=====================================================================
Found a 204 line (728 tokens) duplication in the following files: 
Starting at line 39 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/ImageLoader.java
Starting at line 39 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/renderer/style/ImageLoader.java
class ImageLoader implements Runnable {
    /** The logger for the rendering module. */
    private static final Logger LOGGER = Logger.getLogger("org.geotools.rendering");

    /** The images managed by the loader */
    private static Map images = new HashMap();

    /** A canvas used as the image observer on the tracker */
    private static Canvas obs = new Canvas();

    /** Used to track the images loading status */
    private static MediaTracker tracker = new MediaTracker(obs);

    /** Currently loading image */
    private static int imageID = 1;

    /** A maximum time to wait for the image to load */
    private static long timeout = 10000;

    /** Location of the loading image */
    private URL location;

    /** Still waiting for the image? */
    private boolean waiting = true;

    /**
     * Returns the timeout for aborting an image loading sequence
     *
     * @return the timeout in milliseconds
     */
    public static long getTimeout() {
        return timeout;
    }

    /**
     * Sets the maximum time to wait for getting an external image. Set it to -1 to wait
     * undefinitely
     *
     * @param newTimeout the new timeout value in milliseconds
     */
    public static void setTimeout(long newTimeout) {
        timeout = newTimeout;
    }

    /**
     * Add an image to be loaded by the ImageLoader
     *
     * @param location the image location
     * @param interactive if true the methods returns immediatly, otherwise waits for the image to
     *        be loaded
     */
    private void add(URL location, boolean interactive) {
        int imgId = imageID;
        this.location = location;
        LOGGER.finest("adding image, interactive? " + interactive);

        Thread t = new Thread(this);
        t.start();

        if (interactive) {
            LOGGER.finest("fast return");

            return;
        } else {
            waiting = true;

            long elapsed = 0;
            final long step = 500;

            while (waiting && (elapsed < timeout || timeout < 0)) {
                LOGGER.finest("waiting..." + waiting);

                try {
                    Thread.sleep(step);
                    elapsed += step;

                    if (LOGGER.isLoggable(Level.FINEST)) {
                        LOGGER.finest("Waiting for image " + location + ", elapsed " + elapsed
                            + " milliseconds");
                    }
                } catch (InterruptedException e) {
                    LOGGER.warning(e.toString());
                }
            }

            if (LOGGER.isLoggable(Level.FINEST)) {
                LOGGER.finest(imgId + " complete?: " + (isFlagUp(imgId, MediaTracker.COMPLETE)));
                LOGGER.finest(imgId + " abort?: " + (isFlagUp(imgId, MediaTracker.ABORTED)));
                LOGGER.finest(imgId + " error?: " + (isFlagUp(imgId, MediaTracker.ERRORED)));
                LOGGER.finest(imgId + " loading?: " + (isFlagUp(imgId, MediaTracker.LOADING)));
                LOGGER.finest(imgId + "slow return " + waiting);
            }

            return;
        }
    }

    /**
     * Checks the state of the current tracker against a flag
     *
     * @param id the image id
     * @param flag the flag to be checked
     *
     * @return true if the flag is up
     */
    private boolean isFlagUp(int id, int flag) {
        return (tracker.statusID(id, true) & flag) == flag;
    }

    /**
     * Fetch a buffered image from the loader, if interactive is false then the loader will wait
     * for  the image to be available before returning, used by printers and file output
     * renderers. If interactive is true and the image is ready then return, if image is not ready
     * start loading it  and return null. The renderer is responsible for finding an alternative
     * to use.
     *
     * @param location the url of the image to be fetched
     * @param interactive boolean to signal if the loader should wait for the image to be ready.
     *
     * @return the buffered image or null
     */
    public BufferedImage get(URL location, boolean interactive) {
        if (images.containsKey(location)) {
            LOGGER.finest("found it");

            return (BufferedImage) images.get(location);
        } else {
            if (!interactive) {
                images.put(location, null);
            }

            LOGGER.finest("adding " + location);
            add(location, interactive);

            return (BufferedImage) images.get(location);
        }
    }

    /**
     * Runs the loading thread
     */
    public void run() {
        int myID = 0;
        Image img = null;

        try {
            img = Toolkit.getDefaultToolkit().createImage(location);
            myID = imageID++;
            tracker.addImage(img, myID);
        } catch (Exception e) {
            LOGGER.warning("Exception fetching image from " + location + "\n" + e);
            images.remove(location);
            waiting = false;

            return;
        }

        try {
            while ((tracker.statusID(myID, true) & MediaTracker.LOADING) != 0) {
                tracker.waitForID(myID, 500);
                LOGGER.finest(myID + "loading - waiting....");
            }
        } catch (InterruptedException ie) {
            LOGGER.warning(ie.toString());
        }

        int state = tracker.statusID(myID, true);

        if (state == MediaTracker.ERRORED) {
            LOGGER.finer("" + myID + " Error loading");
            // images.remove(location);
            waiting = false;

            return;
        }

        if ((state & MediaTracker.COMPLETE) == MediaTracker.COMPLETE) {
            LOGGER.finest("" + myID + "completed load");

            int iw = img.getWidth(obs);
            int ih = img.getHeight(obs);
            BufferedImage bi = new BufferedImage(iw, ih, BufferedImage.TYPE_INT_ARGB);
            Graphics2D big = bi.createGraphics();
            big.drawImage(img, 0, 0, obs);
            images.put(location, bi);

            waiting = false;

            return;
        }

        LOGGER.finer("" + myID + " whoops - some other outcome " + state);
        waiting = false;

        return;
    }
    
    /**
     * Resets the image cache
     */
    public void reset() {
        images.clear();
    }
}
=====================================================================
Found a 107 line (463 tokens) duplication in the following files: 
Starting at line 44 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/tests/unit/org/geotools/validation/attributes/RangeFeatureValidationTest.java
Starting at line 44 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/tests/unit/org/geotools/validation/attributes/NullZeroValidationTest.java
	public NullZeroValidationTest(String arg0) {
		super(arg0);
	}

	/*
	 * @see TestCase#setUp()
	 */
	protected void setUp() throws Exception {
		GeometryFactory gf = new GeometryFactory();
		test = new RangeValidation();
		super.setUp();
		
		type = DataUtilities.createType(getName()+".road",
		"id:0,*geom:LineString,name:String");
		Coordinate[] coords = new Coordinate[]{ new Coordinate(1, 1), new Coordinate( 2, 2), new Coordinate (4, 2), new Coordinate (5, 1)};

		
		feature = type.create(new Object[] {
				new Integer(1),
				gf.createLineString(coords),
				"r1",
			},
			"road.rd1"
		);
		
		results = new RoadValidationResults();
	}

	/*
	 * @see TestCase#tearDown()
	 */
	protected void tearDown() throws Exception {
		test = null;
		super.tearDown();
	}

	public void testRangeFeatureValidation() throws Exception {
		test.setPath("id");
		
		
		assertTrue(test.validate(feature, type, results));
		assertEquals(0,results.failedFeatures.size());
		test.setMin(5);
		assertTrue(!test.validate(feature, type, results));
		assertEquals(1,results.failedFeatures.size());		
	}

	public void testValidate() {
		//test.validate(feature, type, results);
	}

	public void testSetName() {
		test.setName("foo");
		assertEquals("foo", test.getName());
	}

	public void testGetName() {
		test.setName("bork");
		assertEquals("bork", test.getName());
	}

	public void testSetDescription() {
		test.setDescription("foo");
		assertEquals("foo", test.getDescription());
	}

	public void testGetDescription() {
		test.setDescription("bork");
		assertEquals("bork", test.getDescription());
	}

	public void testGetPriority() {
		//TODO Implement getPriority().
	}

	public void testGetMax() {
		test.setMax(100);
		assertEquals(100, test.getMax());
	}

	public void testGetMin() {
		test.setMin(10);
		assertEquals(10, test.getMin());
	}

	public void testGetPath() {
		test.setPath("path");
		assertEquals("path", test.getPath());
	}

	public void testSetMax() {
		test.setMax(500);
		assertEquals(500, test.getMax());

	}

	public void testSetMin() {
		test.setMin(5);
		assertEquals(5, test.getMin());
	}

	public void testSetPath() {
		test.setPath("path2");
		assertEquals("path2", test.getPath());
	}

}
=====================================================================
Found a 58 line (427 tokens) duplication in the following files: 
Starting at line 50 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/Java2DMark.java
Starting at line 37 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/renderer/style/Java2DMark.java
    static Shape X;

    static {
        cross = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
        cross.moveTo(0.5f, 0.125f);
        cross.lineTo(0.125f, 0.125f);
        cross.lineTo(0.125f, 0.5f);
        cross.lineTo(-0.125f, 0.5f);
        cross.lineTo(-0.125f, 0.125f);
        cross.lineTo(-0.5f, 0.125f);
        cross.lineTo(-0.5f, -0.125f);
        cross.lineTo(-0.125f, -0.125f);
        cross.lineTo(-0.125f, -0.5f);
        cross.lineTo(0.125f, -0.5f);
        cross.lineTo(0.125f, -0.125f);
        cross.lineTo(0.5f, -0.125f);
        cross.lineTo(0.5f, 0.125f);

        AffineTransform at = new AffineTransform();
        at.rotate(Math.PI / 4.0);
        X = cross.createTransformedShape(at);
        star = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
        star.moveTo(0.191f, 0.0f);
        star.lineTo(0.25f, 0.344f);
        star.lineTo(0.0f, 0.588f);
        star.lineTo(0.346f, 0.638f);
        star.lineTo(0.5f, 0.951f);
        star.lineTo(0.654f, 0.638f);
        star.lineTo(1.0f, 0.588f); // max = 7.887
        star.lineTo(0.75f, 0.344f);
        star.lineTo(0.89f, 0f);
        star.lineTo(0.5f, 0.162f);
        star.lineTo(0.191f, 0.0f);
        at = new AffineTransform();
        at.translate(-.5, -.5);
        star.transform(at);
        triangle = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
        triangle.moveTo(0f, 1f);
        triangle.lineTo(0.866f, -.5f);
        triangle.lineTo(-0.866f, -.5f);
        triangle.lineTo(0f, 1f);
        at = new AffineTransform();

        at.translate(0, -.25);
        at.scale(.5, .5);

        triangle.transform(at);

        arrow = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
        arrow.moveTo(0f, -.5f);
        arrow.lineTo(.5f, 0f);
        arrow.lineTo(0f, .5f);
        arrow.lineTo(0f, .1f);
        arrow.lineTo(-.5f, .1f);
        arrow.lineTo(-.5f, -.1f);
        arrow.lineTo(0f, -.1f);
        arrow.lineTo(0f, -.5f);
    }
=====================================================================
Found a 50 line (403 tokens) duplication in the following files: 
Starting at line 35 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/FilterTransformer.java
Starting at line 60 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/XMLEncoder.java
    private static Map comparisions = new HashMap();

    /** Map of spatial types to sql representation */
    private static Map spatial = new HashMap();

    /** Map of logical types to sql representation */
    private static Map logical = new HashMap();

    /** Map of expression types to sql representation */
    private static Map expressions = new HashMap();

    static {
        comparisions.put(new Integer(AbstractFilter.COMPARE_EQUALS),
            "PropertyIsEqualTo");
        comparisions.put(new Integer(AbstractFilter.COMPARE_GREATER_THAN),
            "PropertyIsGreaterThan");
        comparisions.put(new Integer(AbstractFilter.COMPARE_GREATER_THAN_EQUAL),
            "PropertyIsGreaterThanOrEqualTo");
        comparisions.put(new Integer(AbstractFilter.COMPARE_LESS_THAN),
            "PropertyIsLessThan");
        comparisions.put(new Integer(AbstractFilter.COMPARE_LESS_THAN_EQUAL),
            "PropertyIsLessThanOrEqualTo");
        comparisions.put(new Integer(AbstractFilter.LIKE), "PropertyIsLike");
        comparisions.put(new Integer(AbstractFilter.NULL), "PropertyIsNull");
        comparisions.put(new Integer(AbstractFilter.BETWEEN),
            "PropertyIsBetween");

        expressions.put(new Integer(DefaultExpression.MATH_ADD), "Add");
        expressions.put(new Integer(DefaultExpression.MATH_DIVIDE), "Div");
        expressions.put(new Integer(DefaultExpression.MATH_MULTIPLY), "Mul");
        expressions.put(new Integer(DefaultExpression.MATH_SUBTRACT), "Sub");
        expressions.put(new Integer(DefaultExpression.FUNCTION), "Function");

        //more to come
        spatial.put(new Integer(AbstractFilter.GEOMETRY_EQUALS), "Equals");
        spatial.put(new Integer(AbstractFilter.GEOMETRY_DISJOINT), "Disjoint");
        spatial.put(new Integer(AbstractFilter.GEOMETRY_INTERSECTS),
            "Intersects");
        spatial.put(new Integer(AbstractFilter.GEOMETRY_TOUCHES), "Touches");
        spatial.put(new Integer(AbstractFilter.GEOMETRY_CROSSES), "Crosses");
        spatial.put(new Integer(AbstractFilter.GEOMETRY_WITHIN), "Within");
        spatial.put(new Integer(AbstractFilter.GEOMETRY_CONTAINS), "Contains");
        spatial.put(new Integer(AbstractFilter.GEOMETRY_OVERLAPS), "Overlaps");
        spatial.put(new Integer(AbstractFilter.GEOMETRY_BEYOND), "Beyond");
        spatial.put(new Integer(AbstractFilter.GEOMETRY_BBOX), "BBOX");

        logical.put(new Integer(AbstractFilter.LOGIC_AND), "And");
        logical.put(new Integer(AbstractFilter.LOGIC_OR), "Or");
        logical.put(new Integer(AbstractFilter.LOGIC_NOT), "Not");
    }
=====================================================================
Found a 79 line (397 tokens) duplication in the following files: 
Starting at line 66 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/tests/unit/org/geotools/filter/SQLEncoderPostgisTest.java
Starting at line 53 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/tests/unit/org/geotools/filter/FilterTestSupport.java
    }

    protected void setUp() throws SchemaException, IllegalAttributeException {
        if (setup) {
            return;
        } else {
            prepareFeatures();
        }

        setup = true;
    }

    protected void prepareFeatures()
        throws SchemaException, IllegalAttributeException {
        //_log.getLoggerRepository().setThreshold(Level.INFO);
        // Create the schema attributes
        LOGGER.finer("creating flat feature...");

        AttributeType geometryAttribute = attFactory.newAttributeType("testGeometry",
                LineString.class);
        LOGGER.finer("created geometry attribute");

        AttributeType booleanAttribute = attFactory.newAttributeType("testBoolean",
                Boolean.class);
        LOGGER.finer("created boolean attribute");

        AttributeType charAttribute = attFactory.newAttributeType("testCharacter",
                Character.class);
        AttributeType byteAttribute = attFactory.newAttributeType("testByte",
                Byte.class);
        AttributeType shortAttribute = attFactory.newAttributeType("testShort",
                Short.class);
        AttributeType intAttribute = attFactory.newAttributeType("testInteger",
                Integer.class);
        AttributeType longAttribute = attFactory.newAttributeType("testLong",
                Long.class);
        AttributeType floatAttribute = attFactory.newAttributeType("testFloat",
                Float.class);
        AttributeType doubleAttribute = attFactory.newAttributeType("testDouble",
                Double.class);
        AttributeType stringAttribute = attFactory.newAttributeType("testString",
                String.class);

        AttributeType[] types = {
            geometryAttribute, booleanAttribute, charAttribute, byteAttribute,
            shortAttribute, intAttribute, longAttribute, floatAttribute,
            doubleAttribute, stringAttribute
        };

        // Builds the schema
        testSchema = FeatureTypeFactory.newFeatureType(types,"testSchema");

        GeometryFactory geomFac = new GeometryFactory();

        // Creates coordinates for the linestring
        Coordinate[] coords = new Coordinate[3];
        coords[0] = new Coordinate(1, 2);
        coords[1] = new Coordinate(3, 4);
        coords[2] = new Coordinate(5, 6);

        // Builds the test feature
        Object[] attributes = new Object[10];
        attributes[0] = geomFac.createLineString(coords);
        attributes[1] = new Boolean(true);
        attributes[2] = new Character('t');
        attributes[3] = new Byte("10");
        attributes[4] = new Short("101");
        attributes[5] = new Integer(1002);
        attributes[6] = new Long(10003);
        attributes[7] = new Float(10000.4);
        attributes[8] = new Double(100000.5);
        attributes[9] = "test string data";

        // Creates the feature itself
        testFeature = testSchema.create(attributes);
        LOGGER.finer("...flat feature created");

        //_log.getLoggerRepository().setThreshold(Level.DEBUG);
    }
=====================================================================
Found a 60 line (367 tokens) duplication in the following files: 
Starting at line 63 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/tests/unit/org/geotools/filter/MathTest.java
Starting at line 61 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/tests/unit/org/geotools/filter/AttributeTest.java
                }, "test");

        Feature[] f = new Feature[3];
        f[0] = schema.create(new Object[] {
                    new Integer(12), new GeometryCollection(null, null, -1),
                    "first"
                });
        f[1] = schema.create(new Object[] {
                    new Integer(3), new GeometryCollection(null, null, -1),
                    "second"
                });
        f[2] = schema.create(new Object[] {
                    new Integer(15), new GeometryCollection(null, null, -1),
                    "third"
                });

        return f;
    }

    public void testTypeMissmatch() throws Exception {
        Feature[] f = sampleFeatures();

        //the following are intentionaly backwards
        AttributeExpressionImpl e1 = new AttributeExpressionImpl(schema, "value");
        AttributeExpressionImpl e2 = new AttributeExpressionImpl(schema, "name");
        boolean pass = false;
        Object value = null;
        value = e1.getValue(f[0]);

        if (value instanceof Integer) {
            pass = true;
        }

        assertTrue("String expresion returned an Integer", pass);
        pass = false;

        value = e2.getValue(f[0]);

        if (value instanceof String) {
            pass = true;
        }

        assertTrue("Integer expresion returned a String", pass);
    }

    public void testSetupAndExtraction() throws Exception {
        //this should move out to a more configurable system run from scripts
        //but we can start with a set of hard coded tests
        Feature[] f = sampleFeatures();

        AttributeExpressionImpl e1 = new AttributeExpressionImpl(schema, "value");
        AttributeExpressionImpl e2 = new AttributeExpressionImpl(schema, "name");

        assertEquals(12d, ((Integer) e1.getValue(f[0])).doubleValue(), 0);
        assertEquals(3d, ((Integer) e1.getValue(f[1])).doubleValue(), 0);
        assertEquals(15d, ((Integer) e1.getValue(f[2])).doubleValue(), 0);
        assertEquals("first", (String) e2.getValue(f[0]));
        assertEquals("second", (String) e2.getValue(f[1]));
    }
}
=====================================================================
Found a 53 line (342 tokens) duplication in the following files: 
Starting at line 2438 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/LiteRenderer.java
Starting at line 296 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/renderer/j2d/SLDRenderedGeometries.java
        double[] first = new double[2];
        double[] previous = new double[2];
        type = pi.currentSegment(coords);
        first[0] = coords[0];
        first[1] = coords[1];
        previous[0] = coords[0];
        previous[1] = coords[1];

        if (LOGGER.isLoggable(Level.FINEST)) {
            LOGGER.finest("starting at " + first[0] + "," + first[1]);
        }

        pi.next();

        while (!pi.isDone()) {
            type = pi.currentSegment(coords);

            switch (type) {
            case PathIterator.SEG_MOVETO:

                // nothing to do?
                if (LOGGER.isLoggable(Level.FINEST)) {
                    LOGGER.finest("moving to " + coords[0] + "," + coords[1]);
                }

                break;

            case PathIterator.SEG_CLOSE:

                // draw back to first from previous
                coords[0] = first[0];
                coords[1] = first[1];

                if (LOGGER.isLoggable(Level.FINEST)) {
                    LOGGER.finest("closing from " + previous[0] + "," + previous[1] + " to "
                        + coords[0] + "," + coords[1]);
                }

            // no break here - fall through to next section
            case PathIterator.SEG_LINETO:

                // draw from previous to coords
                if (LOGGER.isLoggable(Level.FINEST)) {
                    LOGGER.finest("drawing from " + previous[0] + "," + previous[1] + " to "
                        + coords[0] + "," + coords[1]);
                }

                double dx = coords[0] - previous[0];
                double dy = coords[1] - previous[1];
                double len = Math.sqrt((dx * dx) + (dy * dy)); // - imageWidth;

                double theta = Math.atan2(dx, dy);
                dx = (Math.sin(theta) * imageSize);
=====================================================================
Found a 100 line (337 tokens) duplication in the following files: 
Starting at line 95 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/CrossesIntegrity.java
Starting at line 96 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/OverlapsIntegrity.java
	public OverlapsIntegrity()
	{
		super();
		usedIDs = new HashSet();	//TODO: remove me later, memory inefficient
	}
	
	
	/* (non-Javadoc)
	 * @see org.geotools.validation.IntegrityValidation#validate(java.util.Map, com.vividsolutions.jts.geom.Envelope, org.geotools.validation.ValidationResults)
	 */
	public boolean validate(Map layers, Envelope envelope,
			ValidationResults results) throws Exception 
	{
		LOGGER.finer("Starting test "+getName()+" ("+getClass().getName()+")" );
		String typeRef1 = getGeomTypeRefA();
		LOGGER.finer( typeRef1 +": looking up FeatureSource " );    	
		FeatureSource geomSource1 = (FeatureSource) layers.get( typeRef1 );
		LOGGER.finer( typeRef1 +": found "+ geomSource1.getSchema().getTypeName() );
		
		String typeRef2 = getGeomTypeRefB();
		if (typeRef2 == EMPTY || typeRef1.equals(typeRef2))
			return validateSingleLayer(geomSource1, isExpected(), results, envelope);
		else
		{
			LOGGER.finer( typeRef2 +": looking up FeatureSource " );        
			FeatureSource geomSource2 = (FeatureSource) layers.get( typeRef2 );
			LOGGER.finer( typeRef2 +": found "+ geomSource2.getSchema().getTypeName() );
			return validateMultipleLayers(geomSource1, geomSource2, isExpected(), results, envelope);
		}	
	
	}


	/**
	 * <b>validateMultipleLayers Purpose:</b> <br>
	 * <p>
	 * This validation tests for a geometry overlaps another geometry. 
	 * Uses JTS' Geometry.overlaps(Geometry) and  Geometry.contains(Geometry)method.
	 * The DE-9IM intersection matrix for overlaps is:
     * T*T***T** (for two points or two surfaces)
     * 1*T***T** (for two curves) 
     * Contains DE-9IM intersection matrix is T*F**F***.
	 * </p>
	 * 
	 * <b>Description:</b><br>
	 * <p>
	 * The function filters the FeatureSources using the given bounding box.
	 * It creates iterators over both filtered FeatureSources. It calls overlaps() and contains()using the
	 * geometries in the FeatureSource layers. Tests the results of the method call against
	 * the given expected results. Returns true if the returned results and the expected results 
	 * are true, false otherwise.
	 * 
	 * </p>
	 * 
	 * Author: bowens<br>
	 * Created on: Apr 27, 2004<br>
	 * @param featureSourceA - the FeatureSource to pull the original geometries from. This geometry is the one that is tested for overlaping with the other
	 * @param featureSourceB - the FeatureSource to pull the other geometries from - these geometries will be those that may overlap the first geometry
	 * @param expected - boolean value representing the user's expected outcome of the test
	 * @param results - ValidationResults
	 * @param bBox - Envelope - the bounding box within which to perform the overlaps() and contains()
	 * @return boolean result of the test
	 * @throws Exception - IOException if iterators improperly closed
	 */
	private boolean validateMultipleLayers(	FeatureSource featureSourceA, 
											FeatureSource featureSourceB, 
											boolean expected, 
											ValidationResults results, 
											Envelope bBox) 
	throws Exception
	{
		boolean success = true;
		
		FilterFactory ff = FilterFactory.createFilterFactory();
		Filter filter = null;

		filter = (Filter) ff.createBBoxExpression(bBox);

		FeatureResults featureResultsA = featureSourceA.getFeatures(filter);
		FeatureResults featureResultsB = featureSourceB.getFeatures(filter);
		
		FeatureReader fr1 = null;
		FeatureReader fr2 = null;
		try 
		{
			fr1 = featureResultsA.reader();

			if (fr1 == null)
				return success;
						
			while (fr1.hasNext())
			{
				Feature f1 = fr1.next();
				Geometry g1 = f1.getDefaultGeometry();
				fr2 = featureResultsB.reader();
				
				while (fr2 != null && fr2.hasNext())
				{
					Feature f2 = fr2.next();
					Geometry g2 = f2.getDefaultGeometry();
=====================================================================
Found a 97 line (335 tokens) duplication in the following files: 
Starting at line 56 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/DisjointIntegrity.java
Starting at line 58 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/ContainsIntegrity.java
Starting at line 64 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/WithinIntegrity.java
Starting at line 66 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/TouchesIntegrity.java
Starting at line 58 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/IntersectsIntegrity.java
	public IntersectsIntegrity()
	{
		super();
	}
	
	
	/* (non-Javadoc)
	 * @see org.geotools.validation.IntegrityValidation#validate(java.util.Map, com.vividsolutions.jts.geom.Envelope, org.geotools.validation.ValidationResults)
	 */
	public boolean validate(Map layers, Envelope envelope,
			ValidationResults results) throws Exception 
	{
		LOGGER.finer("Starting test "+getName()+" ("+getClass().getName()+")" );
		String typeRef1 = getGeomTypeRefA();
		LOGGER.finer( typeRef1 +": looking up FeatureSource " );    	
		FeatureSource geomSource1 = (FeatureSource) layers.get( typeRef1 );
		LOGGER.finer( typeRef1 +": found "+ geomSource1.getSchema().getTypeName() );
		
		String typeRef2 = getGeomTypeRefB();
		if (typeRef2 == EMPTY || typeRef1.equals(typeRef2))
			return validateSingleLayer(geomSource1, isExpected(), results, envelope);
		else
		{
			LOGGER.finer( typeRef2 +": looking up FeatureSource " );        
			FeatureSource geomSource2 = (FeatureSource) layers.get( typeRef2 );
			LOGGER.finer( typeRef2 +": found "+ geomSource2.getSchema().getTypeName() );
			return validateMultipleLayers(geomSource1, geomSource2, isExpected(), results, envelope);
		}	
	
	}


	/**
	 * <b>validateMultipleLayers Purpose:</b> <br>
	 * <p>
	 * This validation tests for a geometry crosses another geometry. 
	 * Uses JTS' Geometry.crosses(Geometry) method.
	 * 
	 * </p>
	 * 
	 * <b>Description:</b><br>
	 * <p>
	 * The function filters the FeatureSources using the given bounding box.
	 * It creates iterators over both filtered FeatureSources. It calls intersects() using the
	 * geometries in the FeatureSource layers. Tests the results of the method call against
	 * the given expected results. Returns true if the returned results and the expected results 
	 * are true, false otherwise.
	 * 
	 * </p>
	 * 
	 * Author: bowens<br>
	 * Created on: Apr 27, 2004<br>
	 * @param featureSourceA - the FeatureSource to pull the original geometries from. This geometry is the one that is tested for intersecting with the other
	 * @param featureSourceB - the FeatureSource to pull the other geometries from - these geometries will be those that may intersect the first geometry
	 * @param expected - boolean value representing the user's expected outcome of the test
	 * @param results - ValidationResults
	 * @param bBox - Envelope - the bounding box within which to perform the intersects()
	 * @return boolean result of the test
	 * @throws Exception - IOException if iterators improperly closed
	 */
	private boolean validateMultipleLayers(	FeatureSource featureSourceA, 
											FeatureSource featureSourceB, 
											boolean expected, 
											ValidationResults results, 
											Envelope bBox) 
	throws Exception
	{
		boolean success = true;
		
		FilterFactory ff = FilterFactory.createFilterFactory();
		Filter filter = null;

		filter = (Filter) ff.createBBoxExpression(bBox);

		FeatureResults featureResultsA = featureSourceA.getFeatures(filter);
		FeatureResults featureResultsB = featureSourceB.getFeatures(filter);
		
		FeatureReader fr1 = null;
		FeatureReader fr2 = null;
		try 
		{
			fr1 = featureResultsA.reader();

			if (fr1 == null)
				return false;
						
			while (fr1.hasNext())
			{
				Feature f1 = fr1.next();
				Geometry g1 = f1.getDefaultGeometry();
				fr2 = featureResultsB.reader();
				
				while (fr2 != null && fr2.hasNext())
				{
					Feature f2 = fr2.next();
					Geometry g2 = f2.getDefaultGeometry();
					if(g1.intersects(g2) != expected )
=====================================================================
Found a 104 line (329 tokens) duplication in the following files: 
Starting at line 59 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/DisjointIntegrity.java
Starting at line 88 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/RelateIntegrity.java
	}

	/* (non-Javadoc)
	 * @see org.geotools.validation.IntegrityValidation#validate(java.util.Map, com.vividsolutions.jts.geom.Envelope, org.geotools.validation.ValidationResults)
	 */
	public boolean validate(Map layers, Envelope envelope,
			ValidationResults results) throws Exception 
	{
		LOGGER.finer("Starting test "+getName()+" ("+getClass().getName()+")" );
		String typeRef1 = getGeomTypeRefA();
		LOGGER.finer( typeRef1 +": looking up FeatureSource " );    	
		FeatureSource geomSource1 = (FeatureSource) layers.get( typeRef1 );
		LOGGER.finer( typeRef1 +": found "+ geomSource1.getSchema().getTypeName() );
	
		String typeRef2 = getGeomTypeRefB();
		if (typeRef2 == EMPTY || typeRef1.equals(typeRef2))
			return validateSingleLayer(geomSource1, isExpected(), results, envelope);
		else
		{
			LOGGER.finer( typeRef2 +": looking up FeatureSource " );        
			FeatureSource geomSource2 = (FeatureSource) layers.get( typeRef2 );
			LOGGER.finer( typeRef2 +": found "+ geomSource2.getSchema().getTypeName() );
			return validateMultipleLayers(geomSource1, geomSource2, isExpected(), results, envelope);
		}	

	}


	/**
	 * <b>validateMultipleLayers Purpose:</b> <br>
	 * <p>
	 * This validation tests for a geometry crosses another geometry. 
	 * Uses JTS' Geometry.crosses(Geometry) method.
	 * 
	 * </p>
	 * 
	 * <b>Description:</b><br>
	 * <p>
	 * The function filters the FeatureSources using the given bounding box.
	 * It creates iterators over both filtered FeatureSources. It calls relate() using the
	 * geometries in the FeatureSource layers. Tests the results of the method call against
	 * the given expected results. Returns true if the returned results and the expected results 
	 * are true, false otherwise.
	 * 
	 * The following is taken from JTS documentation for Geometry.relate():
	 * "Returns true if the elements in the DE-9IM intersection matrix for the two Geometrys match the elements in intersectionPattern  , which may be:
     * 0
     * 1
     * 2
     * T ( = 0, 1 or 2)
     * F ( = -1)
     * * ( = -1, 0, 1 or 2) 
     * For more information on the DE-9IM, see the OpenGIS Simple Features Specification."
     * 
     * 
	 * </p>
	 * 
	 * Author: bowens<br>
	 * Created on: Apr 27, 2004<br>
	 * @param featureSourceA - the FeatureSource to pull the original geometries from. 
	 * @param featureSourceB - the FeatureSource to pull the other geometries from 
	 * @param expected - boolean value representing the user's expected outcome of the test
	 * @param results - ValidationResults
	 * @param bBox - Envelope - the bounding box within which to perform the intersects()
	 * @return boolean result of the test
	 * @throws Exception - IOException if iterators improperly closed
	 */
	private boolean validateMultipleLayers(	FeatureSource featureSourceA, 
											FeatureSource featureSourceB, 
											boolean expected, 
											ValidationResults results, 
											Envelope bBox) 
	throws Exception
	{
		boolean success = true;
	
		FilterFactory ff = FilterFactory.createFilterFactory();
		Filter filter = null;

		filter = (Filter) ff.createBBoxExpression(bBox);

		FeatureResults featureResultsA = featureSourceA.getFeatures(filter);
		FeatureResults featureResultsB = featureSourceB.getFeatures(filter);
	
		FeatureReader fr1 = null;
		FeatureReader fr2 = null;
		try 
		{
			fr1 = featureResultsA.reader();

			if (fr1 == null)
				return false;
					
			while (fr1.hasNext())
			{
				Feature f1 = fr1.next();
				Geometry g1 = f1.getDefaultGeometry();
				fr2 = featureResultsB.reader();
			
				while (fr2 != null && fr2.hasNext())
				{
					Feature f2 = fr2.next();
					Geometry g2 = f2.getDefaultGeometry();
					if(g1.relate(g2, de9im) != expected)
=====================================================================
Found a 36 line (316 tokens) duplication in the following files: 
Starting at line 434 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/rendering-styling/tests/unit/org/geotools/styling/RenderStyleTest.java
Starting at line 344 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/rendering-styling/tests/unit/org/geotools/styling/RenderingGridCoverageTest.java
        final double scalex = width / dataWidth;
        final double scaley = height / dataHeigth;
            
        java.net.URL base = getClass().getResource("rs-testData/");

        AffineTransform at = new AffineTransform();
        at.translate(0, height);
        at.scale(scalex, -scaley);

        if (INTERACTIVE) {
            java.awt.Frame frame = new java.awt.Frame("Mark test (" + renderer.getClass().getName());
            frame.addWindowListener(new java.awt.event.WindowAdapter() {
                    public void windowClosing(java.awt.event.WindowEvent e) {
                        e.getWindow().dispose();
                    }
                });

            java.awt.Panel p = new java.awt.Panel();
            frame.add(p);
            frame.setSize(width, height);
            frame.setLocation(0, 0);
            frame.setVisible(true);
            renderer.paint((Graphics2D) p.getGraphics(), p.getBounds(), at);

            Thread.sleep(5000);
            frame.dispose();
        }

        java.awt.image.BufferedImage image = new java.awt.image.BufferedImage(width, height,
                java.awt.image.BufferedImage.TYPE_INT_RGB);
        java.awt.Graphics2D g = (Graphics2D) image.getGraphics();
        g.setColor(java.awt.Color.white);
        g.fillRect(0, 0, width, height);
        renderer.paint(g, new java.awt.Rectangle(0, 0, width, height), at);

        java.io.File file = new java.io.File(base.getPath(),
=====================================================================
Found a 77 line (301 tokens) duplication in the following files: 
Starting at line 200 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/resources/src/org/geotools/util/WeakValueHashMap.java
Starting at line 151 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/resources/src/org/geotools/util/WeakHashSet.java
    public WeakHashSet() {
        table = new Entry[MIN_CAPACITY];
        threshold = Math.round(table.length*LOAD_FACTOR);
        lastRehashTime = System.currentTimeMillis();
    }

    /**
     * Invoked by {@link Entry} when an element has been collected
     * by the garbage collector. This method will remove the weak reference
     * from {@link #table}.
     */
    private synchronized void removeEntry(final Entry toRemove) {
        assert valid() : count;
        final int i = toRemove.index;
        // Index 'i' may not be valid if the reference 'toRemove'
        // has been already removed in a previous rehash.
        if (i < table.length) {
            Entry prev = null;
            Entry e = table[i];
            while (e != null) {
                if (e == toRemove) {
                    if (prev != null) {
                        prev.next = e.next;
                    } else {
                        table[i] = e.next;
                    }
                    count--;
                    assert valid();

                    // If the number of elements has dimunished
                    // significatively, rehash the table.
                    if (count <= threshold/4) {
                        rehash(false);
                    }
                    // We must not continue the loop, since
                    // variable 'e' is no longer valid.
                    return;
                }
                prev = e;
                e = e.next;
            }
        }
        assert valid();
        /*
         * If we reach this point, its mean that reference 'toRemove' has not
         * been found. This situation may occurs if 'toRemove' has already been
         * removed in a previous run of {@link #rehash}.
         */
    }

    /**
     * Rehash {@link #table}.
     *
     * @param augmentation <code>true</code> if this method is invoked
     *        for augmenting {@link #table}, or <code>false</code> if
     *        it is invoked for making the table smaller.
     */
    private void rehash(final boolean augmentation)
    {
        assert Thread.holdsLock(this);
        assert valid();
        final long currentTime = System.currentTimeMillis();
        final int capacity = Math.max(Math.round(count/(LOAD_FACTOR/2)), count+MIN_CAPACITY);
        if (augmentation ? (capacity<=table.length) :
                           (capacity>=table.length || currentTime-lastRehashTime<HOLD_TIME))
        {
            return;
        }
        lastRehashTime = currentTime;
        final Entry[] oldTable = table;
        table     = new Entry[capacity];
        threshold = Math.round(capacity*LOAD_FACTOR);
        for (int i=0; i<oldTable.length; i++) {
            for (Entry old=oldTable[i]; old!=null;) {
                final Entry e=old;
                old=old.next; // On retient 'next' tout de suite car sa valeur va changer...
                final Object obj_e = e.get();
=====================================================================
Found a 53 line (286 tokens) duplication in the following files: 
Starting at line 1334 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/LiteRenderer.java
Starting at line 565 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/renderer/style/SLDStyleFactory.java
    }

    /**
     * Returns the first font associated to the feature that can be found on the current machine
     *
     * @param feature The feature whose font is to be found
     * @param fonts An array of fonts dependent of the feature, the first that is found on the
     *        current machine is returned
     *
     * @return The first of the specified fonts found on this machine or null if none found
     */
    private java.awt.Font getFont(Feature feature, Font[] fonts) {
        if (fontFamilies == null) {
            GraphicsEnvironment ge = GraphicsEnvironment.getLocalGraphicsEnvironment();
            fontFamilies = new HashSet();

            List f = Arrays.asList(ge.getAvailableFontFamilyNames());
            fontFamilies.addAll(f);

            if (LOGGER.isLoggable(Level.FINEST)) {
                LOGGER.finest("there are " + fontFamilies.size() + " fonts available");
            }
        }

        java.awt.Font javaFont = null;

        int styleCode = 0;
        int size = 6;
        String requestedFont = "";

        for (int k = 0; k < fonts.length; k++) {
            requestedFont = fonts[k].getFontFamily().getValue(feature).toString();

            if (LOGGER.isLoggable(Level.FINEST)) {
                LOGGER.finest("trying to load " + requestedFont);
            }

            if (loadedFonts.containsKey(requestedFont)) {
                javaFont = (java.awt.Font) loadedFonts.get(requestedFont);

                String reqStyle = (String) fonts[k].getFontStyle().getValue(feature);

                if (fontStyleLookup.containsKey(reqStyle)) {
                    styleCode = ((Integer) fontStyleLookup.get(reqStyle)).intValue();
                } else {
                    styleCode = java.awt.Font.PLAIN;
                }

                String reqWeight = (String) fonts[k].getFontWeight().getValue(feature);

                if (reqWeight.equalsIgnoreCase("Bold")) {
                    styleCode = styleCode | java.awt.Font.BOLD;
                }
=====================================================================
Found a 19 line (272 tokens) duplication in the following files: 
Starting at line 29 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gtopo30/tests/unit/org/geotools/data/gtopo30/GT30HeaderTest.java
Starting at line 48 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gtopo30/tests/unit/org/geotools/data/gtopo30/GT30HeaderTest.java
      URL headerURL = getTestResource("DEM_MORE.HDR");
      GT30Header header = new GT30Header(headerURL);
      assertEquals("Byteorder", header.getProperty(GT30Header.BYTEORDER), "M");
      assertEquals("Layout", header.getProperty(GT30Header.LAYOUT), "BIL");
      assertEquals("NRows", header.getProperty(GT30Header.NROWS), new Integer(6000));
      assertEquals("BCols", header.getProperty(GT30Header.NCOLS), new Integer(4800));
      assertEquals("NBands", header.getProperty(GT30Header.NBANDS), new Integer(1));
      assertEquals("NBits", header.getProperty(GT30Header.NBITS), new Integer(16));
      assertEquals("BandRowBytes", header.getProperty(GT30Header.BANDROWBYTES), new Integer(9600));
      assertEquals("TotalRowBytes", header.getProperty(GT30Header.TOTALROWBYTES), new Integer(9600));
      assertEquals("BandGapBytes", header.getProperty(GT30Header.BANDGAPBYTES), new Integer(0));
      assertEquals("NoData", header.getProperty(GT30Header.NODATA), new Integer(-9999));
      assertEquals("ULXMap", header.getProperty(GT30Header.ULXMAP), new Double(-19.99583333333333));
      assertEquals("ULYMap", header.getProperty(GT30Header.ULYMAP), new Double(89.99583333333334));
      assertEquals("XDim", header.getProperty(GT30Header.XDIM), new Double(0.00833333333333));
      assertEquals("YDim", header.getProperty(GT30Header.YDIM), new Double(0.00833333333333));
  }
  
  public void testHeaderSource() throws Exception  {
=====================================================================
Found a 85 line (265 tokens) duplication in the following files: 
Starting at line 58 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/DisjointIntegrity.java
Starting at line 98 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/CrossesIntegrity.java
		usedIDs = new HashSet();	//TODO: remove me later, memory inefficient
	}
	
	
	/* (non-Javadoc)
	 * @see org.geotools.validation.IntegrityValidation#validate(java.util.Map, com.vividsolutions.jts.geom.Envelope, org.geotools.validation.ValidationResults)
	 */
	public boolean validate(Map layers, Envelope envelope,
			ValidationResults results) throws Exception 
	{
		LOGGER.finer("Starting test "+getName()+" ("+getClass().getName()+")" );
		String typeRef1 = getGeomTypeRefA();
		LOGGER.finer( typeRef1 +": looking up FeatureSource " );    	
		FeatureSource geomSource1 = (FeatureSource) layers.get( typeRef1 );
		LOGGER.finer( typeRef1 +": found "+ geomSource1.getSchema().getTypeName() );
		
		String typeRef2 = getGeomTypeRefB();
		if (typeRef2 == EMPTY || typeRef1.equals(typeRef2))
			return validateSingleLayer(geomSource1, isExpected(), results, envelope);
		else
		{
			LOGGER.finer( typeRef2 +": looking up FeatureSource " );        
			FeatureSource geomSource2 = (FeatureSource) layers.get( typeRef2 );
			LOGGER.finer( typeRef2 +": found "+ geomSource2.getSchema().getTypeName() );
			return validateMultipleLayers(geomSource1, geomSource2, isExpected(), results, envelope);
		}	
	
	}


	/**
	 * <b>validateMultipleLayers Purpose:</b> <br>
	 * <p>
	 * This validation tests for a geometry crosses another geometry.
     * Uses JTS' Geometry.crosses(Geometry) method.
     * The DE-9IM intersection matrix for crosses is
   	 * T*T****** (for a point and a curve, a point and an area or a line and an area)
   	 * 0******** (for two curves)
	 * </p>
	 * 
	 * <b>Description:</b><br>
	 * <p>
	 * The function filters the FeatureSources using the given bounding box.
	 * It creates iterators over both filtered FeatureSources. It calls overlaps() and contains()using the
	 * geometries in the FeatureSource layers. Tests the results of the method call against
	 * the given expected results. Returns true if the returned results and the expected results 
	 * are true, false otherwise.
	 * 
	 * </p>
	 * 
	 * Author: bowens<br>
	 * Created on: Apr 27, 2004<br>
	 * @param featureSourceA - the FeatureSource to pull the original geometries from. This geometry is the one that is tested for overlaping with the other
	 * @param featureSourceB - the FeatureSource to pull the other geometries from - these geometries will be those that may overlap the first geometry
	 * @param expected - boolean value representing the user's expected outcome of the test
	 * @param results - ValidationResults
	 * @param bBox - Envelope - the bounding box within which to perform the overlaps() and contains()
	 * @return boolean result of the test
	 * @throws Exception - IOException if iterators improperly closed
	 */
	private boolean validateMultipleLayers(	FeatureSource featureSourceA, 
											FeatureSource featureSourceB, 
											boolean expected, 
											ValidationResults results, 
											Envelope bBox) 
	throws Exception
	{
		boolean success = true;
		
		FilterFactory ff = FilterFactory.createFilterFactory();
		Filter filter = null;

		filter = (Filter) ff.createBBoxExpression(bBox);

		FeatureResults featureResultsA = featureSourceA.getFeatures(filter);
		FeatureResults featureResultsB = featureSourceB.getFeatures(filter);
		
		FeatureReader fr1 = null;
		FeatureReader fr2 = null;
		try 
		{
			fr1 = featureResultsA.reader();

			if (fr1 == null)
				return success;
=====================================================================
Found a 80 line (265 tokens) duplication in the following files: 
Starting at line 67 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/spatial/LineNoSelfOverlappingValidation.java
Starting at line 68 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/spatial/LineNoSelfIntersectValidation.java
    }

    /**
     * Override getPriority.
     * 
     * <p>
     * Sets the priority level of this validation. This is set by the
     * programmer and is a measure of the expense of this plugin
     * </p>
     *
     * @return A made up priority for this validation.
     *
     * @see org.geotools.validation.Validation#getPriority()
     */
    public int getPriority() {
        return PRIORITY_COMPLEX;
    }

    /**
     * Override validate.
     * 
     * <p>
     * Tests to see if a geometry intersects itself. It does not detect if a
     * segment of a LineString doubles back on itself for one segment, then
     * terminates. A different validation is needed to test overlapping. Uses
     * JTS' intersect routine.
     * </p>
     *
     * @param feature The Feature to be validated.
     * @param type The FeatureTypeInfo of the feature.
     * @param results The storage for error messages.
     *
     * @return True if the feature does not self intersect.
     *
     * @see org.geotools.validation.FeatureValidation#validate(org.geotools.feature.Feature,
     *      org.geotools.feature.FeatureTypeInfo,
     *      org.geotools.validation.ValidationResults)
     */
    public boolean validate(Feature feature, FeatureType type,
        ValidationResults results) {
        LOGGER.setLevel(Level.ALL);

        LineString line = null;
        try {
            line = getDefaultLineString( feature );
        }
        catch( ClassCastException unLine ){            
            results.error(feature,"Geometry is required to be a LineString");
            System.out.println( feature.getID()+"  name: "+getName() );
            System.out.println( feature.getID()+"   ref: "+getTypeRef() );
            System.out.println( feature.getID()+"   ref: "+getTypeRefs() );            
        }
        if (line == null) {
            // Ignore null geometry (user can check with nullZero )
            return true;
        }
        if (line.getNumPoints() < 2) {
            results.warning(feature,"LineString contains too few points");            
            return false;
        }
        GeometryFactory gf = new GeometryFactory();

        int numPoints = line.getNumPoints();

        // break up the LineString into line segments
        LineString[] segments = new LineString[numPoints - 1];

        for (int i = 0; i < (numPoints - 1); i++) {
            Coordinate[] coords = new Coordinate[] {
                    line.getCoordinateN(i), line.getCoordinateN(i + 1)
                };
            segments[i] = gf.createLineString(coords);
        }

        // intersect all of the line segments with each other
        for (int i = 0; i < segments.length; i++) // for each line segment
         {
            for (int j = 0; j < segments.length; j++) // intersect with every other line segment
             {
                if ((i != j) && ((i - 1) != j) && ((i + 1) != j)) // if they aren't the same segment
=====================================================================
Found a 84 line (263 tokens) duplication in the following files: 
Starting at line 88 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/RelateIntegrity.java
Starting at line 99 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/CrossesIntegrity.java
	}
	
	
	/* (non-Javadoc)
	 * @see org.geotools.validation.IntegrityValidation#validate(java.util.Map, com.vividsolutions.jts.geom.Envelope, org.geotools.validation.ValidationResults)
	 */
	public boolean validate(Map layers, Envelope envelope,
			ValidationResults results) throws Exception 
	{
		LOGGER.finer("Starting test "+getName()+" ("+getClass().getName()+")" );
		String typeRef1 = getGeomTypeRefA();
		LOGGER.finer( typeRef1 +": looking up FeatureSource " );    	
		FeatureSource geomSource1 = (FeatureSource) layers.get( typeRef1 );
		LOGGER.finer( typeRef1 +": found "+ geomSource1.getSchema().getTypeName() );
		
		String typeRef2 = getGeomTypeRefB();
		if (typeRef2 == EMPTY || typeRef1.equals(typeRef2))
			return validateSingleLayer(geomSource1, isExpected(), results, envelope);
		else
		{
			LOGGER.finer( typeRef2 +": looking up FeatureSource " );        
			FeatureSource geomSource2 = (FeatureSource) layers.get( typeRef2 );
			LOGGER.finer( typeRef2 +": found "+ geomSource2.getSchema().getTypeName() );
			return validateMultipleLayers(geomSource1, geomSource2, isExpected(), results, envelope);
		}	
	
	}


	/**
	 * <b>validateMultipleLayers Purpose:</b> <br>
	 * <p>
	 * This validation tests for a geometry crosses another geometry.
     * Uses JTS' Geometry.crosses(Geometry) method.
     * The DE-9IM intersection matrix for crosses is
   	 * T*T****** (for a point and a curve, a point and an area or a line and an area)
   	 * 0******** (for two curves)
	 * </p>
	 * 
	 * <b>Description:</b><br>
	 * <p>
	 * The function filters the FeatureSources using the given bounding box.
	 * It creates iterators over both filtered FeatureSources. It calls overlaps() and contains()using the
	 * geometries in the FeatureSource layers. Tests the results of the method call against
	 * the given expected results. Returns true if the returned results and the expected results 
	 * are true, false otherwise.
	 * 
	 * </p>
	 * 
	 * Author: bowens<br>
	 * Created on: Apr 27, 2004<br>
	 * @param featureSourceA - the FeatureSource to pull the original geometries from. This geometry is the one that is tested for overlaping with the other
	 * @param featureSourceB - the FeatureSource to pull the other geometries from - these geometries will be those that may overlap the first geometry
	 * @param expected - boolean value representing the user's expected outcome of the test
	 * @param results - ValidationResults
	 * @param bBox - Envelope - the bounding box within which to perform the overlaps() and contains()
	 * @return boolean result of the test
	 * @throws Exception - IOException if iterators improperly closed
	 */
	private boolean validateMultipleLayers(	FeatureSource featureSourceA, 
											FeatureSource featureSourceB, 
											boolean expected, 
											ValidationResults results, 
											Envelope bBox) 
	throws Exception
	{
		boolean success = true;
		
		FilterFactory ff = FilterFactory.createFilterFactory();
		Filter filter = null;

		filter = (Filter) ff.createBBoxExpression(bBox);

		FeatureResults featureResultsA = featureSourceA.getFeatures(filter);
		FeatureResults featureResultsB = featureSourceB.getFeatures(filter);
		
		FeatureReader fr1 = null;
		FeatureReader fr2 = null;
		try 
		{
			fr1 = featureResultsA.reader();

			if (fr1 == null)
				return success;
=====================================================================
Found a 41 line (262 tokens) duplication in the following files: 
Starting at line 330 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/rendering-styling/tests/unit/org/geotools/styling/TextStyleTest.java
Starting at line 291 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/rendering-styling/tests/unit/org/geotools/styling/DefaultMarkTest.java
        Raster data = image.getData();
        Raster data2 = image2.getData();
        int[] pixel1 = null;
        int[] pixel2 = null;
        boolean isBlack = false;

        for (int x = 0; x < data.getWidth(); x++) {
            for (int y = 0; y < data.getHeight(); y++) {
                pixel1 = data.getPixel(x, y, pixel1);
                pixel2 = data2.getPixel(x, y, pixel2);

                if ((notBlack(pixel1)) && (notBlack(pixel2))) { //Since text is black and fonts are not stable across platforms, ignore pixels where at least one is black.

                    for (int band = 0; band < data2.getNumBands(); band++) {
                        assertEquals("mismatch in image comparison at (x: " + x + " y: " + y
                            + " band: " + band + ")", pixel1[band], pixel2[band]);
                    }
                }
            }
        }
    }

    private boolean notBlack(int[] pixel) {
        boolean isBlack = true;
        int x = 0;

        while (isBlack && (x < pixel.length)) {
            isBlack = (pixel[x] == 0);
            x++;
        }

        return !(isBlack);
    }

    private Point makeSamplePoint(final com.vividsolutions.jts.geom.GeometryFactory geomFac,
        double x, double y) {
        com.vividsolutions.jts.geom.Coordinate c = new com.vividsolutions.jts.geom.Coordinate(x, y);
        Point point = geomFac.createPoint(c);

        return point;
    }
=====================================================================
Found a 59 line (257 tokens) duplication in the following files: 
Starting at line 57 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/spatial/PointCoveredByPolygonBoundaryValidation.java
Starting at line 57 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/spatial/PointCoveredByPolygonValidation.java
    public PointCoveredByPolygonValidation() {
        super();
    }

    /**
     * Ensure Point is covered by the Polygon.
     * 
     * <p></p>
     *
     * @param layers a HashMap of key="TypeName" value="FeatureSource"
     * @param envelope The bounding box of modified features
     * @param results Storage for the error and warning messages
     *
     * @return True if no features intersect. If they do then the validation
     *         failed.
     *
     * @throws Exception DOCUMENT ME!
     *
     * @see org.geotools.validation.IntegrityValidation#validate(java.util.Map,
     *      com.vividsolutions.jts.geom.Envelope,
     *      org.geotools.validation.ValidationResults)
     */
    public boolean validate(Map layers, Envelope envelope,
        ValidationResults results) throws Exception {
        FeatureSource pointSource = (FeatureSource) layers.get(getPointTypeRef());
        FeatureSource polySource = (FeatureSource) layers.get(getRestrictedPolygonTypeRef());

        Object[] polys = polySource.getFeatures().collection().toArray();
        Object[] points = pointSource.getFeatures().collection().toArray();

        if (!envelope.contains(polySource.getBounds())) {
            results.error((Feature) polys[0],
                "Point Feature Source is not contained within the Envelope provided.");

            return false;
        }

        if (!envelope.contains(pointSource.getBounds())) {
            results.error((Feature) points[0],
                "Line Feature Source is not contained within the Envelope provided.");

            return false;
        }

        for (int i = 0; i < points.length; i++) {
            Feature tmp = (Feature) points[i];
            Geometry gt = tmp.getDefaultGeometry();

            if (gt instanceof Polygon) {
            	Polygon ls = (Polygon) gt;

                boolean r = false;
                for (int j = 0; j < polys.length && !r; j++) {
                    Feature tmp2 = (Feature) polys[j];
                    Geometry gt2 = tmp2.getDefaultGeometry();

                    if (gt2 instanceof Point) {
                    	Point pt = (Point) gt2;
                        if(!ls.contains(pt)){
=====================================================================
Found a 59 line (255 tokens) duplication in the following files: 
Starting at line 56 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/spatial/PointInsidePolygonValidation.java
Starting at line 57 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/spatial/PointCoveredByPolygonBoundaryValidation.java
    public PointCoveredByPolygonBoundaryValidation() {
        super();
    }

    /**
     * Ensure Point is covered by the Polygon Boundary.
     * 
     * <p></p>
     *
     * @param layers a HashMap of key="TypeName" value="FeatureSource"
     * @param envelope The bounding box of modified features
     * @param results Storage for the error and warning messages
     *
     * @return True if no features intersect. If they do then the validation
     *         failed.
     *
     * @throws Exception DOCUMENT ME!
     *
     * @see org.geotools.validation.IntegrityValidation#validate(java.util.Map,
     *      com.vividsolutions.jts.geom.Envelope,
     *      org.geotools.validation.ValidationResults)
     */
    public boolean validate(Map layers, Envelope envelope,
        ValidationResults results) throws Exception {
        FeatureSource pointSource = (FeatureSource) layers.get(getPointTypeRef());
        FeatureSource polySource = (FeatureSource) layers.get(getRestrictedPolygonTypeRef());

        Object[] polys = polySource.getFeatures().collection().toArray();
        Object[] points = pointSource.getFeatures().collection().toArray();

        if (!envelope.contains(polySource.getBounds())) {
            results.error((Feature) polys[0],
                "Point Feature Source is not contained within the Envelope provided.");

            return false;
        }

        if (!envelope.contains(pointSource.getBounds())) {
            results.error((Feature) points[0],
                "Line Feature Source is not contained within the Envelope provided.");

            return false;
        }

        for (int i = 0; i < points.length; i++) {
            Feature tmp = (Feature) points[i];
            Geometry gt = tmp.getDefaultGeometry();

            if (gt instanceof Polygon) {
            	Polygon ls = (Polygon) gt;

                boolean r = false;
                for (int j = 0; j < polys.length && !r; j++) {
                    Feature tmp2 = (Feature) polys[j];
                    Geometry gt2 = tmp2.getDefaultGeometry();

                    if (gt2 instanceof Point) {
                    	Point pt = (Point) gt2;
                        if(!ls.getBoundary().contains(pt)){
=====================================================================
Found a 34 line (244 tokens) duplication in the following files: 
Starting at line 185 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/LiteRenderer.java
Starting at line 122 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/renderer/style/SLDStyleFactory.java
    private static final Canvas obs = new Canvas();

    static { //static block to populate the lookups
        joinLookup.put("miter", new Integer(BasicStroke.JOIN_MITER));
        joinLookup.put("bevel", new Integer(BasicStroke.JOIN_BEVEL));
        joinLookup.put("round", new Integer(BasicStroke.JOIN_ROUND));

        capLookup.put("butt", new Integer(BasicStroke.CAP_BUTT));
        capLookup.put("round", new Integer(BasicStroke.CAP_ROUND));
        capLookup.put("square", new Integer(BasicStroke.CAP_SQUARE));

        fontStyleLookup.put("normal", new Integer(java.awt.Font.PLAIN));
        fontStyleLookup.put("italic", new Integer(java.awt.Font.ITALIC));
        fontStyleLookup.put("oblique", new Integer(java.awt.Font.ITALIC));
        fontStyleLookup.put("bold", new Integer(java.awt.Font.BOLD));

        /**
         * A list of wellknownshapes that we know about: square, circle, triangle, star, cross, x.
         * Note arrow is an implementation specific mark.
         */
        wellKnownMarks.add("Square");
        wellKnownMarks.add("Triangle");
        wellKnownMarks.add("Cross");
        wellKnownMarks.add("Circle");
        wellKnownMarks.add("Star");
        wellKnownMarks.add("X");
        wellKnownMarks.add("Arrow");
        wellKnownMarks.add("square");
        wellKnownMarks.add("triangle");
        wellKnownMarks.add("cross");
        wellKnownMarks.add("circle");
        wellKnownMarks.add("star");
        wellKnownMarks.add("x");
        wellKnownMarks.add("arrow");
=====================================================================
Found a 39 line (232 tokens) duplication in the following files: 
Starting at line 390 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/rendering-styling/tests/unit/org/geotools/styling/RenderingGridCoverageTest.java
Starting at line 285 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/rendering-styling/tests/unit/org/geotools/styling/DefaultMarkTest.java
                "DefaultMarkTest_" + renderer.getClass().getName().replace('.', '_') + ".png");

        RenderedImage image2 = (RenderedImage) JAI.create("fileload", file2.toString());

        assertNotNull("Failed to load exemplar image", image2);

        Raster data = image.getData();
        Raster data2 = image2.getData();
        int[] pixel1 = null;
        int[] pixel2 = null;
        boolean isBlack = false;

        for (int x = 0; x < data.getWidth(); x++) {
            for (int y = 0; y < data.getHeight(); y++) {
                pixel1 = data.getPixel(x, y, pixel1);
                pixel2 = data2.getPixel(x, y, pixel2);

                if ((notBlack(pixel1)) && (notBlack(pixel2))) { //Since text is black and fonts are not stable across platforms, ignore pixels where at least one is black.

                    for (int band = 0; band < data2.getNumBands(); band++) {
                        assertEquals("mismatch in image comparison at (x: " + x + " y: " + y
                            + " band: " + band + ")", pixel1[band], pixel2[band]);
                    }
                }
            }
        }
    }

    private boolean notBlack(int[] pixel) {
        boolean isBlack = true;
        int x = 0;

        while (isBlack && (x < pixel.length)) {
            isBlack = (pixel[x] == 0);
            x++;
        }

        return !(isBlack);
    }
=====================================================================
Found a 38 line (231 tokens) duplication in the following files: 
Starting at line 70 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/tests/unit/org/geotools/filter/DOMParserTest.java
Starting at line 81 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/tests/unit/org/geotools/filter/ParserTest.java
    }

    public void setUp() throws SchemaException, IllegalAttributeException {
        super.setUp();

        FeatureTypeFactory feaTypeFactory = FeatureTypeFactory.createTemplate(testSchema);
        AttributeType doubleAttribute2 = attFactory.newAttributeType("testZeroDouble",
                Double.class);
        feaTypeFactory.addType(doubleAttribute2);
        testSchema = feaTypeFactory.getFeatureType();

        GeometryFactory geomFac = new GeometryFactory();

        // Creates coordinates for the linestring
        Coordinate[] coords = new Coordinate[3];
        coords[0] = new Coordinate(1, 2);
        coords[1] = new Coordinate(3, 4);
        coords[2] = new Coordinate(5, 6);

        // Builds the test feature
        Object[] attributes = new Object[11];
        attributes[0] = geomFac.createLineString(coords);
        attributes[1] = new Boolean(true);
        attributes[2] = new Character('t');
        attributes[3] = new Byte("10");
        attributes[4] = new Short("101");
        attributes[5] = new Integer(1002);
        attributes[6] = new Long(10003);
        attributes[7] = new Float(10000.4);
        attributes[8] = new Double(100000.5);
        attributes[9] = "test string data";
        attributes[10] = new Double(0.0);

        // Creates the feature itself
        testFeature = testSchema.create(attributes);
    }

    public void test1() throws Exception {
=====================================================================
Found a 54 line (228 tokens) duplication in the following files: 
Starting at line 55 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/spatial/PolygonNotCoveredByPolygonValidation.java
Starting at line 55 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/spatial/PolygonCoveredByPolygonValidation.java
    public PolygonCoveredByPolygonValidation() {
        super();
    }

    /**
     * Ensure Polygon is covered by the Polygon.
     * 
     * <p></p>
     *
     * @param layers a HashMap of key="TypeName" value="FeatureSource"
     * @param envelope The bounding box of modified features
     * @param results Storage for the error and warning messages
     *
     * @return True if no features intersect. If they do then the validation
     *         failed.
     *
     * @throws Exception DOCUMENT ME!
     *
     * @see org.geotools.validation.IntegrityValidation#validate(java.util.Map,
     *      com.vividsolutions.jts.geom.Envelope,
     *      org.geotools.validation.ValidationResults)
     */
    public boolean validate(Map layers, Envelope envelope,
        ValidationResults results) throws Exception {
        FeatureSource polySource1 = (FeatureSource) layers.get(getPolygonTypeRef());
        FeatureSource polySource2 = (FeatureSource) layers.get(getRestrictedPolygonTypeRef());

        Object[] poly1 = polySource1.getFeatures().collection().toArray();
        Object[] poly2 = polySource2.getFeatures().collection().toArray();

        if (!envelope.contains(polySource1.getBounds())) {
            results.error((Feature) poly1[0],
                "Polygon Feature Source is not contained within the Envelope provided.");

            return false;
        }

        if (!envelope.contains(polySource2.getBounds())) {
            results.error((Feature) poly1[0],
                "Restricted Polygon Feature Source is not contained within the Envelope provided.");

            return false;
        }

        for (int i = 0; i < poly2.length; i++) {
            Feature tmp = (Feature) poly2[i];
            Geometry gt = tmp.getDefaultGeometry();

            for (int j = 0; j < poly1.length; j++) {
                Feature tmp2 = (Feature) poly1[j];
                Geometry gt2 = tmp2.getDefaultGeometry();

                if (gt2.within(gt)) {
                    return true;
=====================================================================
Found a 85 line (227 tokens) duplication in the following files: 
Starting at line 154 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/DisjointIntegrity.java
Starting at line 156 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/ContainsIntegrity.java
Starting at line 163 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/WithinIntegrity.java
Starting at line 193 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/RelateIntegrity.java
Starting at line 165 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/TouchesIntegrity.java
Starting at line 156 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/IntersectsIntegrity.java
						results.error( f1, f1.getDefaultGeometry().getGeometryType()+" "+getGeomTypeRefA()+" intersects "+getGeomTypeRefB()+"("+f2.getID()+"), Result was not "+expected );
						success = false;
					}
				}		
			}
		}finally
		{
			/** Close the connections too the feature readers*/
			try {
				fr1.close();
				if (fr2 != null)
					fr2.close();
			} catch (IOException e4) {
				e4.printStackTrace();
				throw e4;
			}
		}
				
		return success;
	}



	/**
	 * <b>validateSingleLayer Purpose:</b> <br>
	 * <p>
	 * This validation tests for a geometry that intersects with itself. 
	 * Uses JTS' Geometry.intersects(Geometry) method.
	 * </p>
	 * 
	 * <b>Description:</b><br>
	 * <p>
	 * The function filters the FeatureSource using the given bounding box.
	 * It creates iterators over the filtered FeatureSource. It calls intersects() using the
	 * geometries in the FeatureSource layer. Tests the results of the method call against
	 * the given expected results. Returns true if the returned results and the expected results 
	 * are true, false otherwise.
	 * 
	 * </p>	 * 
	 * Author: bowens<br>
	 * Created on: Apr 27, 2004<br>
	 * @param featureSourceA - the FeatureSource to pull the original geometries from. 
	 * @param expected - boolean value representing the user's expected outcome of the test
	 * @param results - ValidationResults
	 * @param bBox - Envelope - the bounding box within which to perform the intersects()
	 * @return boolean result of the test
	 * @throws Exception - IOException if iterators improperly closed
	 */
	private boolean validateSingleLayer(FeatureSource featureSourceA, 
										boolean expected, 
										ValidationResults results, 
										Envelope bBox) 
	throws Exception
	{
		boolean success = true;
		
		FilterFactory ff = FilterFactory.createFilterFactory();
		Filter filter = null;

		filter = (Filter) ff.createBBoxExpression(bBox);

		FeatureResults featureResults = featureSourceA.getFeatures(filter);
		
		FeatureReader fr1 = null;
		FeatureReader fr2 = null;
		try 
		{
			fr1 = featureResults.reader();

			if (fr1 == null)
				return false;
					
			while (fr1.hasNext())
			{
				Feature f1 = fr1.next();
				Geometry g1 = f1.getDefaultGeometry();
				fr2 = featureResults.reader();
				
				while (fr2 != null && fr2.hasNext())
				{
					Feature f2 = fr2.next();
					Geometry g2 = f2.getDefaultGeometry();
					if (!f1.getID().equals(f2.getID()))	// if they are the same feature, move onto the next one
					{
						if(g1.intersects(g2) != expected )
=====================================================================
Found a 56 line (218 tokens) duplication in the following files: 
Starting at line 179 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/mysql/src/org/geotools/data/mysql/MySQLDataStore.java
Starting at line 506 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/src/org/geotools/data/postgis/PostgisDataStore.java
            if (Character.isLetter(ch) || (ch == '_')) {
                sql.append("'");
                sql.append(fid);
                sql.append("'");
            } else if (Character.isDigit(ch)) {
                try {
                    long number = Long.parseLong(fid);
                    sql.append(number);
                } catch (NumberFormatException badNumber) {
                    sql.append(fid);
                }
            } else {
                sql.append(fid);
            }

            sql.append(", ");
        }

        for (int j = 0; j < attributes.length; j++) {
            if (types[j].isGeometry()) {
                String geomName = types[j].getName();
                int srid = ftInfo.getSRID(geomName);
                String geoText = getGeometryText((Geometry) attributes[j], srid);
                sql.append(geoText);

                //String geoText = geometryWriter.write((Geometry) attributes[j]);
                //sql.append("GeometryFromText('" + geoText + "', " + srid + ")");
            } else {
                attrValue = addQuotes(attributes[j]);
                sql.append(attrValue);
            }

            if (j < (attributes.length - 1)) {
                sql.append(", ");
            }
        }

        sql.append(");");

        return sql.toString();
    }

    /**
     * Adds quotes to an object for storage in postgis.  The object should be a
     * string or a number.  To perform an insert strings need quotes around
     * them, and numbers work fine with quotes, so this method can be called
     * on unknown objects.
     *
     * @param value The object to add quotes to.
     *
     * @return a string representation of the object with quotes.
     */
    private String addQuotes(Object value) {
        String retString;

        if (value != null) {
=====================================================================
Found a 48 line (213 tokens) duplication in the following files: 
Starting at line 62 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/spatial/LineIntersectsLineWithNodeValidation.java
Starting at line 60 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/spatial/LineEndPointCoveredByLineValidation.java
    public LineEndPointCoveredByLineValidation() {
        super();
    }

    /**
     * Ensure Line End Point is covered by the Line.
     * 
     * <p></p>
     *
     * @param layers a HashMap of key="TypeName" value="FeatureSource"
     * @param envelope The bounding box of modified features
     * @param results Storage for the error and warning messages
     *
     * @return True if no features intersect. If they do then the validation
     *         failed.
     *
     * @throws Exception DOCUMENT ME!
     *
     * @see org.geotools.validation.IntegrityValidation#validate(java.util.Map,
     *      com.vividsolutions.jts.geom.Envelope,
     *      org.geotools.validation.ValidationResults)
     */
    public boolean validate(Map layers, Envelope envelope,
        ValidationResults results) throws Exception {

    	boolean r = true;
    	
        FeatureSource fsLine = (FeatureSource) layers.get(getLineTypeRef());
        FeatureResults frLine = fsLine.getFeatures();
        FeatureCollection fcLine = frLine.collection();
        FeatureIterator fLine = fcLine.features();
        
        FeatureSource fsRLine = (FeatureSource) layers.get(getRestrictedLineTypeRef());
        FeatureResults frRLine = fsRLine.getFeatures();
        FeatureCollection fcRLine = frRLine.collection();
                
        while(fLine.hasNext()){
        	Feature line = fLine.next();
        	FeatureIterator fRLine = fcRLine.features();
        	Geometry lineGeom = line.getDefaultGeometry();
        	if(envelope.contains(lineGeom.getEnvelopeInternal())){
        		// 	check for valid comparison
        		if(LineString.class.isAssignableFrom(lineGeom.getClass())){
        			while(fRLine.hasNext()){
        				Feature rLine = fRLine.next();
        				Geometry rLineGeom = rLine.getDefaultGeometry(); 
        				if(envelope.contains(rLineGeom.getEnvelopeInternal())){
        					if(LineString.class.isAssignableFrom(rLineGeom.getClass())){
=====================================================================
Found a 100 line (211 tokens) duplication in the following files: 
Starting at line 49 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gcs-coverage/src/org/geotools/resources/gcs/Resources.java
Starting at line 49 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/resources/src/org/geotools/resources/rsc/Resources.java
public class Resources extends ResourceBundle {
    /**
     * Construct a resource bundle using english language.
     * This is the default when no resource are available
     * in user language.
     */
    public Resources() {
        super(// Set 'true' in front of language to use as default.
              false ? Resources_fr.FILEPATH :
               true ? Resources_en.FILEPATH :
               null);
    }

    /**
     * Construct a resource bundle
     * using the specified UTF8 file.
     */
    Resources(final String filepath) {
        super(filepath);
    }

    /**
     * Returns resources in the given locale.
     *
     * @param  local The locale, or <code>null</code> for the default locale.
     * @return Resources in the given locale.
     * @throws MissingResourceException if resources can't be found.
     */
    public static Resources getResources(Locale locale) throws MissingResourceException {
        if (locale==null) {
            locale = Locale.getDefault();
        }
        return (Resources) getBundle(Resources.class.getName(), locale);
        /*
         * We rely on cache capability of {@link java.util.ResourceBundle}.
         */
    }

    /**
     * Gets a string for the given key from this resource bundle or one of its
     * parents.
     *
     * @param  key The key for the desired string.
     * @return The string for the given key.
     * @throws MissingResourceException If no object for the given key can be
     * found.
     */
    public static String format(final int key) throws MissingResourceException {
        return getResources(null).getString(key);
    }

    /**
     * Gets a string for the given key are replace all occurence of "{0}"
     * with values of <code>arg0</code>.
     *
     * @param  key The key for the desired string.
     * @param  arg0 Value to substitute to "{0}".
     * @return The formatted string for the given key.
     * @throws MissingResourceException If no object for the given key can be
     *         found.
     */
    public static String format(final int     key,
                                final Object arg0) throws MissingResourceException {
        return getResources(null).getString(key, arg0);
    }

    /**
     * Gets a string for the given key are replace all occurence of "{0}",
     * "{1}", with values of <code>arg0</code>, <code>arg1</code>.
     *
     * @param  key The key for the desired string.
     * @param  arg0 Value to substitute to "{0}".
     * @param  arg1 Value to substitute to "{1}".
     * @return The formatted string for the given key.
     * @throws MissingResourceException If no object for the given key can be
     *         found.
     */
    public static String format(final int     key,
                                final Object arg0,
                                final Object arg1) throws MissingResourceException {
        return getResources(null).getString(key, arg0, arg1);
    }

    /**
     * Gets a string for the given key are replace all occurence of "{0}",
     * "{1}", with values of <code>arg0</code>, <code>arg1</code>, etc.
     *
     * @param  key The key for the desired string.
     * @param  arg0 Value to substitute to "{0}".
     * @param  arg1 Value to substitute to "{1}".
     * @param  arg2 Value to substitute to "{2}".
     * @return The formatted string for the given key.
     * @throws MissingResourceException If no object for the given key can be found.
     */
    public static String format(final int     key,
                                final Object arg0,
                                final Object arg1,
                                final Object arg2) throws MissingResourceException {
        return getResources(null).getString(key, arg0, arg1, arg2);
    }
=====================================================================
Found a 29 line (209 tokens) duplication in the following files: 
Starting at line 96 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/shapefile/src/org/geotools/data/shapefile/ShapefileDataStore.java
Starting at line 77 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/shapefile/src/org/geotools/data/shapefile/ShapefileDataSource.java
  public ShapefileDataSource(URL url) throws java.net.MalformedURLException {
    
    String filename = null;
    if (url == null) {
      throw new NullPointerException("Null URL for ShapefileDataSource");
    }
    try {
      filename = java.net.URLDecoder.decode(url.toString(),"US-ASCII");
    } catch (java.io.UnsupportedEncodingException use) {
      throw new java.net.MalformedURLException(
      "Unable to decode " + url + " cause " + use.getMessage()
      );
    }
    
    String shpext = ".shp";
    String dbfext = ".dbf";
    String shxext = ".shx";
    
    if(filename.endsWith(shpext) || filename.endsWith(dbfext) || filename.endsWith(shxext)) {
      filename = filename.substring(0, filename.length() - 4);
    } else if(filename.endsWith(".SHP") || filename.endsWith(".DBF") || filename.endsWith(".SHX")) {
      filename = filename.substring(0, filename.length() - 4);
      shpext = ".SHP";
      dbfext = ".DBF";
      shxext = ".SHX";
    }
    shpURL = new URL(filename + shpext);
    dbfURL = new URL(filename + dbfext);
    shxURL = new URL(filename + shxext);
=====================================================================
Found a 43 line (207 tokens) duplication in the following files: 
Starting at line 62 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/spatial/LineCoveredByPolygonBoundaryValidation.java
Starting at line 81 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/spatial/LineCoveredByPolygonValidation.java
    }

    /**
     * Check that lineTypeRef is convered by polygonTypeRef.
     * 
     * <p>
     * Detailed description...
     * </p>
     *
     * @param layers Map of FeatureSource by "dataStoreID:typeName"
     * @param envelope The bounding box that encloses the unvalidated data
     * @param results Used to coallate results information
     *
     * @return <code>true</code> if all the features pass this test.
     *
     * @throws Exception DOCUMENT ME!
     */
    public boolean validate(Map layers, Envelope envelope,
        ValidationResults results) throws Exception {

    	boolean r = true;
    	
        FeatureSource fsLine = (FeatureSource) layers.get(getLineTypeRef());
        FeatureResults frLine = fsLine.getFeatures();
        FeatureCollection fcLine = frLine.collection();
        FeatureIterator fLine = fcLine.features();
        
        FeatureSource fsPoly = (FeatureSource) layers.get(getRestrictedPolygonTypeRef());
        FeatureResults frPoly = fsPoly.getFeatures();
        FeatureCollection fcPoly = frPoly.collection();
                
        while(fLine.hasNext()){
        	Feature line = fLine.next();
        	FeatureIterator fPoly = fcPoly.features();
        	Geometry lineGeom = line.getDefaultGeometry();
        	if(envelope.contains(lineGeom.getEnvelopeInternal())){
        		// 	check for valid comparison
        		if(LineString.class.isAssignableFrom(lineGeom.getClass())){
        			while(fPoly.hasNext()){
        				Feature poly = fPoly.next();
        				Geometry polyGeom = poly.getDefaultGeometry(); 
        				if(envelope.contains(polyGeom.getEnvelopeInternal())){
        					if(Polygon.class.isAssignableFrom(polyGeom.getClass())){
=====================================================================
Found a 42 line (207 tokens) duplication in the following files: 
Starting at line 492 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/src/org/geotools/data/postgis/PostgisDataSource.java
Starting at line 661 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/src/org/geotools/data/postgis/PostgisFeatureStore.java
        throws IOException {
        //one to one relationship for now, so typeName is not used.
        //String tableName = query.getTypeName();
        tableName = this.tableName;

        boolean useLimit = (unpacker.getUnSupported() == null);
        Filter filter = unpacker.getSupported();
        LOGGER.fine("Filter in making sql is " + filter);

        StringBuffer sqlStatement = new StringBuffer("SELECT ");
        sqlStatement.append(fidColumn);

        AttributeType[] attributeTypes = getAttTypes(query);
        int numAttributes = attributeTypes.length;
        LOGGER.finer("making sql for " + numAttributes + " attributes");

        for (int i = 0; i < numAttributes; i++) {
            String curAttName = attributeTypes[i].getName();

            if (Geometry.class.isAssignableFrom(attributeTypes[i].getType())) {
                sqlStatement.append(", AsText(force_2d(\"" + curAttName
                    + "\"))");

                //REVISIT, see getIdColumn note.
            } else if (fidColumn.equals(curAttName)) {
                //do nothing, already covered by fid
            } else {
                sqlStatement.append(", \"" + curAttName + "\"");
            }
        }

        String where = "";

        if (filter != null) {
            try {
                where = encoder.encode(filter);
            } catch (SQLEncoderException sqle) {
                String message = "Encoder error" + sqle.getMessage();
                LOGGER.warning(message);
                throw new DataSourceException(message, sqle);
            }
        }
=====================================================================
Found a 44 line (205 tokens) duplication in the following files: 
Starting at line 147 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ParseException.java
Starting at line 40 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/TokenMgrError.java
   protected static final String addEscapes(String str) {
      StringBuffer retval = new StringBuffer();
      char ch;
      for (int i = 0; i < str.length(); i++) {
        switch (str.charAt(i))
        {
           case 0 :
              continue;
           case '\b':
              retval.append("\\b");
              continue;
           case '\t':
              retval.append("\\t");
              continue;
           case '\n':
              retval.append("\\n");
              continue;
           case '\f':
              retval.append("\\f");
              continue;
           case '\r':
              retval.append("\\r");
              continue;
           case '\"':
              retval.append("\\\"");
              continue;
           case '\'':
              retval.append("\\\'");
              continue;
           case '\\':
              retval.append("\\\\");
              continue;
           default:
              if ((ch = str.charAt(i)) < 0x20 || ch > 0x7e) {
                 String s = "0000" + Integer.toString(ch, 16);
                 retval.append("\\u" + s.substring(s.length() - 4, s.length()));
              } else {
                 retval.append(ch);
              }
              continue;
        }
      }
      return retval.toString();
   }
=====================================================================
Found a 98 line (202 tokens) duplication in the following files: 
Starting at line 49 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gui/src/org/geotools/resources/gui/Resources.java
Starting at line 49 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/resources/renderer/Resources.java
public class Resources extends ResourceBundle {
    /**
     * Construct a resource bundle using english language.
     * This is the default when no resource are available
     * in user language.
     */
    public Resources() {
        super(Resources_en.FILEPATH);
    }

    /**
     * Construct a resource bundle
     * using the specified UTF8 file.
     */
    Resources(final String filepath) {
        super(filepath);
    }

    /**
     * Returns resources in the given locale.
     *
     * @param  local The locale, or <code>null</code> for the default locale.
     * @return Resources in the given locale.
     * @throws MissingResourceException if resources can't be found.
     */
    public static Resources getResources(Locale locale) throws MissingResourceException {
        if (locale==null) {
            locale = Locale.getDefault();
        }
        return (Resources) getBundle(Resources.class.getName(), locale);
        /*
         * We rely on cache capability of {@link java.util.ResourceBundle}.
         */
    }

    /**
     * Gets a string for the given key from this resource bundle or one of its
     * parents.
     *
     * @param  key The key for the desired string.
     * @return The string for the given key.
     * @throws MissingResourceException If no object for the given key can be
     * found.
     */
    public static String format(final int key) throws MissingResourceException {
        return getResources(null).getString(key);
    }

    /**
     * Gets a string for the given key are replace all occurence of "{0}"
     * with values of <code>arg0</code>.
     *
     * @param  key The key for the desired string.
     * @param  arg0 Value to substitute to "{0}".
     * @return The formatted string for the given key.
     * @throws MissingResourceException If no object for the given key can be
     *         found.
     */
    public static String format(final int     key,
                                final Object arg0) throws MissingResourceException {
        return getResources(null).getString(key, arg0);
    }

    /**
     * Gets a string for the given key are replace all occurence of "{0}",
     * "{1}", with values of <code>arg0</code>, <code>arg1</code>.
     *
     * @param  key The key for the desired string.
     * @param  arg0 Value to substitute to "{0}".
     * @param  arg1 Value to substitute to "{1}".
     * @return The formatted string for the given key.
     * @throws MissingResourceException If no object for the given key can be
     *         found.
     */
    public static String format(final int     key,
                                final Object arg0,
                                final Object arg1) throws MissingResourceException {
        return getResources(null).getString(key, arg0, arg1);
    }

    /**
     * Gets a string for the given key are replace all occurence of "{0}",
     * "{1}", with values of <code>arg0</code>, <code>arg1</code>, etc.
     *
     * @param  key The key for the desired string.
     * @param  arg0 Value to substitute to "{0}".
     * @param  arg1 Value to substitute to "{1}".
     * @param  arg2 Value to substitute to "{2}".
     * @return The formatted string for the given key.
     * @throws MissingResourceException If no object for the given key can be found.
     */
    public static String format(final int     key,
                                final Object arg0,
                                final Object arg1,
                                final Object arg2) throws MissingResourceException {
        return getResources(null).getString(key, arg0, arg1, arg2);
    }
}
=====================================================================
Found a 33 line (201 tokens) duplication in the following files: 
Starting at line 396 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/rendering-styling/tests/unit/org/geotools/styling/RenderingGridCoverageTest.java
Starting at line 330 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/rendering-styling/tests/unit/org/geotools/styling/TextStyleTest.java
        Raster data = image1.getData();
        Raster data2 = image2.getData();
        int[] pixel1 = null;
        int[] pixel2 = null;
        boolean isBlack = false;

        for (int x = 0; x < data.getWidth(); x++) {
            for (int y = 0; y < data.getHeight(); y++) {
                pixel1 = data.getPixel(x, y, pixel1);
                pixel2 = data2.getPixel(x, y, pixel2);

                if ((notBlack(pixel1)) && (notBlack(pixel2))) { //Since text is black and fonts are not stable across platforms, ignore pixels where at least one is black.

                    for (int band = 0; band < data2.getNumBands(); band++) {
                        assertEquals("mismatch in image comparison at (x: " + x + " y: " + y
                            + " band: " + band + ")", pixel1[band], pixel2[band]);
                    }
                }
            }
        }
    }

    private boolean notBlack(int[] pixel) {
        boolean isBlack = true;
        int x = 0;

        while (isBlack && (x < pixel.length)) {
            isBlack = (pixel[x] == 0);
            x++;
        }

        return !(isBlack);
    }
=====================================================================
Found a 50 line (198 tokens) duplication in the following files: 
Starting at line 56 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/spatial/PointCoveredByLineValidation.java
Starting at line 57 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/spatial/PointCoveredByEndPointOfLineValidation.java
    public PointCoveredByEndPointOfLineValidation() {
        super();
    }

    /**
     * Ensure Point is covered by a Line end point.
     * 
     * <p></p>
     *
     * @param layers a HashMap of key="TypeName" value="FeatureSource"
     * @param envelope The bounding box of modified features
     * @param results Storage for the error and warning messages
     *
     * @return True if no features intersect. If they do then the validation
     *         failed.
     *
     * @throws Exception DOCUMENT ME!
     *
     * @see org.geotools.validation.IntegrityValidation#validate(java.util.Map,
     *      com.vividsolutions.jts.geom.Envelope,
     *      org.geotools.validation.ValidationResults)
     */
    public boolean validate(Map layers, Envelope envelope,
        ValidationResults results) throws Exception {
        FeatureSource lineSource = (FeatureSource) layers.get(getRestrictedLineTypeRef());
        FeatureSource pointSource = (FeatureSource) layers.get(getPointTypeRef());

        Object[] points = pointSource.getFeatures().collection().toArray();
        Object[] lines = lineSource.getFeatures().collection().toArray();

        if (!envelope.contains(pointSource.getBounds())) {
            results.error((Feature) points[0],
                "Point Feature Source is not contained within the Envelope provided.");

            return false;
        }

        if (!envelope.contains(lineSource.getBounds())) {
            results.error((Feature) lines[0],
                "Line Feature Source is not contained within the Envelope provided.");

            return false;
        }

        for (int i = 0; i < lines.length; i++) {
            Feature tmp = (Feature) lines[i];
            Geometry gt = tmp.getDefaultGeometry();

            if (gt instanceof LineString) {
                LineString ls = (LineString) gt;
=====================================================================
Found a 28 line (197 tokens) duplication in the following files: 
Starting at line 200 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/tests/unit/org/geotools/filter/DOMParserTest.java
Starting at line 234 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/tests/unit/org/geotools/filter/DOMParserTest.java
    public Filter parseDocumentFirst(String uri) throws Exception {
        Filter filter = null;
        DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
        DocumentBuilder db = dbf.newDocumentBuilder();
        Document dom = db.parse(uri);
        LOGGER.fine("parsing " + uri);

        // first grab a filter node
        NodeList nodes = dom.getElementsByTagName("Filter");

        for (int j = 0; j < nodes.getLength(); j++) {
            Element filterNode = (Element) nodes.item(j);
            NodeList list = filterNode.getChildNodes();
            Node child = null;

            for (int i = 0; i < list.getLength(); i++) {
                child = list.item(i);

                if ((child == null)
                        || (child.getNodeType() != Node.ELEMENT_NODE)) {
                    continue;
                }

                filter = FilterDOMParser.parseFilter(child);
                assertNotNull("Null filter returned", filter);
                LOGGER.finer("filter: " + filter.getClass().toString());
                LOGGER.fine("parsed: " + filter.toString());
                LOGGER.finer("result " + filter.contains(testFeature));
=====================================================================
Found a 40 line (192 tokens) duplication in the following files: 
Starting at line 446 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/wmsserver/src/org/geotools/wms/WMSServlet.java
Starting at line 667 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/wmsserver/src/org/geotools/wms/WMSServlet.java
        } catch (WMSException wmsexp) {
            doException(wmsexp.getCode(), wmsexp.getMessage(), request,
                response, exceptions);
            return;
        } catch (Exception exp) {
            doException(null,
                "Unknown exception : " + exp + " : " + exp.getStackTrace()[0] +
                exp.getMessage(), request, response, exceptions);
            return;
        }

        // Write the response
        response.setContentType(format);

        OutputStream out = response.getOutputStream();

        // avoid caching in browser
        response.setHeader("Pragma", "no-cache");
        response.setHeader("Cache-Control", "no-cache");
        response.setDateHeader("Expires", 0);

        try {
            formatImageOutputStream(format, image, out);
        } catch (Exception exp) {
            exp.printStackTrace();
            LOGGER.severe(
                "Unable to complete image generation after response started : " +
                exp + exp.getMessage());

            if (exp instanceof SecurityException) {
                response.sendError(500,
                    "Image generation failed because of: " +
                    exp.getStackTrace()[0] +
                    " JAI may not have 'write' and 'delete' permissions in temp folder");
            } else {
                response.sendError(500,
                    "Image generation failed because of: " +
                    exp.getStackTrace()[0] + "Check JAI configuration");
            }
        }//finally{
=====================================================================
Found a 44 line (188 tokens) duplication in the following files: 
Starting at line 644 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/resources/src/org/geotools/resources/NumberParser.java
Starting at line 702 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/resources/src/org/geotools/resources/NumberParser.java
        low  = (b <  m );
        high = (b+m > tens );
        if ( q >= 10 ){
          // bummer, dude
          throw new RuntimeException( "Assertion botch: excessivly large digit "+q);
        } else if ( (q == 0) && ! high ){
          // oops. Usually ignore leading zero.
          decExp--;
        } else {
          digits[ndigit++] = (char)('0' + q);
        }
    /*
     * HACK! Java spec sez that we always have at least
     * one digit after the . in either F- or E-form output.
     * Thus we will need more than one digit if we're using
     * E-form
     */
        if ( decExp <= -3 || decExp >= 8 ){
          high = low = false;
        }
        while( ! low && ! high ){
          q = (int) ( b / s );
          b = 10 * ( b % s );
          m *= 10;
          if ( q >= 10 ){
            // bummer, dude
            throw new RuntimeException( "Assertion botch: excessivly large digit "+q);
          }
          if ( m > 0L ){
            low  = (b <  m );
            high = (b+m > tens );
          } else {
            // hack -- m might overflow!
            // in this case, it is certainly > b,
            // which won't
            // and b+m > tens, too, since that has overflowed
            // either!
            low = true;
            high = true;
          }
          digits[ndigit++] = (char)('0' + q);
        }
        lowDigitDifference = (b<<1) - tens;
      }
=====================================================================
Found a 32 line (186 tokens) duplication in the following files: 
Starting at line 328 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/shapefile/tests/unit/org/geotools/data/shapefile/ShapefileDataStoreTest.java
Starting at line 217 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/shapefile/tests/unit/org/geotools/data/shapefile/ShapefileDataSourceTest.java
    FeatureCollection fc = s.getFeatures();
    FeatureIterator fci = fc.features();
    
    // verify
    while (fci.hasNext()) {
      Feature f = fci.next();
      Geometry fromShape = f.getDefaultGeometry();
      
      if (fromShape instanceof GeometryCollection) {
        if ( ! (geom instanceof GeometryCollection) ) {
          fromShape = ((GeometryCollection)fromShape).getGeometryN(0);
        }
      }
      try {
        Coordinate[] c1 = geom.getCoordinates();
        Coordinate[] c2 = fromShape.getCoordinates();
        for (int cc = 0, ccc = c1.length; cc < ccc; cc++) {
            //System.out.println(c1[cc] + "," + c2[cc]);
          if (d3)
            assertTrue(c1[cc].equals3D(c2[cc]));
          else
            assertTrue(c1[cc].equals2D(c2[cc]));
        }
      } catch (Throwable t) {
        fail("Bogus : " + Arrays.asList(geom.getCoordinates()) + " : " + Arrays.asList(fromShape.getCoordinates()));
      }
      
      
    }
    
    tmpFile.delete();
  }
=====================================================================
Found a 91 line (186 tokens) duplication in the following files: 
Starting at line 56 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gui/src/org/geotools/resources/gui/Resources.java
Starting at line 59 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/resources/src/org/geotools/resources/rsc/Resources.java
               null);
    }

    /**
     * Construct a resource bundle
     * using the specified UTF8 file.
     */
    Resources(final String filepath) {
        super(filepath);
    }

    /**
     * Returns resources in the given locale.
     *
     * @param  local The locale, or <code>null</code> for the default locale.
     * @return Resources in the given locale.
     * @throws MissingResourceException if resources can't be found.
     */
    public static Resources getResources(Locale locale) throws MissingResourceException {
        if (locale==null) {
            locale = Locale.getDefault();
        }
        return (Resources) getBundle(Resources.class.getName(), locale);
        /*
         * We rely on cache capability of {@link java.util.ResourceBundle}.
         */
    }

    /**
     * Gets a string for the given key from this resource bundle or one of its
     * parents.
     *
     * @param  key The key for the desired string.
     * @return The string for the given key.
     * @throws MissingResourceException If no object for the given key can be
     * found.
     */
    public static String format(final int key) throws MissingResourceException {
        return getResources(null).getString(key);
    }

    /**
     * Gets a string for the given key are replace all occurence of "{0}"
     * with values of <code>arg0</code>.
     *
     * @param  key The key for the desired string.
     * @param  arg0 Value to substitute to "{0}".
     * @return The formatted string for the given key.
     * @throws MissingResourceException If no object for the given key can be
     *         found.
     */
    public static String format(final int     key,
                                final Object arg0) throws MissingResourceException {
        return getResources(null).getString(key, arg0);
    }

    /**
     * Gets a string for the given key are replace all occurence of "{0}",
     * "{1}", with values of <code>arg0</code>, <code>arg1</code>.
     *
     * @param  key The key for the desired string.
     * @param  arg0 Value to substitute to "{0}".
     * @param  arg1 Value to substitute to "{1}".
     * @return The formatted string for the given key.
     * @throws MissingResourceException If no object for the given key can be
     *         found.
     */
    public static String format(final int     key,
                                final Object arg0,
                                final Object arg1) throws MissingResourceException {
        return getResources(null).getString(key, arg0, arg1);
    }

    /**
     * Gets a string for the given key are replace all occurence of "{0}",
     * "{1}", with values of <code>arg0</code>, <code>arg1</code>, etc.
     *
     * @param  key The key for the desired string.
     * @param  arg0 Value to substitute to "{0}".
     * @param  arg1 Value to substitute to "{1}".
     * @param  arg2 Value to substitute to "{2}".
     * @return The formatted string for the given key.
     * @throws MissingResourceException If no object for the given key can be found.
     */
    public static String format(final int     key,
                                final Object arg0,
                                final Object arg1,
                                final Object arg2) throws MissingResourceException {
        return getResources(null).getString(key, arg0, arg1, arg2);
    }
}
=====================================================================
Found a 14 line (186 tokens) duplication in the following files: 
Starting at line 96 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/tests/unit/org/geotools/renderer/lite/LiteShapeTest.java
Starting at line 549 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/rendering-styling/tests/unit/org/geotools/styling/RenderStyleTest.java
    private Polygon makeSamplePolygon(final GeometryFactory geomFac, double xoff, double yoff) {
        Coordinate[] polygonCoordinates = new Coordinate[10];
        polygonCoordinates[0] = new Coordinate(70 + xoff, 70 + yoff);
        polygonCoordinates[1] = new Coordinate(60 + xoff, 90 + yoff);
        polygonCoordinates[2] = new Coordinate(60 + xoff, 110 + yoff);
        polygonCoordinates[3] = new Coordinate(70 + xoff, 120 + yoff);
        polygonCoordinates[4] = new Coordinate(90 + xoff, 110 + yoff);
        polygonCoordinates[5] = new Coordinate(110 + xoff, 120 + yoff);
        polygonCoordinates[6] = new Coordinate(130 + xoff, 110 + yoff);
        polygonCoordinates[7] = new Coordinate(130 + xoff, 90 + yoff);
        polygonCoordinates[8] = new Coordinate(110 + xoff, 70 + yoff);
        polygonCoordinates[9] = new Coordinate(70 + xoff, 70 + yoff);

        try {
=====================================================================
Found a 92 line (185 tokens) duplication in the following files: 
Starting at line 56 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gui/src/org/geotools/resources/gui/Resources.java
Starting at line 59 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gcs-coverage/src/org/geotools/resources/gcs/Resources.java
                null);
    }
    
    /**
     * Construct a resource bundle
     * using the specified UTF8 file.
     */
    Resources(final String filepath) {
        super(filepath);
    }
    
    /**
     * Returns resources in the given locale.
     *
     * @param  local The locale, or <code>null</code> for the default locale.
     * @return Resources in the given locale.
     * @throws MissingResourceException if resources can't be found.
     */
    public static Resources getResources(Locale locale) throws MissingResourceException {
        if (locale==null) {
            locale = Locale.getDefault();
        }
        return (Resources) getBundle(Resources.class.getName(), locale);
        /*
         * We rely on cache capability of {@link java.util.ResourceBundle}.
         */
    }
    
    /**
     * Gets a string for the given key from this resource bundle or one of its parents.
     *
     * @param  key The key for the desired string.
     * @return The string for the given key.
     * @throws MissingResourceException If no object for the given key can be found.
     */
    public static String format(final int key) throws MissingResourceException {
        return getResources(null).getString(key);
    }
    
    /**
     * Gets a string for the given key are replace all occurence of "{0}"
     * with values of <code>arg0</code>.
     *
     * @param  key The key for the desired string.
     * @param  arg0 Value to substitute to "{0}".
     * @return The formatted string for the given key.
     * @throws MissingResourceException If no object for the given key can be found.
     */
    public static String format(final int    key,
                                final Object arg0)
        throws MissingResourceException
    {
        return getResources(null).getString(key, arg0);
    }
    
    /**
     * Gets a string for the given key are replace all occurence of "{0}",
     * "{1}", with values of <code>arg0</code>, <code>arg1</code>.
     *
     * @param  key The key for the desired string.
     * @param  arg0 Value to substitute to "{0}".
     * @param  arg1 Value to substitute to "{1}".
     * @return The formatted string for the given key.
     * @throws MissingResourceException If no object for the given key can be found.
     */
    public static String format(final int    key,
                                final Object arg0,
                                final Object arg1)
        throws MissingResourceException
    {
        return getResources(null).getString(key, arg0, arg1);
    }
    
    /**
     * Gets a string for the given key are replace all occurence of "{0}",
     * "{1}", with values of <code>arg0</code>, <code>arg1</code>, etc.
     *
     * @param  key The key for the desired string.
     * @param  arg0 Value to substitute to "{0}".
     * @param  arg1 Value to substitute to "{1}".
     * @param  arg2 Value to substitute to "{2}".
     * @return The formatted string for the given key.
     * @throws MissingResourceException If no object for the given key can be found.
     */
    public static String format(final int    key,
                                final Object arg0,
                                final Object arg1,
                                final Object arg2)
        throws MissingResourceException
    {
        return getResources(null).getString(key, arg0, arg1, arg2);
    }
=====================================================================
Found a 39 line (177 tokens) duplication in the following files: 
Starting at line 79 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gmldatasource/src/org/geotools/gml/TestParser.java
Starting at line 46 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/tests/unit/org/geotools/validation/LakesValidationTest.java
				LakesTestHandler contentHandler = new LakesTestHandler();
				GMLFilterGeometry geometryFilter = new GMLFilterGeometry(contentHandler);
				GMLFilterDocument documentFilter = new GMLFilterDocument(geometryFilter);
				XMLReader parser = XMLReaderFactory.createXMLReader(
				"org.apache.xerces.parsers.SAXParser");

				parser.setContentHandler(documentFilter);
				parser.parse(uri);
			} catch (IOException e) {
				System.out.println("Error reading uri: " + uri);
			} catch (SAXException e) {
				System.out.println("Error in parsing: " + e.getMessage());
			}
		}

		public static void parseFeatures(String uri) {
			System.out.println("Parsing the flat feature collection in this GML "
					+ "resource:" + uri);

			try {
				GMLDataSource data = new GMLDataSource(uri);
				FeatureCollection featureCollection = data.getFeatures(Query.ALL);

				Iterator i = featureCollection.iterator();

				while (i.hasNext()) {
					System.out.println("Parsed feature is ... " + i.next());
				}
			} catch (DataSourceException e) {
				System.out.println(
						"TestParser->parseFeatures DataSourceException: "
						+ e.toString());
			}

			//parsedFeatures.
			// chains all the appropriate filters together (in correct order)
			// and initiates parsing
		}	
}
=====================================================================
Found a 20 line (168 tokens) duplication in the following files: 
Starting at line 78 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/tests/unit/org/geotools/renderer/lite/LiteShapeTest.java
Starting at line 530 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/rendering-styling/tests/unit/org/geotools/styling/RenderStyleTest.java
        return !(isBlack);
    }

    private LineString makeSampleLineString(final GeometryFactory geomFac, double xoff, double yoff) {
        Coordinate[] linestringCoordinates = new Coordinate[8];
        linestringCoordinates[0] = new Coordinate(50.0d + xoff, 50.0d + yoff);
        linestringCoordinates[1] = new Coordinate(60.0d + xoff, 50.0d + yoff);
        linestringCoordinates[2] = new Coordinate(60.0d + xoff, 60.0d + yoff);
        linestringCoordinates[3] = new Coordinate(70.0d + xoff, 60.0d + yoff);
        linestringCoordinates[4] = new Coordinate(70.0d + xoff, 70.0d + yoff);
        linestringCoordinates[5] = new Coordinate(80.0d + xoff, 70.0d + yoff);
        linestringCoordinates[6] = new Coordinate(80.0d + xoff, 80.0d + yoff);
        linestringCoordinates[7] = new Coordinate(130.0d + xoff, 300.0d + yoff);

        LineString line = geomFac.createLineString(linestringCoordinates);

        return line;
    }

    private Polygon makeSamplePolygon(final GeometryFactory geomFac, double xoff, double yoff) {
=====================================================================
Found a 24 line (165 tokens) duplication in the following files: 
Starting at line 1544 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/LiteRenderer.java
Starting at line 1612 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/LiteRenderer.java
        float radius = ((Number) halo.getRadius().getValue(feature)).floatValue();

        Point2D mapCentre = new java.awt.geom.Point2D.Double(x, y);
        Point2D graphicCentre = new java.awt.geom.Point2D.Double();
        temp.transform(mapCentre, graphicCentre);
        labelAT.translate(graphicCentre.getX(), graphicCentre.getY());

        if (LOGGER.isLoggable(Level.FINER)) {
            LOGGER.finer("rotation " + rotation);
        }

        double shearY = temp.getShearY();
        double scaleY = temp.getScaleY();
        double scaleX = temp.getScaleX();
        double originalRotation = Math.atan(shearY / scaleY);

        if (LOGGER.isLoggable(Level.FINER)) {
            LOGGER.finer("originalRotation " + originalRotation);
        }

        labelAT.rotate(rotation - originalRotation);

        double xToyRatio = Math.abs(scaleX / scaleY);
        labelAT.scale(xToyRatio, 1.0 / xToyRatio);
=====================================================================
Found a 22 line (165 tokens) duplication in the following files: 
Starting at line 1378 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/LiteRenderer.java
Starting at line 1409 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/LiteRenderer.java
                String reqStyle = (String) fonts[k].getFontStyle().getValue(feature);

                if (fontStyleLookup.containsKey(reqStyle)) {
                    styleCode = ((Integer) fontStyleLookup.get(reqStyle))
                        .intValue();
                } else {
                    styleCode = java.awt.Font.PLAIN;
                }

                String reqWeight = (String) fonts[k].getFontWeight().getValue(feature);

                if (reqWeight.equalsIgnoreCase("Bold")) {
                    styleCode = styleCode | java.awt.Font.BOLD;
                }

                if ((fonts[k].getFontSize() == null)
                        || (fonts[k].getFontSize().getValue(feature) == null)) {
                    size = 10;
                } else {
                    size = ((Number) fonts[k].getFontSize().getValue(feature))
                        .intValue();
                }
=====================================================================
Found a 41 line (163 tokens) duplication in the following files: 
Starting at line 254 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/shapefile/tests/unit/org/geotools/data/shapefile/ShapefileDataStoreTest.java
Starting at line 155 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/shapefile/tests/unit/org/geotools/data/shapefile/ShapefileDataSourceTest.java
    tmpFile.delete();
  }
  
  public void testGeometriesWriting() throws Exception {
    
    
    String[] wktResources = new String[] {
      "point",
      "multipoint",
      "line",
      "multiline",
      "polygon",
      "multipolygon"
    };
    
    PrecisionModel pm = new PrecisionModel();
    for (int i = 0; i < wktResources.length; i++) {
      Geometry geom = readGeometry(wktResources[i]);
      String testName = wktResources[i];
      try {
        
        runWriteReadTest(geom,false);
        make3D(geom);
        testName += "3d";
        runWriteReadTest(geom,true);
      } catch (Throwable e) {
        throw new Exception("Error in " + testName,e); 
      }
      
    }
    
  }
  
  private void make3D(Geometry g) {
    Coordinate[] c = g.getCoordinates();
    for (int i = 0, ii = c.length; i < ii; i++) {
      c[i].z = 42 + i;
    }
  }
  
  private void runWriteReadTest(Geometry geom,boolean d3) throws Exception {
=====================================================================
Found a 24 line (160 tokens) duplication in the following files: 
Starting at line 103 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/tests/unit/org/geotools/renderer/lite/Rendering2DTest.java
Starting at line 97 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/wmsserver/tests/unit/org/geotools/renderer/LegendImageGeneratorTest.java
        StyleFactory sFac = StyleFactory.createStyleFactory();

        //The following is complex, and should be built from
        //an SLD document and not by hand
        PointSymbolizer pointsym = sFac.createPointSymbolizer();
        pointsym.setGraphic(sFac.getDefaultGraphic());

        LineSymbolizer linesym = sFac.createLineSymbolizer();
        Stroke myStroke = sFac.getDefaultStroke();
        myStroke.setColor(filterFactory.createLiteralExpression("#0000ff"));
        myStroke.setWidth(filterFactory.createLiteralExpression(new Integer(5)));
        LOGGER.info("got new Stroke " + myStroke);
        linesym.setStroke(myStroke);

        PolygonSymbolizer polysym = sFac.createPolygonSymbolizer();
        Fill myFill = sFac.getDefaultFill();
        myFill.setColor(filterFactory.createLiteralExpression("#ff0000"));
        polysym.setFill(myFill);
        polysym.setStroke(sFac.getDefaultStroke());

        Rule rule = sFac.createRule();
        rule.setSymbolizers(new Symbolizer[] { polysym });

        FeatureTypeStyle fts = sFac.createFeatureTypeStyle(new Rule[] { rule });
=====================================================================
Found a 45 line (160 tokens) duplication in the following files: 
Starting at line 113 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/Java2DMark.java
Starting at line 94 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/renderer/style/Java2DMark.java
    }

    public static Shape getWellKnownMark(String wellKnownName) {
        LOGGER.finer("fetching mark of name " + wellKnownName);

        if (wellKnownName.equalsIgnoreCase("cross")) {
            LOGGER.finer("returning cross");

            return cross;
        }

        if (wellKnownName.equalsIgnoreCase("circle")) {
            LOGGER.finer("returning circle");

            return new java.awt.geom.Ellipse2D.Double(-.5, -.5, 1., 1.);
        }

        if (wellKnownName.equalsIgnoreCase("triangle")) {
            LOGGER.finer("returning triangle");

            return triangle;
        }

        if (wellKnownName.equalsIgnoreCase("X")) {
            LOGGER.finer("returning X");

            return X;
        }

        if (wellKnownName.equalsIgnoreCase("star")) {
            LOGGER.finer("returning star");

            return star;
        }

        if (wellKnownName.equalsIgnoreCase("arrow")) {
            LOGGER.finer("returning arrow");

            return arrow;
        }

        // failing that return a square?
        LOGGER.finer("returning square");

        return new Rectangle2D.Double(-.5, -.5, 1., 1.);
=====================================================================
Found a 20 line (151 tokens) duplication in the following files: 
Starting at line 63 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/shapefile/tests/unit/org/geotools/data/shapefile/ShapefileDataStoreTest.java
Starting at line 61 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/shapefile/tests/unit/org/geotools/data/shapefile/ShapefileDataSourceTest.java
    assertEquals("Number of Attributes",253,types.length);
  }
  
  public void testEnvelope() throws Exception {
    FeatureCollection features = loadFeatures(STATE_POP, null);
    ShapefileDataSource s = new ShapefileDataSource(getTestResource(STATE_POP));
    assertEquals(features.getBounds(), s.getBounds());
  }
  
  public void testLoadAndVerify() throws Exception {
    FeatureCollection features = loadFeatures(STATE_POP,null);
    
    assertEquals("Number of Features loaded",49,features.size());
    
    FeatureType schema = firstFeature(features).getFeatureType();
    assertNotNull(schema.getDefaultGeometry());
    assertEquals("Number of Attributes",253,schema.getAttributeTypes().length);
    assertEquals("Value of statename is wrong",firstFeature(features).getAttribute("STATE_NAME"),"Illinois");
    assertEquals("Value of land area is wrong",((Double)firstFeature(features).getAttribute("LAND_KM")).doubleValue(),143986.61,0.001);
  }
=====================================================================
Found a 15 line (150 tokens) duplication in the following files: 
Starting at line 155 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/proj4j/src/org/geotools/proj4j/Transformer.java
Starting at line 193 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/proj4j/src/org/geotools/proj4j/Transformer.java
                z[io] = z[io] - defn.datum.getParams()[2];
            }
        }
        else if( defn.datum.datumType == Datum.PJD_7PARAM ) {
            for(int i = 0; i < point_count; i++ ) {
                io = i * point_offset;
                double x_out, y_out, z_out;
                double Dx_BF = defn.datum.getParams()[0];//not elegent!
                double Dy_BF = defn.datum.getParams()[1];//and possibly expensive
                double Dz_BF = defn.datum.getParams()[2];//sigh, no macros in Java
                double Rx_BF = defn.datum.getParams()[3];//...
                double Ry_BF = defn.datum.getParams()[4];//still, keeps it readable
                double Rz_BF = defn.datum.getParams()[5];//if a little verbose
                double M_BF  = defn.datum.getParams()[6];//could do with a better solution though.
                x_out = M_BF*(       x[io] + Rz_BF*y[io] - Ry_BF*z[io]) - Dx_BF;
=====================================================================
Found a 23 line (149 tokens) duplication in the following files: 
Starting at line 69 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/sldstyling/src/org/geotools/styling/SLDTransformer.java
Starting at line 292 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/sldstyling/src/org/geotools/styling/XMLEncoder.java
            out.write("<Stroke>\n");

            if (stroke.getGraphicFill() != null) {
                stroke.getGraphicFill().accept(this);
            }

            if (stroke.getGraphicStroke() != null) {
                stroke.getGraphicStroke().accept(this);
            }

            encodeCssParam("stroke", stroke.getColor());
            encodeCssParam("stroke-linecap", stroke.getLineCap());
            encodeCssParam("stroke-linejoin", stroke.getLineJoin());
            encodeCssParam("stroke-opacity", stroke.getOpacity());
            encodeCssParam("stroke-width", stroke.getWidth());
            encodeCssParam("stroke-dashoffset", stroke.getDashOffset());

            float[] dash = stroke.getDashArray();
            StringBuffer sb = new StringBuffer();

            for (int i = 0; i < dash.length; i++) {
                sb.append(dash[i] + " ");
            }
=====================================================================
Found a 38 line (148 tokens) duplication in the following files: 
Starting at line 235 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/rendering-styling/tests/unit/org/geotools/styling/TextStyleTest.java
Starting at line 204 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/rendering-styling/tests/unit/org/geotools/styling/DefaultMarkTest.java
        performTestOnRenderer(new LiteRenderer(context), "builder");
    }

    /**
     * Test j2d renderer
     */
    public void testJ2DRendererXml() throws Exception {
        MapContext map = new DefaultMapContext();
        map.addLayer(buildFeatureCollection(), loadStyleFromXml());
        
        StyledMapRenderer sr = new StyledMapRenderer(null);
        sr.setMapContext(map);
        performTestOnRenderer(sr, "xml");
    }
    
     /**
     * Test j2d renderer
     */
    public void testJ2DRendererBuilder() throws Exception {
		MapContext map = new DefaultMapContext();
	   map.addLayer(buildFeatureCollection(), loadStyleFromXml());
        
	   StyledMapRenderer sr = new StyledMapRenderer(null);
	   sr.setMapContext(map);
        performTestOnRenderer(sr, "builder");
    }


    /**
     * Perform test on the passed renderer, which must be already configured with its context
     */
    private void performTestOnRenderer(Renderer2D renderer, String fileSuffix)
        throws Exception {
        java.net.URL base = getClass().getResource("rs-testData");
        
        AffineTransform at = new AffineTransform();
        at.translate(0, 400);
        at.scale(9, -9);
=====================================================================
Found a 22 line (148 tokens) duplication in the following files: 
Starting at line 437 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/legend/src/org/geotools/gui/swing/sldeditor/style/full/TreeStyleEditor.java
Starting at line 328 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/legend/src/org/geotools/gui/swing/sldeditor/style/full/FullStyleEditor.java
        return treeEditor.getStyle();
    }

    public static void main(String[] args) throws Exception {
        AttributeType geom = AttributeTypeFactory.newAttributeType("geom",
                com.vividsolutions.jts.geom.Polygon.class);
        AttributeType[] attributeTypes = new AttributeType[] {
                geom, AttributeTypeFactory.newAttributeType("name", String.class),
                AttributeTypeFactory.newAttributeType("population", Long.class)
            };

        FeatureType ft = DefaultFeatureTypeFactory.newFeatureType(attributeTypes, "demo", "",
                false, null, (GeometryAttributeType) geom);
        FeatureTypeStyle featureStyle = styleBuilder.createFeatureTypeStyle(SymbolizerUtils
                .getDefaultSymbolizer(ft));
        Rule r = featureStyle.getRules()[0];
        r.setName("Rule1");
        featureStyle.setName("FeatureTypeStyle1");

        Style style = styleBuilder.createStyle();
        style.addFeatureTypeStyle(featureStyle);
        FormUtils.show(new FullStyleEditor(ft, style));
=====================================================================
Found a 27 line (143 tokens) duplication in the following files: 
Starting at line 82 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gui/tests/unit/org/geotools/gui/swing/tables/FeatureTableModelTest.java
Starting at line 90 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/tests/unit/org/geotools/filter/SQLEncoderPostgisTest.java
        LOGGER.finer("created boolean attribute");

        AttributeType charAttribute = attFactory.newAttributeType("testCharacter",
                Character.class);
        AttributeType byteAttribute = attFactory.newAttributeType("testByte",
                Byte.class);
        AttributeType shortAttribute = attFactory.newAttributeType("testShort",
                Short.class);
        AttributeType intAttribute = attFactory.newAttributeType("testInteger",
                Integer.class);
        AttributeType longAttribute = attFactory.newAttributeType("testLong",
                Long.class);
        AttributeType floatAttribute = attFactory.newAttributeType("testFloat",
                Float.class);
        AttributeType doubleAttribute = attFactory.newAttributeType("testDouble",
                Double.class);
        AttributeType stringAttribute = attFactory.newAttributeType("testString",
                String.class);

        AttributeType[] types = {
            geometryAttribute, booleanAttribute, charAttribute, byteAttribute,
            shortAttribute, intAttribute, longAttribute, floatAttribute,
            doubleAttribute, stringAttribute
        };

        // Builds the schema
        testSchema = FeatureTypeFactory.newFeatureType(types, "testSchema");
=====================================================================
Found a 15 line (139 tokens) duplication in the following files: 
Starting at line 624 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/renderer/array/GenericArray.java
Starting at line 664 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/renderer/array/GenericArray.java
        public Character(final char[] array) {
            super(XArray.isSorted(array));
            this.array = array;
            for (int i=array.length; --i>=0;) {
                final double value = array[i];
                if (value<minimum) minimum=value;
                if (value>maximum) maximum=value;
            }
        }
        public int    sizeof      ()         {return 16;}
        public int    length      ()         {return array.length;}
        public double getAsDouble (int i)    {return array[i];}
        public float  getAsFloat  (int i)    {return array[i];}
        public int    getAsInteger(int i)    {return array[i];}
        protected int binarySearch(double v) {return Arrays.binarySearch(array, (char)Math.floor(v));}
=====================================================================
Found a 24 line (139 tokens) duplication in the following files: 
Starting at line 149 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/tests/unit/org/geotools/data/postgis/PostgisTest.java
Starting at line 195 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/tests/unit/org/geotools/data/postgis/PostgisLockingTest.java
        postgis = new PostgisLockingDataSource(connection, TABLE);
        collection = postgis.getFeatures(query);

        Feature feature = (Feature) collection.iterator().next();
        LOGGER.fine("name feature is " + feature + ", and feature type is "
            + feature.getFeatureType());

        String[] fidsOnly = new String[0];
        query.setPropertyNames(fidsOnly);
        collection = postgis.getFeatures(query);
        feature = (Feature) collection.iterator().next();
        LOGGER.fine("fid feature is " + feature + ", and feature type is "
            + feature.getFeatureType());

        String[] badAtts = { "bull", "blorg" };
        query.setPropertyNames(badAtts);

        try {
            collection = postgis.getFeatures(query);
            fail("exception should be thrown for non matching propertyNames");
        } catch (DataSourceException dse) {
            assertTrue(dse != null);
        }
    }
=====================================================================
Found a 21 line (139 tokens) duplication in the following files: 
Starting at line 1401 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/LiteRenderer.java
Starting at line 621 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/renderer/style/SLDStyleFactory.java
                return javaFont.deriveFont(styleCode, size);
            }

            if (LOGGER.isLoggable(Level.FINEST)) {
                LOGGER.finest("not already loaded");
            }

            if (fontFamilies.contains(requestedFont)) {
                String reqStyle = (String) fonts[k].getFontStyle().getValue(feature);

                if (fontStyleLookup.containsKey(reqStyle)) {
                    styleCode = ((Integer) fontStyleLookup.get(reqStyle)).intValue();
                } else {
                    styleCode = java.awt.Font.PLAIN;
                }

                String reqWeight = (String) fonts[k].getFontWeight().getValue(feature);

                if (reqWeight.equalsIgnoreCase("Bold")) {
                    styleCode = styleCode | java.awt.Font.BOLD;
                }
=====================================================================
Found a 34 line (137 tokens) duplication in the following files: 
Starting at line 457 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/wmsserver/src/org/geotools/wms/WMSServlet.java
Starting at line 818 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/wmsserver/src/org/geotools/wms/WMSServlet.java
            }
            response.setContentType(format);

            OutputStream out = response.getOutputStream();

            // avoid caching in browser
            response.setHeader("Pragma", "no-cache");
            response.setHeader("Cache-Control", "no-cache");
            response.setDateHeader("Expires", 0);

            try {
                formatImageOutputStream(format, image, out);
            } catch (Exception exp) {
                exp.printStackTrace();
                LOGGER.severe(
                    "Unable to complete image generation after response started : " +
                    exp + exp.getMessage());

                if (exp instanceof SecurityException) {
                    response.sendError(500,
                        "Image generation failed because of: " +
                        exp.getStackTrace()[0] +
                        " JAI may not have 'write' and 'delete' permissions in temp folder");
                } else {
                    response.sendError(500,
                        "Image generation failed because of: " +
                        exp.getStackTrace()[0] + "Check JAI configuration");
                }
            }finally{

                out.close();
                image = null;
            }
         } else {
=====================================================================
Found a 56 line (135 tokens) duplication in the following files: 
Starting at line 101 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gcs-coverage/src/org/geotools/gp/Hints.java
Starting at line 126 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/renderer/j2d/Hints.java
    public static final RenderingHints.Key PREFETCH = new Hints(3, Boolean.class);

    /**
     * The class name for {@link #valueClass}.
     */
    private final String className;

    /**
     * Base class of all values for this key. Will be created from {@link #className}
     * only when first required, in order to avoid too early class loading.
     */
    private Class valueClass;

    /**
     * Construct a new key.
     *
     * @param id An ID. Must be unique for all instances of {@link Key}.
     * @param valueClass Base class of all valid values.
     */
    private Hints(final int id, final Class valueClass) {
        super(id);
        this.valueClass = valueClass;
        this.className  = valueClass.getName();
    }

    /**
     * Construct a new key. This constructor is used when a class loading should
     * be deferred until first needed.
     *
     * @param id An ID. Must be unique for all instances of {@link Key}.
     * @param className Name of base class for all valid values.
     */
    private Hints(final int id, final String className) {
        super(id);
        this.className = className;
        try {
            assert !Class.forName(className).isPrimitive();
        } catch (ClassNotFoundException exception) {
            throw new AssertionError(exception);
        }
    }

    /**
     * Returns <code>true</code> if the specified object is a valid value for this key.
     *
     * @param  value The object to test for validity.
     * @return <code>true</code> if the value is valid; <code>false</code> otherwise.
     */
    public boolean isCompatibleValue(final Object value) {
        if (value == null) {
            return false;
        }
        if (valueClass == null) try {
            valueClass = Class.forName(className);
        } catch (ClassNotFoundException exception) {
            Utilities.unexpectedException("org.geotools.renderer", "Hints", "isCompatibleValue",
=====================================================================
Found a 25 line (135 tokens) duplication in the following files: 
Starting at line 1432 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/LiteRenderer.java
Starting at line 645 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/renderer/style/SLDStyleFactory.java
                if (LOGGER.isLoggable(Level.FINEST)) {
                    LOGGER.finest("requesting " + requestedFont + " " + styleCode + " " + size);
                }

                javaFont = new java.awt.Font(requestedFont, styleCode, size);
                loadedFonts.put(requestedFont, javaFont);

                return javaFont;
            }

            if (LOGGER.isLoggable(Level.FINEST)) {
                LOGGER.finest("not a system font");
            }

            // may be its a file or url
            InputStream is = null;

            if (requestedFont.startsWith("http") || requestedFont.startsWith("file:")) {
                try {
                    URL url = new URL(requestedFont);
                    is = url.openStream();
                } catch (MalformedURLException mue) {
                    // this may be ok - but we should mention it
                    if (LOGGER.isLoggable(Level.INFO)) {
                        LOGGER.info("Bad url in SLDStyleFactory " + requestedFont + "\n" + mue);
=====================================================================
Found a 34 line (134 tokens) duplication in the following files: 
Starting at line 118 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/shapefile/src/org/geotools/data/shapefile/shp/MultiLineHandler.java
Starting at line 136 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/shapefile/src/org/geotools/data/shapefile/shp/PolygonHandler.java
    if (shapeType == ShapeType.POLYGONZ) {
      //z
      buffer.position(buffer.position() + 2 * 8);
      
      for (int t = 0; t < numPoints; t++) {
        coords[t].z = buffer.getDouble();
      }
    }
    
    int offset = 0;
    int start;
    int finish;
    int length;
    
    for (int part = 0; part < numParts; part++) {
      start = partOffsets[part];
      
      if (part == (numParts - 1)) {
        finish = numPoints;
      } else {
        finish = partOffsets[part + 1];
      }
      
      length = finish - start;
      
      // Use the progressive CCW algorithm.
      // basically the area algorithm for polygons
      // which also tells us vertex order based upon the
      // sign of the area.
      Coordinate[] points = new Coordinate[length];
      //double area = 0;
      //int sx = offset;
      for (int i = 0; i < length; i++) {
        points[i] = coords[offset++];
=====================================================================
Found a 44 line (134 tokens) duplication in the following files: 
Starting at line 57 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/opengis/src/org/opengis/ct/CT_Parameter.java
Starting at line 63 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/opengis/src/org/opengis/cs/CS_ProjectionParameter.java
    public CS_ProjectionParameter(final String name, final double value)
    {
        this.name  = name;
        this.value = value;
    }

    /**
     * Returns a hash value for this parameter.
     * This value need not remain consistent between
     * different implementations of the same class.
     */
    public int hashCode()
    {
        final long longCode = Double.doubleToLongBits(value);
        int code = (int)(longCode >>> 32) ^ (int)longCode;
        if (name!=null) code ^= name.hashCode();
        return code;
    }

    /**
     * Returns a copy of this parameter.
     */
    public Object clone()
    {
        try
        {
            return super.clone();
        }
        catch (CloneNotSupportedException exception)
        {
            // Should not happen, since we are cloneable.
            throw new InternalError(exception.getMessage());
        }
    }

    /**
     * Compares the specified object with
     * this parameter for equality.
     */
    public boolean equals(final Object object)
    {
        if (object!=null && getClass().equals(object.getClass()))
        {
            final CS_ProjectionParameter that = (CS_ProjectionParameter) object;
=====================================================================
Found a 15 line (134 tokens) duplication in the following files: 
Starting at line 93 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/spatial/LineCoveredByPolygonBoundaryValidation.java
Starting at line 89 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/spatial/LineNotTouchingPolygonInteriorValidation.java
        FeatureResults frPoly = fsPoly.getFeatures();
        FeatureCollection fcPoly = frPoly.collection();
                
        while(fLine.hasNext()){
        	Feature line = fLine.next();
        	FeatureIterator fPoly = fcPoly.features();
        	Geometry lineGeom = line.getDefaultGeometry();
        	if(envelope.contains(lineGeom.getEnvelopeInternal())){
        		// 	check for valid comparison
        		if(LineString.class.isAssignableFrom(lineGeom.getClass())){
        			while(fPoly.hasNext()){
        				Feature poly = fPoly.next();
        				Geometry polyGeom = poly.getDefaultGeometry(); 
        				if(envelope.contains(polyGeom.getEnvelopeInternal())){
        					if(Polygon.class.isAssignableFrom(polyGeom.getClass())){
=====================================================================
Found a 28 line (134 tokens) duplication in the following files: 
Starting at line 817 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gcs-coverage/src/org/geotools/gc/GridCoverage.java
Starting at line 843 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gcs-coverage/src/org/geotools/gc/GridCoverage.java
Starting at line 869 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gcs-coverage/src/org/geotools/gc/GridCoverage.java
    public double[] evaluate(final Point2D coord, final double[] dest)
        throws CannotEvaluateException
    {
        final Point2D pixel = gridGeometry.inverseTransform(coord);
        final double fx = pixel.getX();
        final double fy = pixel.getY();
        if (!Double.isNaN(fx) && !Double.isNaN(fy)) {
            final int x = (int)Math.round(fx);
            final int y = (int)Math.round(fy);
            if (image.getBounds().contains(x,y)) { // getBounds() returns a cached instance.
                return image.getTile(image.XToTileX(x), image.YToTileY(y)).getPixel(x, y, dest);
            }
        }
        throw new PointOutsideCoverageException(coord);
    }
    
    /**
     * Returns a debug string for the specified coordinate.   This method produces a
     * string with pixel coordinates and pixel values for all bands (with geophysics
     * values or category name in parenthesis). Example for a 1-banded image:
     *
     * <blockquote><pre>(1171,1566)=[196 (29.6 0C)]</pre></blockquote>
     *
     * @param  coord The coordinate point where to evaluate.
     * @return A string with pixel coordinates and pixel values at the specified location,
     *         or <code>null</code> if <code>coord</code> is outside coverage.
     */
    public synchronized String getDebugString(final CoordinatePoint coord) {
=====================================================================
Found a 60 line (131 tokens) duplication in the following files: 
Starting at line 193 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/CrossesIntegrity.java
Starting at line 197 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/relate/OverlapsIntegrity.java
					System.out.println("Does the one contain the other?->" + g1.contains(g2));
					if(g1.overlaps(g2) != expected || g1.contains(g2) != expected)
					{
						results.error( f1, f1.getDefaultGeometry().getGeometryType()+" "+getGeomTypeRefA()+" overlapped "+getGeomTypeRefB()+"("+f2.getID()+"), Result was not "+expected );
						success = false;
					}
				}		
			}
		}finally
		{
			/** Close the connections to the feature readers*/
			try {
				fr1.close();
				if (fr2 != null)
					fr2.close();
			} catch (IOException e4) {
				e4.printStackTrace();
				throw e4;
			}
		}
		
		return success;
	}

	/**
	 * <b>validateSingleLayer Purpose:</b> <br>
	 * <p>
	 * This validation tests for a geometry that overlaps with itself. 
	 * Uses JTS' Geometry.overlaps(Geometry) and  Geometry.contains(Geometry)method.
	 * The DE-9IM intersection matrix for overlaps is:
     * T*T***T** (for two points or two surfaces)
     * 1*T***T** (for two curves) 
     * Contains DE-9IM intersection matrix is T*F**F***.
	 * </p>
	 * 
	 * <b>Description:</b><br>
	 * <p>
	 * The function filters the FeatureSource using the given bounding box.
	 * It creates iterators over the filtered FeatureSource. It calls overlaps() and contains() using the
	 * geometries in the FeatureSource layer. Tests the results of the method calls against
	 * the given expected results. Returns true if the returned results and the expected results 
	 * are true, false otherwise.
	 * 
	 * </p>	 * 
	 * Author: bowens<br>
	 * Created on: Apr 27, 2004<br>
	 * @param featureSourceA - the FeatureSource to pull the original geometries from. This geometry is the one that is tested for overlapping itself
	 * @param expected - boolean value representing the user's expected outcome of the test
	 * @param results - ValidationResults
	 * @param bBox - Envelope - the bounding box within which to perform the overlaps() and contains()
	 * @return boolean result of the test
	 * @throws Exception - IOException if iterators improperly closed
	 */
	private boolean validateSingleLayer(FeatureSource featureSourceA, 
										boolean expected, 
										ValidationResults results, 
										Envelope bBox) 
	throws Exception
	{
		boolean success = true;
=====================================================================
Found a 10 line (131 tokens) duplication in the following files: 
Starting at line 421 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gtopo30/src/org/geotools/data/gtopo30/GTopo30DataSource.java
Starting at line 305 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/rendering-styling/tests/unit/org/geotools/styling/RenderingGridCoverageTest.java
        GeometryFactory geometryFactory = new GeometryFactory(); 
        Rectangle2D rect = gc.getEnvelope().toRectangle2D();
        Coordinate[] coord = new Coordinate[5];
        coord[0] = new Coordinate(rect.getMinX(), rect.getMinY());
        coord[1] = new Coordinate(rect.getMaxX(), rect.getMinY());
        coord[2] = new Coordinate(rect.getMaxX(), rect.getMaxY());
        coord[3] = new Coordinate(rect.getMinX(), rect.getMaxY());
        coord[4] = new Coordinate(rect.getMinX(), rect.getMinY());

        Feature feature = null;
=====================================================================
Found a 29 line (130 tokens) duplication in the following files: 
Starting at line 834 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/src/org/geotools/data/postgis/PostgisDataSource.java
Starting at line 205 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/src/org/geotools/data/postgis/PostgisFeatureStore.java
    private Set getFidSet(Connection conn) throws IOException {
        Set fids = new HashSet();
        Statement statement = null;

        try {
            LOGGER.finer("entering fid set");

            //conn = getConnection();
            statement = conn.createStatement();

            DefaultQuery query = new DefaultQuery();
            query.setPropertyNames(new String[0]);

            SQLUnpacker unpacker = new SQLUnpacker(encoder.getCapabilities());

            //REVISIT: redo unpacker-this has to be called first, or it breaks.
            unpacker.unPackAND(null);

            String sql = makeSql(unpacker, (Query) query);
            ResultSet result = statement.executeQuery(sql);

            while (result.next()) {
                //REVISIT: this formatting could be done after the remove,
                //would speed things up, but also would make that code ugly.
                fids.add(createFid(result.getString(1)));
            }
        } catch (SQLException sqle) {
            String message = CONN_ERROR + sqle.getMessage();
            LOGGER.warning(message);
=====================================================================
Found a 31 line (129 tokens) duplication in the following files: 
Starting at line 295 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gcs-coverage/src/org/geotools/gp/Interpolator.java
Starting at line 325 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gcs-coverage/src/org/geotools/gp/Interpolator.java
    public float[] evaluate(final Point2D coord, float[] dest) throws CannotEvaluateException {
        if (fallback!=null) {
            dest = super.evaluate(coord, dest);
        }
        try {
            final Point2D pixel = toGrid.transform(coord, null);
            final double x = pixel.getX();
            final double y = pixel.getY();
            if (!Double.isNaN(x) && !Double.isNaN(y)) {
                dest = interpolate(x, y, dest, 0, image.getNumBands());
                if (dest != null) {
                    return dest;
                }
            }
        } catch (TransformException exception) {
            throw new CannotEvaluateException(coord, exception);
        }
        throw new PointOutsideCoverageException(coord);
    }
    
    /**
     * Return an sequence of double values for a given two-dimensional point in the coverage.
     *
     * @param  coord The coordinate point where to evaluate.
     * @param  dest  An array in which to store values, or <code>null</code>.
     * @return An array containing values.
     * @throws CannotEvaluateException if the values can't be computed at the specified coordinate.
     *         More specifically, {@link PointOutsideCoverageException} is thrown if the evaluation
     *         failed because the input point has invalid coordinates.
     */
    public double[] evaluate(final Point2D coord, double[] dest) throws CannotEvaluateException {
=====================================================================
Found a 19 line (128 tokens) duplication in the following files: 
Starting at line 295 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gcs-coverage/src/org/geotools/gp/Interpolator.java
Starting at line 355 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gcs-coverage/src/org/geotools/gp/Interpolator.java
    public double[] evaluate(final Point2D coord, double[] dest) throws CannotEvaluateException {
        if (fallback!=null) {
            dest = super.evaluate(coord, dest);
        }
        try {
            final Point2D pixel = toGrid.transform(coord, null);
            final double x = pixel.getX();
            final double y = pixel.getY();
            if (!Double.isNaN(x) && !Double.isNaN(y)) {
                dest = interpolate(x, y, dest, 0, image.getNumBands());
                if (dest != null) {
                    return dest;
                }
            }
        } catch (TransformException exception) {
            throw new CannotEvaluateException(coord, exception);
        }
        throw new PointOutsideCoverageException(coord);
    }
=====================================================================
Found a 22 line (127 tokens) duplication in the following files: 
Starting at line 562 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/src/org/geotools/data/postgis/PostgisDataSource.java
Starting at line 754 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/src/org/geotools/data/postgis/PostgisFeatureStore.java
        AttributeType[] schemaTypes = getSchema().getAttributeTypes();

        if (query.retrieveAllProperties()) {
            return schemaTypes;
        } else {
            List attNames = Arrays.asList(query.getPropertyNames());
            AttributeType[] retAttTypes = new AttributeType[attNames.size()];
            int retPos = 0;

            for (int i = 0, n = schemaTypes.length; i < n; i++) {
                String schemaTypeName = schemaTypes[i].getName();

                if (attNames.contains(schemaTypeName)) {
                    retAttTypes[retPos++] = schemaTypes[i];
                }
            }

            //TODO: better error reporting, and completely test this method.
            if (attNames.size() != retPos) {
                String msg = "attempted to request a property, "
                    + attNames.get(0) + " that is not part of the schema ";
                throw new IOException(msg);
=====================================================================
Found a 29 line (125 tokens) duplication in the following files: 
Starting at line 676 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/wmsserver/src/org/geotools/wms/WMSServlet.java
Starting at line 818 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/wmsserver/src/org/geotools/wms/WMSServlet.java
            }
            response.setContentType(format);

            OutputStream out = response.getOutputStream();

            // avoid caching in browser
            response.setHeader("Pragma", "no-cache");
            response.setHeader("Cache-Control", "no-cache");
            response.setDateHeader("Expires", 0);

            try {
                formatImageOutputStream(format, image, out);
            } catch (Exception exp) {
                exp.printStackTrace();
                LOGGER.severe(
                    "Unable to complete image generation after response started : " +
                    exp + exp.getMessage());

                if (exp instanceof SecurityException) {
                    response.sendError(500,
                        "Image generation failed because of: " +
                        exp.getStackTrace()[0] +
                        " JAI may not have 'write' and 'delete' permissions in temp folder");
                } else {
                    response.sendError(500,
                        "Image generation failed because of: " +
                        exp.getStackTrace()[0] + "Check JAI configuration");
                }
            }finally{
=====================================================================
Found a 15 line (124 tokens) duplication in the following files: 
Starting at line 605 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/renderer/style/SLDStyleFactory.java
Starting at line 629 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/renderer/style/SLDStyleFactory.java
                String reqStyle = (String) fonts[k].getFontStyle().getValue(feature);

                if (fontStyleLookup.containsKey(reqStyle)) {
                    styleCode = ((Integer) fontStyleLookup.get(reqStyle)).intValue();
                } else {
                    styleCode = java.awt.Font.PLAIN;
                }

                String reqWeight = (String) fonts[k].getFontWeight().getValue(feature);

                if (reqWeight.equalsIgnoreCase("Bold")) {
                    styleCode = styleCode | java.awt.Font.BOLD;
                }

                size = ((Number) fonts[k].getFontSize().getValue(feature)).intValue();
=====================================================================
Found a 17 line (124 tokens) duplication in the following files: 
Starting at line 656 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gcs-coverage/src/org/geotools/gc/LocalizationGridTransform2D.java
Starting at line 694 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gcs-coverage/src/org/geotools/gc/LocalizationGridTransform2D.java
                              final double[] dstPts, int dstOff, int numPts)
            throws TransformException
        {
            int postIncrement = 0;
            if (srcPts == dstPts && srcOff < dstOff) {
                srcOff += (numPts-1)*2;
                dstOff += (numPts-1)*2;
                postIncrement = -4;
            }
            final Point2D.Double source = new Point2D.Double();
            final Point2D.Double target = new Point2D.Double();
            final AffineTransform tr = new AffineTransform(global);
            while (--numPts >= 0) {
                source.x = srcPts[srcOff++];
                source.y = srcPts[srcOff++];
                inverseTransform(source, target, tr);
                dstPts[dstOff++] = target.x;
=====================================================================
Found a 30 line (123 tokens) duplication in the following files: 
Starting at line 222 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/ExpressionDOMParser.java
Starting at line 252 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/ExpressionDOMParser.java
Starting at line 283 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/ExpressionDOMParser.java
Starting at line 313 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/ExpressionDOMParser.java
                math = FILTER_FACT.createMathExpression(DefaultExpression.MATH_DIVIDE);

                Node value = child.getFirstChild();

                while (value.getNodeType() != Node.ELEMENT_NODE) {
                    value = value.getNextSibling();
                }

                LOGGER.finer("add left value -> " + value + "<-");
                math.addLeftValue(parseExpression(value));
                value = value.getNextSibling();

                while (value.getNodeType() != Node.ELEMENT_NODE) {
                    value = value.getNextSibling();
                }

                LOGGER.finer("add right value -> " + value + "<-");
                math.addRightValue(parseExpression(value));

                return math;
            } catch (IllegalFilterException ife) {
                LOGGER.warning("Unable to build expression " + ife);

                return null;
            }
        }

       

        if (childName.equalsIgnoreCase("PropertyName")) {
=====================================================================
Found a 37 line (122 tokens) duplication in the following files: 
Starting at line 104 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/attributes/UniqueFIDValidation.java
Starting at line 160 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/tests/unit/org/geotools/validation/UniqueFIDIntegrityValidation.java
	}


	/**
	 * Override validate.
	 * <p>
	 * Description ...
	 * </p>
	 * @see org.geotools.validation.IntegrityValidation#validate(java.util.Map, com.vividsolutions.jts.geom.Envelope, org.geotools.validation.ValidationResults)
	 * 
	 * @param layers
	 * @param envelope
	 * @param results
	 * @return
	 */
	public boolean validate(Map layers, Envelope envelope, ValidationResults results) throws Exception{
		
		HashMap FIDs = new HashMap();
		boolean result = true;
		Iterator it = layers.values().iterator();
		
		while (it.hasNext())// for each layer
		{
			FeatureSource featureSource = (FeatureSource) it.next();
			FeatureReader reader = featureSource.getFeatures().reader();
			try {
				 
				while (reader.hasNext())	// for each feature
				{
					Feature feature = reader.next();
					String fid = feature.getID();
					if(FIDs.containsKey(fid))	// if a FID like this one already exists
					{
						results.error(feature, "FID already exists.");
						result = false;
					}
					else
=====================================================================
Found a 35 line (121 tokens) duplication in the following files: 
Starting at line 228 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/LiteShape.java
Starting at line 296 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/LiteShape.java
    public Rectangle2D getBounds2D() {
        Coordinate[] coords = geometry.getEnvelope().getCoordinates();

        // get out corners. the documentation doens't specify in which
        // order the bounding box coordinates are returned
        double x1;
        double y1;
        double x2;
        double y2;

        x1 = x2 = coords[0].x;
        y1 = y2 = coords[0].y;

        
        for (int i = 1; i < 3; i++) {
            double x = coords[i].x;
            double y = coords[i].y;
            

            if (x < x1) {
                x1 = x;
            }

            if (x > x2) {
                x2 = x;
            }

            if (y < y1) {
                y1 = y;
            }

            if (y > y2) {
                y2 = y;
            }
        }
=====================================================================
Found a 41 line (121 tokens) duplication in the following files: 
Starting at line 117 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/mysql/src/org/geotools/data/mysql/MySQLDataStoreFactory.java
Starting at line 139 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/src/org/geotools/data/postgis/PostgisDataStoreFactory.java
        if (!((String) params.get("dbtype")).equalsIgnoreCase("postgis")) {
            return false;
        }

        if (!params.containsKey("host")) {
            return false;
        }

        if (!params.containsKey("user")) {
            return false;
        }

        if (!params.containsKey("database")) {
            return false;
        }

        return true;
    }

    /**
     * Construct a postgis data store using the params.
     *
     * @param params The full set of information needed to construct a live
     *        data source.  Should have  dbtype equal to postgis, as well as
     *        host, user, passwd, database, and table.
     *
     * @return The created DataSource, this may be null if the required
     *         resource was not found or if insufficent parameters were given.
     *         Note that canProcess() should have returned false if the
     *         problem is to do with insuficent parameters.
     *
     * @throws IOException See DataSourceException
     * @throws DataSourceException Thrown if there were any problems creating
     *         or connecting the datasource.
     */
    public DataStore createDataStore(Map params) throws IOException {
        String host = (String) HOST.lookUp(params);
        String user = (String) USER.lookUp(params);
        String passwd = (String) PASSWD.lookUp(params);
        Integer port = (Integer) PORT.lookUp(params);
        String database = (String) DATABASE.lookUp(params);
=====================================================================
Found a 8 line (119 tokens) duplication in the following files: 
Starting at line 38 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gtopo30/tests/unit/org/geotools/data/gtopo30/GT30HeaderTest.java
Starting at line 76 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gtopo30/tests/unit/org/geotools/data/gtopo30/GT30HeaderTest.java
      assertEquals("TotalRowBytes", header.getProperty(GT30Header.TOTALROWBYTES), new Integer(4800));
      assertEquals("BandGapBytes", header.getProperty(GT30Header.BANDGAPBYTES), new Integer(0));
      assertEquals("NoData", header.getProperty(GT30Header.NODATA), new Integer(-9999));
      assertEquals("ULXMap", header.getProperty(GT30Header.ULXMAP), new Double(-19.99583333333333));
      assertEquals("ULYMap", header.getProperty(GT30Header.ULYMAP), new Double(89.99583333333334));
      assertEquals("XDim", header.getProperty(GT30Header.XDIM), new Double(0.00833333333333));
      assertEquals("YDim", header.getProperty(GT30Header.YDIM), new Double(0.00833333333333));
  }
=====================================================================
Found a 35 line (116 tokens) duplication in the following files: 
Starting at line 84 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/src/org/geotools/data/postgis/PostgisLockingDataSourceFactory.java
Starting at line 89 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/src/org/geotools/data/postgis/PostgisDataSourceFactory.java
        if (!params.containsKey("port")) {
            return false;
        }

        return true;
    }

    /**
     * Construct a live data source using the params specifed.
     *
     * @param params The full set of information needed to construct a live
     *        data source.  Should have  dbtype equal to postgis, as well as
     *        host, user, passwd, database, and table.
     *
     * @return The created DataSource, this may be null if the required
     *         resource was not found or if insufficent parameters were given.
     *         Note that canProcess() should have returned false if the
     *         problem is to do with insuficent parameters.
     *
     * @throws DataSourceException Thrown if there were any problems creating
     *         or connecting the datasource.
     */
    public DataSource createDataSource(Map params) throws DataSourceException {
        if (!canProcess(params)) {
            return null;
        }

        String host = (String) params.get("host");
        String user = (String) params.get("user");
        String passwd = (String) params.get("passwd");
        String port = (String) params.get("port");
        String database = (String) params.get("database");
        String table = (String) params.get("table");
        String charSet = (String) params.get("charset");
	String useStrict = (String) params.get("strictbbox");
=====================================================================
Found a 11 line (115 tokens) duplication in the following files: 
Starting at line 305 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/rendering-styling/tests/unit/org/geotools/styling/TextStyleTest.java
Starting at line 265 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/rendering-styling/tests/unit/org/geotools/styling/DefaultMarkTest.java
        java.awt.image.BufferedImage image = new java.awt.image.BufferedImage(w, h,
                java.awt.image.BufferedImage.TYPE_INT_RGB);
        java.awt.Graphics2D g = (Graphics2D) image.getGraphics();
        g.setColor(java.awt.Color.white);
        g.fillRect(0, 0, w, h);
        renderer.paint(g, new java.awt.Rectangle(0, 0, w, h), at);

            
        

        java.io.File file = new java.io.File(base.getPath(),
=====================================================================
Found a 17 line (114 tokens) duplication in the following files: 
Starting at line 1885 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/LiteRenderer.java
Starting at line 1950 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/LiteRenderer.java
                                                      .toString());

        Point2D mapCentre = new java.awt.geom.Point2D.Double(tx, ty);
        Point2D graphicCentre = new java.awt.geom.Point2D.Double();
        temp.transform(mapCentre, graphicCentre);
        markAT.translate(graphicCentre.getX(), graphicCentre.getY());

        double shearY = temp.getShearY();
        double scaleY = temp.getScaleY();

        double originalRotation = Math.atan(shearY / scaleY);

        if (LOGGER.isLoggable(Level.FINER)) {
            LOGGER.finer("originalRotation " + originalRotation);
        }

        markAT.rotate(rotation - originalRotation);
=====================================================================
Found a 15 line (113 tokens) duplication in the following files: 
Starting at line 150 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/resources/src/org/geotools/units/DMSUnit.java
Starting at line 171 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/resources/src/org/geotools/units/DMSUnit.java
            float value = values[i]*divider;
            final int deg,min;
            deg = (int) (value/10000); value -= 10000*deg;
            min = (int) (value/  100); value -=   100*min;
            if (min<=-60 || min>=60) {
                throw new UnitException("Invalid minutes: "+min);
            }
            if (value<=-60 || value>=60) // Accept NaN
            {
                throw new UnitException("Invalid secondes: "+value);
            }
            values[i] = ((value/60) + min)/60 + deg;
        }
        DEGREE.inverseConvert(values, toUnit);
    }
=====================================================================
Found a 50 line (113 tokens) duplication in the following files: 
Starting at line 46 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/tests/unit/org/geotools/validation/RoadNetworkValidationResults.java
Starting at line 45 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/tests/unit/org/geotools/validation/RoadValidationResults.java
	public RoadValidationResults() {
		validationList = new ArrayList();
		failedFeatures = new ArrayList();
		warningFeatures = new ArrayList();
		failureMessages = new ArrayList();
		warningMessages = new ArrayList();
	}

	/**
	 * Override setValidation.
	 * <p>
	 * Description ...
	 * </p>
	 * @see org.geotools.validation.ValidationResults#setValidation(org.geotools.validation.Validation)
	 * 
	 * @param validation
	 */
	public void setValidation(Validation validation) {
		validationList.add(validation);
	}

	/**
	 * Override error.
	 * <p>
	 * Description ...
	 * </p>
	 * @see org.geotools.validation.ValidationResults#error(org.geotools.feature.Feature, java.lang.String)
	 * 
	 * @param feature
	 * @param message
	 */
	public void error(Feature feature, String message) {
		failedFeatures.add(feature);
		failureMessages.add(feature.getID() + ": " + message);
	}

	/**
	 * Override warning.
	 * <p>
	 * Description ...
	 * </p>
	 * @see org.geotools.validation.ValidationResults#warning(org.geotools.feature.Feature, java.lang.String)
	 * 
	 * @param feature
	 * @param message
	 */
	public void warning(Feature feature, String message) {
		warningFeatures.add(feature);
		warningMessages.add(feature.getID() + ": " + message);
	}
=====================================================================
Found a 21 line (112 tokens) duplication in the following files: 
Starting at line 410 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/src/org/geotools/data/postgis/PostgisFeatureStore.java
Starting at line 508 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/src/org/geotools/data/postgis/PostgisFeatureStore.java
        } catch (SQLException sqle) {
            fail = true;
            close(conn, getTransaction(), sqle);

            String message = CONN_ERROR + sqle.getMessage();
            LOGGER.warning(message);
            throw new DataSourceException(message, sqle);
        } catch (SQLEncoderException ence) {
            fail = true;

            String message = "error encoding sql from filter "
                + ence.getMessage();
            LOGGER.warning(message);
            throw new DataSourceException(message, ence);
        } catch (IllegalAttributeException iae) {
            throw new DataSourceException("attribute problem", iae);
        } finally {
            close(statement);
            close(conn, getTransaction(), null);
        }
    }
=====================================================================
Found a 8 line (112 tokens) duplication in the following files: 
Starting at line 29 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gtopo30/tests/unit/org/geotools/data/gtopo30/GT30HeaderTest.java
Starting at line 67 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gtopo30/tests/unit/org/geotools/data/gtopo30/GT30HeaderTest.java
      URL headerURL = getTestResource("SRC.SCH");
      GT30Header header = new GT30Header(headerURL);
      assertEquals("Byteorder", header.getProperty(GT30Header.BYTEORDER), "M");
      assertEquals("Layout", header.getProperty(GT30Header.LAYOUT), "BIL");
      assertEquals("NRows", header.getProperty(GT30Header.NROWS), new Integer(6000));
      assertEquals("BCols", header.getProperty(GT30Header.NCOLS), new Integer(4800));
      assertEquals("NBands", header.getProperty(GT30Header.NBANDS), new Integer(1));
      assertEquals("NBits", header.getProperty(GT30Header.NBITS), new Integer(8));
=====================================================================
Found a 45 line (112 tokens) duplication in the following files: 
Starting at line 162 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/LineIterator.java
Starting at line 161 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/PolygonIterator.java
        } else if (currentCoord == this.coords.length) {
            return SEG_CLOSE;
        } else {
            coords[0] = this.coords[currentCoord].x;
            coords[1] = this.coords[currentCoord].y;
            at.transform(coords, 0, coords, 0, 1);

            return SEG_LINETO;
        }
    }

    /**
     * Returns the coordinates and type of the current path segment in the iteration. The return
     * value is the path-segment type: SEG_MOVETO, SEG_LINETO, SEG_QUADTO, SEG_CUBICTO, or
     * SEG_CLOSE. A float array of length 6 must be passed in and can be used to store the
     * coordinates of the point(s). Each point is stored as a pair of float x,y coordinates.
     * SEG_MOVETO and SEG_LINETO types returns one point, SEG_QUADTO returns two points,
     * SEG_CUBICTO returns 3 points and SEG_CLOSE does not return any points.
     *
     * @param coords an array that holds the data returned from this method
     *
     * @return the path-segment type of the current path segment.
     *
     * @see #SEG_MOVETO
     * @see #SEG_LINETO
     * @see #SEG_QUADTO
     * @see #SEG_CUBICTO
     * @see #SEG_CLOSE
     */
    public int currentSegment(float[] coords) {
        double[] dcoords = new double[2];
        int result = currentSegment(dcoords);
        coords[0] = (float) dcoords[0];
        coords[1] = (float) dcoords[1];

        return result;
    }

    /**
     * Return the winding rule for determining the interior of the path.
     *
     * @return <code>WIND_EVEN_ODD</code> by default.
     */
    public int getWindingRule() {
        return WIND_EVEN_ODD;
=====================================================================
Found a 23 line (112 tokens) duplication in the following files: 
Starting at line 30 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gmldatasource/tests/unit/org/geotools/gml/ServiceTest.java
Starting at line 47 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/tests/unit/org/geotools/data/postgis/ServiceTest.java
public class ServiceTest extends TestCase {
    public ServiceTest(java.lang.String testName) {
        super(testName);
    }

    public static void main(java.lang.String[] args) {
        junit.textui.TestRunner.run(suite());
    }

    public static Test suite() {
        TestSuite suite = new TestSuite(ServiceTest.class);

        return suite;
    }

    public void testIsAvailable() {
        Iterator list = DataSourceFinder.getAvailableDataSources();
        boolean found = false;

        while (list.hasNext()) {
            DataSourceFactorySpi fac = (DataSourceFactorySpi) list.next();

            if (fac instanceof PostgisDataSourceFactory) {
=====================================================================
Found a 20 line (111 tokens) duplication in the following files: 
Starting at line 73 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/spatial/PolygonNotOverlappingLineValidation.java
Starting at line 80 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/validation/src/org/geotools/validation/spatial/PolygonNotCoveredByPolygonValidation.java
        FeatureSource polySource2 = (FeatureSource) layers.get(getRestrictedPolygonTypeRef());

        Object[] poly1 = polySource1.getFeatures().collection().toArray();
        Object[] poly2 = polySource2.getFeatures().collection().toArray();

        if (!envelope.contains(polySource1.getBounds())) {
            results.error((Feature) poly1[0],
                "Polygon Feature Source is not contained within the Envelope provided.");

            return false;
        }

        if (!envelope.contains(polySource2.getBounds())) {
            results.error((Feature) poly1[0],
                "Restricted Polygon Feature Source is not contained within the Envelope provided.");

            return false;
        }

        for (int i = 0; i < poly2.length; i++) {
=====================================================================
Found a 26 line (110 tokens) duplication in the following files: 
Starting at line 846 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
Starting at line 1222 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
        Geometry();
      }
      jj_consume_token(RP);
    } catch (Throwable jjte000) {
    if (jjtc000) {
      jjtree.clearNodeScope(jjtn000);
      jjtc000 = false;
    } else {
      jjtree.popNode();
    }
    if (jjte000 instanceof RuntimeException) {
      {if (true) throw (RuntimeException)jjte000;}
    }
    if (jjte000 instanceof ParseException) {
      {if (true) throw (ParseException)jjte000;}
    }
    {if (true) throw (Error)jjte000;}
    } finally {
    if (jjtc000) {
      jjtree.closeNodeScope(jjtn000, true);
      jjtreeCloseNodeScope(jjtn000);
    }
    }
  }

  final private boolean jj_2_1(int xla) {
=====================================================================
Found a 13 line (110 tokens) duplication in the following files: 
Starting at line 198 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/map/tests/unit/org/geotools/map/MapContextTest.java
Starting at line 251 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/map/tests/unit/org/geotools/map/MapContextTest.java
        context.addLayers(new MapLayer[] { layer3 });
        assertEquals(3, context.getLayerCount());
        assertEquals(0, boundsChangedCount);
        assertEquals(1, layerAddedCount);
        assertEquals(0, layerRemovedCount);
        assertEquals(0, layerChangedCount);
        assertEquals(0, layerMovedCount);
        assertEquals(0, propertyChangeCount);
        assertEquals(2, ((MapLayerListEvent) events.get(0)).getFromIndex());
        assertEquals(2, ((MapLayerListEvent) events.get(0)).getToIndex());
        assertEquals(layer3, ((MapLayerListEvent) events.get(0)).getLayer());

        clearEventTracking();
=====================================================================
Found a 20 line (109 tokens) duplication in the following files: 
Starting at line 205 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/tests/unit/org/geotools/filter/DOMParserTest.java
Starting at line 175 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/tests/unit/org/geotools/filter/XMLEncoderTest.java
        LOGGER.fine("exporting " + uri);

        // first grab a filter node
        NodeList nodes = dom.getElementsByTagName("Filter");

        for (int j = 0; j < nodes.getLength(); j++) {
            Element filterNode = (Element) nodes.item(j);
            NodeList list = filterNode.getChildNodes();
            Node child = null;

            for (int i = 0; i < list.getLength(); i++) {
                child = list.item(i);

                //_log.getLoggerRepository().setThreshold(Level.INFO);
                if ((child == null)
                        || (child.getNodeType() != Node.ELEMENT_NODE)) {
                    continue;
                }

                filter = FilterDOMParser.parseFilter(child);
=====================================================================
Found a 25 line (109 tokens) duplication in the following files: 
Starting at line 1084 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
Starting at line 1115 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
Starting at line 1146 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
Starting at line 1177 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
      jjtn000.token = jj_consume_token(MULTIPOLYGON);
      CoordsList();
    } catch (Throwable jjte000) {
    if (jjtc000) {
      jjtree.clearNodeScope(jjtn000);
      jjtc000 = false;
    } else {
      jjtree.popNode();
    }
    if (jjte000 instanceof RuntimeException) {
      {if (true) throw (RuntimeException)jjte000;}
    }
    if (jjte000 instanceof ParseException) {
      {if (true) throw (ParseException)jjte000;}
    }
    {if (true) throw (Error)jjte000;}
    } finally {
    if (jjtc000) {
      jjtree.closeNodeScope(jjtn000, true);
      jjtreeCloseNodeScope(jjtn000);
    }
    }
  }

  final public void GeometryCollection() throws ParseException {
=====================================================================
Found a 24 line (109 tokens) duplication in the following files: 
Starting at line 848 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
Starting at line 1023 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
      jj_consume_token(RP);
    } catch (Throwable jjte000) {
    if (jjtc000) {
      jjtree.clearNodeScope(jjtn000);
      jjtc000 = false;
    } else {
      jjtree.popNode();
    }
    if (jjte000 instanceof RuntimeException) {
      {if (true) throw (RuntimeException)jjte000;}
    }
    if (jjte000 instanceof ParseException) {
      {if (true) throw (ParseException)jjte000;}
    }
    {if (true) throw (Error)jjte000;}
    } finally {
    if (jjtc000) {
      jjtree.closeNodeScope(jjtn000, true);
      jjtreeCloseNodeScope(jjtn000);
    }
    }
  }

  final public void LineString() throws ParseException {
=====================================================================
Found a 24 line (108 tokens) duplication in the following files: 
Starting at line 206 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
Starting at line 458 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
Starting at line 538 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
          UnaryExpression();
        } catch (Throwable jjte002) {
          if (jjtc002) {
            jjtree.clearNodeScope(jjtn002);
            jjtc002 = false;
          } else {
            jjtree.popNode();
          }
          if (jjte002 instanceof RuntimeException) {
            {if (true) throw (RuntimeException)jjte002;}
          }
          if (jjte002 instanceof ParseException) {
            {if (true) throw (ParseException)jjte002;}
          }
          {if (true) throw (Error)jjte002;}
        } finally {
          if (jjtc002) {
            jjtree.closeNodeScope(jjtn002,  2);
            jjtreeCloseNodeScope(jjtn002);
          }
        }
        break;
      default:
        jj_la1[10] = jj_gen;
=====================================================================
Found a 25 line (108 tokens) duplication in the following files: 
Starting at line 90 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
Starting at line 132 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
        EqualityExpression();
      } catch (Throwable jjte001) {
            if (jjtc001) {
              jjtree.clearNodeScope(jjtn001);
              jjtc001 = false;
            } else {
              jjtree.popNode();
            }
            if (jjte001 instanceof RuntimeException) {
              {if (true) throw (RuntimeException)jjte001;}
            }
            if (jjte001 instanceof ParseException) {
              {if (true) throw (ParseException)jjte001;}
            }
            {if (true) throw (Error)jjte001;}
      } finally {
            if (jjtc001) {
              jjtree.closeNodeScope(jjtn001,  2);
              jjtreeCloseNodeScope(jjtn001);
            }
      }
    }
  }

  final public void EqualityExpression() throws ParseException {
=====================================================================
Found a 26 line (108 tokens) duplication in the following files: 
Starting at line 182 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/src/org/geotools/filter/SQLEncoderPostgis.java
Starting at line 456 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/oraclespatial/src/org/geotools/filter/SQLEncoderOracle.java
            super.visit(literal);
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @param filter
     *
     * @see org.geotools.filter.SQLEncoder#visit(org.geotools.filter.FidFilter)
     */
    public void visit(FidFilter filter) {
        String[] fids = filter.getFids();
        LOGGER.finer("Exporting FID=" + Arrays.asList(fids));

        for (int i = 0; i < fids.length; i++) {
            try {
                out.write(fidColumn);
                out.write(" = '");
                
                int pos;
                
                if ((pos = fids[i].indexOf('.')) != -1) {
                	out.write(fids[i].substring(pos + 1));
                } else {
					out.write(fids[i]);
=====================================================================
Found a 24 line (107 tokens) duplication in the following files: 
Starting at line 1054 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
Starting at line 1085 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
      CoordsList();
    } catch (Throwable jjte000) {
    if (jjtc000) {
      jjtree.clearNodeScope(jjtn000);
      jjtc000 = false;
    } else {
      jjtree.popNode();
    }
    if (jjte000 instanceof RuntimeException) {
      {if (true) throw (RuntimeException)jjte000;}
    }
    if (jjte000 instanceof ParseException) {
      {if (true) throw (ParseException)jjte000;}
    }
    {if (true) throw (Error)jjte000;}
    } finally {
    if (jjtc000) {
      jjtree.closeNodeScope(jjtn000, true);
      jjtreeCloseNodeScope(jjtn000);
    }
    }
  }

  final public void MultiPoint() throws ParseException {
=====================================================================
Found a 24 line (107 tokens) duplication in the following files: 
Starting at line 1023 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
Starting at line 1224 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
      jj_consume_token(RP);
    } catch (Throwable jjte000) {
    if (jjtc000) {
      jjtree.clearNodeScope(jjtn000);
      jjtc000 = false;
    } else {
      jjtree.popNode();
    }
    if (jjte000 instanceof RuntimeException) {
      {if (true) throw (RuntimeException)jjte000;}
    }
    if (jjte000 instanceof ParseException) {
      {if (true) throw (ParseException)jjte000;}
    }
    {if (true) throw (Error)jjte000;}
    } finally {
    if (jjtc000) {
      jjtree.closeNodeScope(jjtn000, true);
      jjtreeCloseNodeScope(jjtn000);
    }
    }
  }

  final private boolean jj_2_1(int xla) {
=====================================================================
Found a 10 line (106 tokens) duplication in the following files: 
Starting at line 470 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/rendering-styling/tests/unit/org/geotools/styling/RenderStyleTest.java
Starting at line 380 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/rendering-styling/tests/unit/org/geotools/styling/RenderingGridCoverageTest.java
                "RenderingGridCoverageTest_" + renderer.getClass().getName().replace('.', '_') + "_"
                + fileSuffix + width + "x" + height + ".png");
        java.io.FileOutputStream out = new java.io.FileOutputStream(file);
        boolean fred = javax.imageio.ImageIO.write(image, "PNG", out);

        if (!fred) {
            System.out.println("Failed to write image to " + file.toString());
        }

        java.io.File file2 = new java.io.File(base.getPath() + "/exemplars/",
=====================================================================
Found a 24 line (106 tokens) duplication in the following files: 
Starting at line 848 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
Starting at line 1054 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
      Coords();
    } catch (Throwable jjte000) {
    if (jjtc000) {
      jjtree.clearNodeScope(jjtn000);
      jjtc000 = false;
    } else {
      jjtree.popNode();
    }
    if (jjte000 instanceof RuntimeException) {
      {if (true) throw (RuntimeException)jjte000;}
    }
    if (jjte000 instanceof ParseException) {
      {if (true) throw (ParseException)jjte000;}
    }
    {if (true) throw (Error)jjte000;}
    } finally {
    if (jjtc000) {
      jjtree.closeNodeScope(jjtn000, true);
      jjtreeCloseNodeScope(jjtn000);
    }
    }
  }

  final public void Polygon() throws ParseException {
=====================================================================
Found a 17 line (106 tokens) duplication in the following files: 
Starting at line 560 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/tests/unit/org/geotools/data/postgis/PostgisDataStoreAPITest.java
Starting at line 580 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/tests/unit/org/geotools/data/postgis/PostgisDataStoreAPITest.java
        FeatureType actual = data.getSchema("river");
        assertEquals("namespace", expected.getNamespace(), actual.getNamespace());
        assertEquals("typeName", expected.getTypeName(), actual.getTypeName());

        //assertEquals( "compare", 0, DataUtilities.compare( expected, actual ));
        assertEquals("attributeCount", expected.getAttributeCount(),
            actual.getAttributeCount());

        for (int i = 0; i < expected.getAttributeCount(); i++) {
            AttributeType expectedAttribute = expected.getAttributeType(i);
            AttributeType actualAttribute = actual.getAttributeType(i);
            assertEquals("attribute " + expectedAttribute.getName(),
                expectedAttribute, actualAttribute);
        }

        assertEquals(expected, actual);
    }
=====================================================================
Found a 18 line (106 tokens) duplication in the following files: 
Starting at line 551 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/sldstyling/src/org/geotools/styling/SLDParser.java
Starting at line 583 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/sldstyling/src/org/geotools/styling/SLDParser.java
        symbol.setStroke((Stroke) null);
        
        NodeList children = root.getChildNodes();
        
        for (int i = 0; i < children.getLength(); i++) {
            Node child = children.item(i);
            
            if ((child == null) || (child.getNodeType() != Node.ELEMENT_NODE)) {
                continue;
            }
            
            if (child.getLocalName().equalsIgnoreCase(geomSt)) {
                symbol.setGeometryPropertyName(parseGeometryName(child));
            }
            
            if (child.getLocalName().equalsIgnoreCase("Stroke")) {
                symbol.setStroke(parseStroke(child));
            }
=====================================================================
Found a 18 line (106 tokens) duplication in the following files: 
Starting at line 234 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/LineIterator.java
Starting at line 230 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/PolygonIterator.java
        } else {
            if (generalize) {
                if (oldCoord == null) {
                    currentCoord++;
                    oldCoord = coords[currentCoord];
                } else {
                    double distx = 0;
                    double disty = 0;

                    do {
                        currentCoord++;

                        if (currentCoord < coords.length) {
                            distx = Math.abs(coords[currentCoord].x - oldCoord.x);
                            disty = Math.abs(coords[currentCoord].y - oldCoord.y);
                        }
                    } while (((distx * xScale) < maxDistance) && ((disty * yScale) < maxDistance)
                            && (currentCoord < coords.length));
=====================================================================
Found a 26 line (105 tokens) duplication in the following files: 
Starting at line 45 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/vpf/src/org/geotools/data/vpf/io/CoordinateDouble.java
Starting at line 45 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/vpf/src/org/geotools/data/vpf/io/CoordinateFloat.java
    public CoordinateFloat(float[][] coords) {
        coordinates = coords;
    }

    /**
     * Describe <code>toString</code> method here.
     *
     * @return a <code>String</code> value
     */
    public String toString() {
        StringBuffer sb = new StringBuffer();

        for (int i = 0; i < coordinates.length; i++) {
            sb.append("(");

            for (int j = 0; j < coordinates[i].length; j++) {
                if (j > 0) {
                    sb.append(", ");
                }
                sb.append(coordinates[i][j]);
            }
            sb.append(")");
        }
        return sb.toString();
    }
}
=====================================================================
Found a 23 line (105 tokens) duplication in the following files: 
Starting at line 177 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
Starting at line 429 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
Starting at line 509 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
          UnaryExpression();
        } catch (Throwable jjte001) {
          if (jjtc001) {
            jjtree.clearNodeScope(jjtn001);
            jjtc001 = false;
          } else {
            jjtree.popNode();
          }
          if (jjte001 instanceof RuntimeException) {
            {if (true) throw (RuntimeException)jjte001;}
          }
          if (jjte001 instanceof ParseException) {
            {if (true) throw (ParseException)jjte001;}
          }
          {if (true) throw (Error)jjte001;}
        } finally {
          if (jjtc001) {
            jjtree.closeNodeScope(jjtn001,  2);
            jjtreeCloseNodeScope(jjtn001);
          }
        }
        break;
      case 43:
=====================================================================
Found a 27 line (105 tokens) duplication in the following files: 
Starting at line 226 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/resources/src/org/geotools/resources/XAffineTransform.java
Starting at line 267 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/resources/src/org/geotools/resources/XAffineTransform.java
            transform.inverseTransform(point, point);
            if (point.x<xmin) xmin=point.x;
            if (point.x>xmax) xmax=point.x;
            if (point.y<ymin) ymin=point.y;
            if (point.y>ymax) ymax=point.y;
        }
        if (dest!=null) {
            dest.setRect(xmin, ymin, xmax-xmin, ymax-ymin);
            return dest;
        }
        return new Rectangle2D.Double(xmin, ymin, xmax-xmin, ymax-ymin);
    }

    /**
     * Calculates the inverse affine transform of a point without bearing in
     * mind the translation.
     *
     * @param transform Affine transform to use.
     * @param source    Point to transform. This rectangle will not be modified.
     * @param dest      Point in which to place the result.  If null, a new
     *                  point will be created.
     *
     * @return The inverse transform of the <code>source</code> point.
     * @throws NoninvertibleTransformException if the affine transform can't be
     *         inverted.
     */
    public static Point2D inverseDeltaTransform(final AffineTransform transform,
=====================================================================
Found a 22 line (104 tokens) duplication in the following files: 
Starting at line 189 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/shapefile/src/org/geotools/data/shapefile/shp/MultiLineHandler.java
Starting at line 406 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/shapefile/src/org/geotools/data/shapefile/shp/PolygonHandler.java
      double[] zExtreame = JTSUtilities.zMinMax(multi.getCoordinates());
      
      if (Double.isNaN(zExtreame[0])) {
        buffer.putDouble(0.0);
        buffer.putDouble(0.0);
      } else {
        buffer.putDouble(zExtreame[0]);
        buffer.putDouble(zExtreame[1]);
      }
      
      for (int t = 0; t < npoints; t++) {
        double z = coords[t].z;
        
        if (Double.isNaN(z)) {
          buffer.putDouble(0.0);
        } else {
          buffer.putDouble(z);
        }
      }
    }
    
    if (shapeType == ShapeType.POLYGONM || shapeType == ShapeType.POLYGONZ) {
=====================================================================
Found a 24 line (104 tokens) duplication in the following files: 
Starting at line 1147 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
Starting at line 1224 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
      jj_consume_token(RP);
    } catch (Throwable jjte000) {
    if (jjtc000) {
      jjtree.clearNodeScope(jjtn000);
      jjtc000 = false;
    } else {
      jjtree.popNode();
    }
    if (jjte000 instanceof RuntimeException) {
      {if (true) throw (RuntimeException)jjte000;}
    }
    if (jjte000 instanceof ParseException) {
      {if (true) throw (ParseException)jjte000;}
    }
    {if (true) throw (Error)jjte000;}
    } finally {
    if (jjtc000) {
      jjtree.closeNodeScope(jjtn000, true);
      jjtreeCloseNodeScope(jjtn000);
    }
    }
  }

  final private boolean jj_2_1(int xla) {
=====================================================================
Found a 22 line (104 tokens) duplication in the following files: 
Starting at line 206 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
Starting at line 290 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
            AdditiveExpression();
          } catch (Throwable jjte002) {
               if (jjtc002) {
                 jjtree.clearNodeScope(jjtn002);
                 jjtc002 = false;
               } else {
                 jjtree.popNode();
               }
               if (jjte002 instanceof RuntimeException) {
                 {if (true) throw (RuntimeException)jjte002;}
               }
               if (jjte002 instanceof ParseException) {
                 {if (true) throw (ParseException)jjte002;}
               }
               {if (true) throw (Error)jjte002;}
          } finally {
               if (jjtc002) {
                 jjtree.closeNodeScope(jjtn002,  2);
                 jjtreeCloseNodeScope(jjtn002);
               }
          }
          break;
=====================================================================
Found a 21 line (103 tokens) duplication in the following files: 
Starting at line 90 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
Starting at line 177 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/filter/src/org/geotools/filter/parser/ExpressionParser.java
          RelationalExpression();
        } catch (Throwable jjte001) {
            if (jjtc001) {
              jjtree.clearNodeScope(jjtn001);
              jjtc001 = false;
            } else {
              jjtree.popNode();
            }
            if (jjte001 instanceof RuntimeException) {
              {if (true) throw (RuntimeException)jjte001;}
            }
            if (jjte001 instanceof ParseException) {
              {if (true) throw (ParseException)jjte001;}
            }
            {if (true) throw (Error)jjte001;}
        } finally {
            if (jjtc001) {
              jjtree.closeNodeScope(jjtn001,  2);
              jjtreeCloseNodeScope(jjtn001);
            }
        }
=====================================================================
Found a 13 line (103 tokens) duplication in the following files: 
Starting at line 540 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/renderer/array/GenericArray.java
Starting at line 584 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/renderer/array/GenericArray.java
            super(XArray.isSorted(array));
            this.array = array;
            for (int i=array.length; --i>=0;) {
                final double value = array[i];
                if (value<minimum) minimum=value;
                if (value>maximum) maximum=value;
            }
        }
        public int    type        ()         {return 2;}
        public int    sizeof      ()         {return 64;}
        public int    length      ()         {return array.length;}
        public double getAsDouble (int i)    {return array[i];}
        public float  getAsFloat  (int i)    {return array[i];}
=====================================================================
Found a 6 line (103 tokens) duplication in the following files: 
Starting at line 281 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/science/src/org/geotools/science/oceano/SeaWater.java
Starting at line 314 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/science/src/org/geotools/science/oceano/SeaWater.java
        final double K0 = ( polynome(T,EOS80_F) + polynome(T,EOS80_G)*SR )*S + polynome(T,EOS80_E);
        final double DK = K0 + (((EOS80_J*SR+polynome(T,EOS80_I))*S+polynome(T,EOS80_H)) + (polynome(T,EOS80_K) + polynome(T,EOS80_M)*S)*P)*P;

        final double K_35_0_P = polynome(P,EOS80_N);
        final double V_S_T_0  = SVAN_S_T_0 + V_35_0_0;
        return (SVAN_S_T_0*( 1.0 - P/K_35_0_P ) + V_S_T_0*P*DK/(K_35_0_P*( K_35_0_P + DK )));
=====================================================================
Found a 13 line (102 tokens) duplication in the following files: 
Starting at line 240 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/renderer/j2d/SLDRenderedGeometries.java
Starting at line 266 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/renderer/j2d/SLDRenderedGeometries.java
                        Paint paint  = ls2d.getContour();
                        if(paint instanceof TexturePaint) {
                            TexturePaint tp = (TexturePaint) paint;
                            BufferedImage image = tp.getImage();
                            Rectangle2D rect = tp.getAnchorRect();
                            AffineTransform at = graphics.getTransform();
                            double width = rect.getWidth() * at.getScaleX();
                            double height = rect.getHeight() * at.getScaleY();
                            Rectangle2D scaledRect = new Rectangle2D.Double(0, 0, width, height);
                            paint = new TexturePaint(image, scaledRect);
                        } 
                        graphics.setPaint(paint);
                        graphics.setStroke(ls2d.getStroke());
=====================================================================
Found a 24 line (102 tokens) duplication in the following files: 
Starting at line 989 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/src/org/geotools/data/postgis/PostgisDataSource.java
Starting at line 388 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/postgis/src/org/geotools/data/postgis/PostgisFeatureStore.java
                FeatureReader iter = features.reader();

                if (iter.hasNext()) {
                    sql = "DELETE FROM \"" + tableName + "\" WHERE ";

                    for (int i = 0; iter.hasNext(); i++) {
                        fid = formatFid(iter.next());
                        sql += (fidColumn + " = " + fid);

                        if (iter.hasNext()) {
                            sql += " OR ";
                        } else {
                            sql += ";";
                        }
                    }

                    LOGGER.fine("our delete says : " + sql);
                    statement.executeUpdate(sql);
                }
            }

            close(statement);
        } catch (SQLException sqle) {
            fail = true;
=====================================================================
Found a 11 line (102 tokens) duplication in the following files: 
Starting at line 388 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gcs-coverage/src/org/geotools/gp/Interpolator.java
Starting at line 456 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gcs-coverage/src/org/geotools/gp/Interpolator.java
Starting at line 535 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gcs-coverage/src/org/geotools/gp/Interpolator.java
                                              double[] dest, int band, final int bandUp)
    {
        final double x0 = Math.floor(x);
        final double y0 = Math.floor(y);
        final int    ix = (int)x0;
        final int    iy = (int)y0;
        if (!(ix>=xmin && ix<xmax && iy>=ymin && iy<ymax)) {
            if (fallback==null) return null;
            if (fallback==this) return dest; // super.evaluate(...) succeed prior to this call.
            return fallback.interpolate(x, y, dest, band, bandUp);
        }
=====================================================================
Found a 22 line (102 tokens) duplication in the following files: 
Starting at line 1482 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/LiteRenderer.java
Starting at line 690 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/renderer/style/SLDStyleFactory.java
                        LOGGER.info("Bad file name in SLDStyleFactory" + requestedFont + "\n" + fne);
                    }
                }
            }

            if (LOGGER.isLoggable(Level.FINEST)) {
                LOGGER.finest("about to load");
            }

            if (is == null) {
                if (LOGGER.isLoggable(Level.INFO)) {
                    LOGGER.info("null input stream");
                }

                continue;
            }

            try {
                javaFont = java.awt.Font.createFont(java.awt.Font.TRUETYPE_FONT, is);
            } catch (FontFormatException ffe) {
                if (LOGGER.isLoggable(Level.INFO)) {
                    LOGGER.info("Font format error in SLDStyleFactory " + requestedFont + "\n"
=====================================================================
Found a 19 line (102 tokens) duplication in the following files: 
Starting at line 23 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/mapinfo/tests/unit/org/geotools/data/mapinfo/TestCaseSupport.java
Starting at line 103 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/shapefile/tests/unit/org/geotools/data/shapefile/TestCaseSupport.java
    }
    
    protected URL getTestResource(String name) {
        URL r = getClass().getResource("/testData/" + name);
        if (r == null)
            throw new RuntimeException("Could not locate resource : " + name);
        return r;
    }
    
    protected InputStream getTestResourceAsStream(String name) {
        InputStream in = getClass().getResourceAsStream("/testData/" + name);
        if (in == null)
            throw new RuntimeException("Could not locate resource : " + name);
        return in;
    }
    
    protected ReadableByteChannel getTestResourceChannel(String name) {
        return java.nio.channels.Channels.newChannel(getTestResourceAsStream(name));
    }
=====================================================================
Found a 16 line (100 tokens) duplication in the following files: 
Starting at line 278 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/resources/src/org/geotools/util/WeakValueHashMap.java
Starting at line 229 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/resources/src/org/geotools/util/WeakHashSet.java
                    final int index=(obj_e.hashCode() & 0x7FFFFFFF) % table.length;
                    e.index = index;
                    e.next  = table[index];
                    table[index]=e;
                } else {
                    count--;
                }
            }
        }
        final Logger logger = Logger.getLogger("org.geotools.util");
        final Level   level = Level.FINEST;
        if (logger.isLoggable(level)) {
            final LogRecord record = new LogRecord(level, "Rehash from " + oldTable.length +
                                                                  " to " +    table.length);
            record.setSourceMethodName(augmentation ? "canonicalize" : "remove");
            record.setSourceClassName("WeakHashSet");
=====================================================================
Found a 23 line (100 tokens) duplication in the following files: 
Starting at line 420 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gcs-coverage/src/org/geotools/util/RangeSet.java
Starting at line 646 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/gcs-coverage/src/org/geotools/util/RangeSet.java
        assert (i1 & 1) == 0 : i1;
        final int n = i1 - (++i0);
        if (n > 0) {
            modCount++;
            final Object old = array;
            final int length = Array.getLength(array);
            array = Array.newInstance(elementType, length - n);
            System.arraycopy(old, 0, array, 0, i0);
            System.arraycopy(old, i1, array, i0, length - i1);
        }
        assert (Array.getLength(array) & 1) == 0;
        return modCountChk != modCount;
    }
    
    /**
     * Remove a range of values from this set. Range may be removed in any order.
     *
     * @param lower The lower value to remove, exclusive.
     * @param upper The upper value to remove, exclusive.
     * @return <code>true</code> if this set changed as a result of the call.
     * @throws IllegalArgumentException if <code>lower</code> is greater than <code>upper</code>.
     */
    public boolean remove(byte lower, byte upper) throws IllegalArgumentException {
=====================================================================
Found a 5 line (100 tokens) duplication in the following files: 
Starting at line 244 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/science/src/org/geotools/science/oceano/SeaWater.java
Starting at line 281 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/science/src/org/geotools/science/oceano/SeaWater.java
        final double K0 = ( polynome(T,EOS80_F) + polynome(T,EOS80_G)*SR )*S + polynome(T,EOS80_E);
        final double DK = K0 + (((EOS80_J*SR+polynome(T,EOS80_I))*S+polynome(T,EOS80_H)) + (polynome(T,EOS80_K) + polynome(T,EOS80_M)*S)*P)*P;

        final double K_35_0_P = polynome(P,EOS80_N);
        final double V_S_T_0  = SVAN_S_T_0 + V_35_0_0;
=====================================================================
Found a 13 line (100 tokens) duplication in the following files: 
Starting at line 1378 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/lite-rendering/src/org/geotools/renderer/lite/LiteRenderer.java
Starting at line 629 of /home/tom/pmd/pmd-web/src/geotools2/geotools-src/renderer/src/org/geotools/renderer/style/SLDStyleFactory.java
                String reqStyle = (String) fonts[k].getFontStyle().getValue(feature);

                if (fontStyleLookup.containsKey(reqStyle)) {
                    styleCode = ((Integer) fontStyleLookup.get(reqStyle)).intValue();
                } else {
                    styleCode = java.awt.Font.PLAIN;
                }

                String reqWeight = (String) fonts[k].getFontWeight().getValue(feature);

                if (reqWeight.equalsIgnoreCase("Bold")) {
                    styleCode = styleCode | java.awt.Font.BOLD;
                }