=====================================================================
Found a 69 line (853 tokens) duplication in the following files: 
Starting at line 134 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Reference/x86/x86ReferenceCompiler.java
Starting at line 194 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Quad/x86/SimpleCompiler.java
            HeapAddress addr = HeapAddress.addressOf(o);
            asm.emit1_Imm32(x86.PUSH_i32, addr.to32BitValue());
            Code2HeapReference r = new Code2HeapReference((CodeAddress) asm.getCurrentAddress().offset(-4), addr);
            data_relocs.add(r);
            if (ALWAYS_TRACE) System.out.println("Code2Heap reference: "+r);
        } else {
            asm.emit1_Imm8(x86.PUSH_i8, (byte)0);
        }
    }
    public final void emitPushMemory(jq_StaticField f) { emitPushMemory(f, asm, data_relocs); }
    public static final void emitPushMemory(jq_StaticField f, x86Assembler asm, List data_relocs) {
        HeapAddress addr = f.getAddress();
        asm.emit2_Mem(x86.PUSH_m, addr.to32BitValue());
        Code2HeapReference r = new Code2HeapReference((CodeAddress) asm.getCurrentAddress().offset(-4), addr);
        data_relocs.add(r);
        if (ALWAYS_TRACE) System.out.println("Code2Heap reference: "+r);
    }
    public final void emitPushMemory8(jq_StaticField f) { emitPushMemory8(f, asm, data_relocs); }
    public static final void emitPushMemory8(jq_StaticField f, x86Assembler asm, List data_relocs) {
        HeapAddress addr = f.getAddress();
        asm.emit2_Mem(x86.PUSH_m, addr.offset(4).to32BitValue()); // hi
        Code2HeapReference r = new Code2HeapReference((CodeAddress) asm.getCurrentAddress().offset(-4), (HeapAddress) addr.offset(4));
        data_relocs.add(r);
        asm.emit2_Mem(x86.PUSH_m, addr.to32BitValue()); // lo
        r = new Code2HeapReference((CodeAddress) asm.getCurrentAddress().offset(-4), addr);
        data_relocs.add(r);
        if (ALWAYS_TRACE) System.out.println("Code2Heap reference: "+r);
    }
    public final void emitPopMemory(jq_StaticField f) { emitPopMemory(f, asm, data_relocs); }
    public static final void emitPopMemory(jq_StaticField f, x86Assembler asm, List data_relocs) {
        HeapAddress addr = f.getAddress();
        asm.emit2_Mem(x86.POP_m, addr.to32BitValue());
        Code2HeapReference r = new Code2HeapReference((CodeAddress) asm.getCurrentAddress().offset(-4), addr);
        data_relocs.add(r);
        if (ALWAYS_TRACE) System.out.println("Code2Heap reference: "+r);
    }
    public final void emitPopMemory8(jq_StaticField f) { emitPopMemory8(f, asm, data_relocs); }
    public static final void emitPopMemory8(jq_StaticField f, x86Assembler asm, List data_relocs) {
        HeapAddress addr = f.getAddress();
        asm.emit2_Mem(x86.POP_m, addr.to32BitValue()); // lo
        Code2HeapReference r = new Code2HeapReference((CodeAddress) asm.getCurrentAddress().offset(-4), addr);
        data_relocs.add(r);
        if (ALWAYS_TRACE) System.out.println("Code2Heap reference: "+r);
        asm.emit2_Mem(x86.POP_m, addr.offset(4).to32BitValue()); // hi
        r = new Code2HeapReference((CodeAddress) asm.getCurrentAddress().offset(-4), (HeapAddress) addr.offset(4));
        data_relocs.add(r);
        if (ALWAYS_TRACE) System.out.println("Code2Heap reference: "+r);
    }
    public final void emitCallMemory(jq_StaticField f) { emitCallMemory(f, asm, data_relocs); }
    public static final void emitCallMemory(jq_StaticField f, x86Assembler asm, List data_relocs) {
        HeapAddress addr = f.getAddress();
        asm.emit2_Mem(x86.CALL_m, addr.to32BitValue());
        Code2HeapReference r = new Code2HeapReference((CodeAddress) asm.getCurrentAddress().offset(-4), addr);
        data_relocs.add(r);
        if (ALWAYS_TRACE) System.out.println("Code2Heap reference: "+r);
    }
    public final void emitFLD64(jq_StaticField f) { emitFLD64(f, asm, data_relocs); }
    public static final void emitFLD64(jq_StaticField f, x86Assembler asm, List data_relocs) {
        HeapAddress addr = f.getAddress();
        asm.emit2_Mem(x86.FLD_m64, addr.to32BitValue());
        Code2HeapReference r = new Code2HeapReference((CodeAddress) asm.getCurrentAddress().offset(-4), addr);
        data_relocs.add(r);
        if (ALWAYS_TRACE) System.out.println("Code2Heap reference: "+r);
    }
    
    public final List getCodeRelocs() { return code_relocs; }
    public final List getDataRelocs() { return data_relocs; }
    
    public static final jq_CompiledCode generate_compile_stub(jq_Method method) {
=====================================================================
Found a 56 line (593 tokens) duplication in the following files: 
Starting at line 233 of /home/tom/data/pmd/pmd-web/src/joeq/Main/TraceFlags.java
Starting at line 494 of /home/tom/data/pmd/pmd-web/src/joeq/Main/Driver.java
                Assert.UNREACHABLE("array parameter doesn't start with {");
            int count = 0;
            while (!s_args[++j].equals("}")) ++count;
            jq_Type elementType = ((jq_Array) type).getElementType();
            if (elementType == PrimordialClassLoader.getJavaLangString()) {
                String[] array = new String[count];
                for (int k = 0; k < count; ++k)
                    array[k] = s_args[j - count + k];
                args[m] = array;
            } else if (elementType == jq_Primitive.BOOLEAN) {
                boolean[] array = new boolean[count];
                for (int k = 0; k < count; ++k)
                    array[k] = Boolean.valueOf(s_args[j - count + k]).booleanValue();
                args[m] = array;
            } else if (elementType == jq_Primitive.BYTE) {
                byte[] array = new byte[count];
                for (int k = 0; k < count; ++k)
                    array[k] = Byte.parseByte(s_args[j - count + k]);
                args[m] = array;
            } else if (elementType == jq_Primitive.SHORT) {
                short[] array = new short[count];
                for (int k = 0; k < count; ++k)
                    array[k] = Short.parseShort(s_args[j - count + k]);
                args[m] = array;
            } else if (elementType == jq_Primitive.CHAR) {
                char[] array = new char[count];
                for (int k = 0; k < count; ++k)
                    array[k] = s_args[j - count + k].charAt(0);
                args[m] = array;
            } else if (elementType == jq_Primitive.INT) {
                int[] array = new int[count];
                for (int k = 0; k < count; ++k)
                    array[k] = Integer.parseInt(s_args[j - count + k]);
                args[m] = array;
            } else if (elementType == jq_Primitive.LONG) {
                long[] array = new long[count];
                for (int k = 0; k < count; ++k)
                    array[k] = Long.parseLong(s_args[j - count + k]);
                args[m] = array;
            } else if (elementType == jq_Primitive.FLOAT) {
                float[] array = new float[count];
                for (int k = 0; k < count; ++k)
                    array[k] = Float.parseFloat(s_args[j - count + k]);
                args[m] = array;
            } else if (elementType == jq_Primitive.DOUBLE) {
                double[] array = new double[count];
                for (int k = 0; k < count; ++k)
                    array[k] = Double.parseDouble(s_args[j - count + k]);
                args[m] = array;
            } else
                Assert.UNREACHABLE("Parsing of type " + type + " is not implemented");
        } else
            Assert.UNREACHABLE("Parsing of type " + type + " is not implemented");
        return j;
    }

=====================================================================
Found a 36 line (371 tokens) duplication in the following files: 
Starting at line 570 of /home/tom/data/pmd/pmd-web/src/joeq/Run_Time/ReflectionImpl.java
Starting at line 509 of /home/tom/data/pmd/pmd-web/src/joeq/Run_Time/ReflectionImpl.java
                        throw new IllegalArgumentException(args[i].getClass()+" is not assignable to "+c);
                    Unsafe.pushArgA(HeapAddress.addressOf(args[i]));
                } else {
                    if (c == jq_Primitive.BYTE) {
                        int v = (int)Reflection.unwrapToByte(args[i]);
                        Unsafe.pushArg(v);
                    } else if (c == jq_Primitive.CHAR) {
                        int v = (int)Reflection.unwrapToChar(args[i]);
                        Unsafe.pushArg(v);
                    } else if (c == jq_Primitive.DOUBLE) {
                        long v = Double.doubleToRawLongBits(Reflection.unwrapToDouble(args[i]));
                        Unsafe.pushArg((int)(v >> 32)); // hi
                        Unsafe.pushArg((int)v);         // lo
                    } else if (c == jq_Primitive.FLOAT) {
                        int v = Float.floatToRawIntBits(Reflection.unwrapToFloat(args[i]));
                        Unsafe.pushArg(v);
                    } else if (c == jq_Primitive.INT) {
                        int v = Reflection.unwrapToInt(args[i]);
                        Unsafe.pushArg(v);
                    } else if (c == jq_Primitive.LONG) {
                        long v = Reflection.unwrapToLong(args[i]);
                        Unsafe.pushArg((int)(v >> 32)); // hi
                        Unsafe.pushArg((int)v);         // lo
                    } else if (c == jq_Primitive.SHORT) {
                        int v = (int)Reflection.unwrapToShort(args[i]);
                        Unsafe.pushArg(v);
                    } else if (c == jq_Primitive.BOOLEAN) {
                        int v = Reflection.unwrapToBoolean(args[i])?1:0;
                        Unsafe.pushArg(v);
                    } else Assert.UNREACHABLE(c.toString());
                }
            }
        } else {
            Assert._assert(params.length == offset);
        }
        try {
=====================================================================
Found a 31 line (198 tokens) duplication in the following files: 
Starting at line 21 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/sun14_win32/java/lang/Class.java
Starting at line 23 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/sun14_linux/java/lang/Class.java
                    ++count;
            }
            java.lang.reflect.Field[] f2 = new java.lang.reflect.Field[count];
            --count;
            for (int i=0, j=-1; j<count; ++i) {
                if (java.lang.reflect.Modifier.isPublic(f[i].getModifiers()))
                    f2[++j] = f[i];
            }
            f = f2;
        }
        return f;
    }
    private java.lang.reflect.Method[] getDeclaredMethods0(boolean publicOnly) {
        java.lang.reflect.Method[] f = getMethods0(java.lang.reflect.Member.DECLARED);
        if (publicOnly) {
            // TODO.
        }
        return f;
    }
    private java.lang.reflect.Constructor[] getDeclaredConstructors0(boolean publicOnly) {
        java.lang.reflect.Constructor[] f = getConstructors0(java.lang.reflect.Member.DECLARED);
        if (publicOnly) {
            // TODO.
        }
        return f;
    }
    
    private static boolean desiredAssertionStatus0(Class clazz) {
        // TODO.
        return false;
    }
=====================================================================
Found a 21 line (196 tokens) duplication in the following files: 
Starting at line 1454 of /home/tom/data/pmd/pmd-web/src/joeq/Clazz/jq_Class.java
Starting at line 1509 of /home/tom/data/pmd/pmd-web/src/joeq/Clazz/jq_Class.java
            if ((params[j] == jq_Primitive.LONG) || (params[j] == jq_Primitive.DOUBLE))
                ++n;
        }
        bc[++k] = (byte)0xb8; // invokestatic
        bc[++k] = (byte)(method_idx>>8);
        bc[++k] = (byte)method_idx;
        jq_Type t = m.getReturnType();
        if (t.isReferenceType()) {
            bc[++k] = (byte)0xb0; // areturn
        } else if (t == jq_Primitive.LONG) {
            bc[++k] = (byte)0xad; // lreturn
        } else if (t == jq_Primitive.FLOAT) {
            bc[++k] = (byte)0xae; // freturn
        } else if (t == jq_Primitive.DOUBLE) {
            bc[++k] = (byte)0xaf; // dreturn
        } else if (t == jq_Primitive.VOID) {
            bc[++k] = (byte)0xb1; // return
        } else {
            bc[++k] = (byte)0xac; // ireturn
        }
        jq_Method stubm = (jq_Method)getDeclaredMember(nd);
=====================================================================
Found a 23 line (188 tokens) duplication in the following files: 
Starting at line 33 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/Common/java/io/RandomAccessFile.java
Starting at line 29 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/Common/java/io/FileInputStream.java
        return b[0]&0xFF;
    }
    private int readBytes(byte b[], int off, int len) throws java.io.IOException {
        return readBytes(b, off, len, this.fd);
    }
    // IBM JDK has this extra fd argument here.
    private int readBytes(byte b[], int off, int len, FileDescriptor fd) throws java.io.IOException {
        int fdnum = fd.fd;
        // check for index out of bounds/null pointer
        if (len < 0) throw new IndexOutOfBoundsException();
        // do bounds check
        byte b2 = b[off+len-1];
        // BUG in Sun's implementation, which we mimic here.  off=b.length and len=0 doesn't throw an error (?)
        if (off < 0) throw new IndexOutOfBoundsException();
        if (len == 0) return 0;
        HeapAddress start = (HeapAddress) HeapAddress.addressOf(b).offset(off);
        int result = SystemInterface.file_readbytes(fdnum, start, len);
        if (result == 0)
            return -1; // EOF
        if (result == -1)
            throw new java.io.IOException();
        return result;
    }
=====================================================================
Found a 24 line (175 tokens) duplication in the following files: 
Starting at line 2855 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Analysis/IPA/CSPAResults.java
Starting at line 2897 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Analysis/IPA/CSPAResults.java
            System.out.println(vPrelation.toStringWithDomains(ts));
            visited.orWith(vPrelation.id());
            // A: v2=v1;
            BDD b = A.relprod(vPrelation, V1set);
            System.out.println("Arguments/Return Values = "+b.satCount(V2set));
            // L: v2=v1.f;
            vPrelation.replaceWith(V1toV2);
            BDD c = L.relprod(vPrelation, V2set); // V1xF
            vPrelation.free();
            BDD d = vP.relprod(c, V1set); // H1xF
            c.free();
            BDD e = hP.relprod(d, H1Fset); // H2
            d.free();
            e.replaceWith(H2toH1);
            BDD f = vP.relprod(e, H1set); // V1
            System.out.println("Loads/Stores = "+f.satCount(V1set));
            e.free();
            vPrelation = b;
            vPrelation.replaceWith(V2toV1);
            vPrelation.orWith(f);
            vPrelation.applyWith(visited.id(), BDDFactory.diff);
        }
    }
    
=====================================================================
Found a 19 line (171 tokens) duplication in the following files: 
Starting at line 55 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/Common/java/io/UnixFileSystem.java
Starting at line 100 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/Common/java/io/Win32FileSystem.java
            if (i == s.length) {
                String[] s2 = new String[s.length<<1];
                System.arraycopy(s, 0, s2, 0, s.length);
                s = s2;
            }
            s[i] = SystemInterface.fromCString(ptr.offset(SystemInterface.readdir_name_offset));
            if (s[i].equals(".") || s[i].equals("..")) --i;
        }
        SystemInterface.fs_closedir(dir);
        String[] ret = new String[i];
        System.arraycopy(s, 0, ret, 0, i);
        return ret;
    }

    public boolean createDirectory(java.io.File file) {
        int res = SystemInterface.fs_mkdir(file.getPath());
        return res == 0;
    }

=====================================================================
Found a 22 line (164 tokens) duplication in the following files: 
Starting at line 65 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/ibm13_linux/Interface.java
Starting at line 65 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/ibm13_win32/Interface.java
                Object[] args = { } ;
                Clazz.jq_Method init_inflaters = k.getOrCreateStaticMethod("init_inflaters", "()V");
                Bootstrap.MethodInvocation mi = new Bootstrap.MethodInvocation(init_inflaters, args);
                jq.on_vm_startup.add(mi);
                System.out.println("Added call to reinitialize java.util.zip.ZipFile.inflaters field on joeq startup: "+mi);
            }
        }
        
        public java.lang.Object mapInstanceField(java.lang.Object o, Clazz.jq_InstanceField f) {
            if (IGNORE_THREAD_LOCALS) {
                jq_Class c = f.getDeclaringClass();
                if (c == PrimordialClassLoader.getJavaLangThread()) {
                    String fieldName = f.getName().toString();
                    if (fieldName.equals("threadLocals"))
                        return java.util.Collections.EMPTY_MAP;
                    if (fieldName.equals("inheritableThreadLocals"))
                        return java.util.Collections.EMPTY_MAP;
                }
            }
            return super.mapInstanceField(o, f);
        }
    }
=====================================================================
Found a 17 line (158 tokens) duplication in the following files: 
Starting at line 133 of /home/tom/data/pmd/pmd-web/src/joeq/Run_Time/ExceptionDeliverer.java
Starting at line 158 of /home/tom/data/pmd/pmd-web/src/joeq/Run_Time/ExceptionDeliverer.java
            CodeAddress ip = sf.ip;
            jq_CompiledCode cc = CodeAllocator.getCodeContaining(ip);
            String s;
            if (cc != null) {
                jq_Method m = cc.getMethod();
                int code_offset = ip.difference(cc.getStart());
                if (m != null) {
                    Utf8 sourcefile = m.getDeclaringClass().getSourceFile();
                    int bc_index = cc.getBytecodeIndex(ip);
                    int line_num = m.getLineNumber(bc_index);
                    s = "\tat "+m+" ("+sourcefile+":"+line_num+" bc:"+bc_index+" off:"+Strings.hex(code_offset)+")";
                } else {
                    s = "\tat <unknown cc> (start:"+cc.getStart().stringRep()+" off:"+Strings.hex(code_offset)+")";
                }
            } else {
                s = "\tat <unknown addr> (ip:"+ip.stringRep()+")";
            }
=====================================================================
Found a 19 line (157 tokens) duplication in the following files: 
Starting at line 408 of /home/tom/data/pmd/pmd-web/src/joeq/Linker/ELF/Section.java
Starting at line 348 of /home/tom/data/pmd/pmd-web/src/joeq/Linker/ELF/Section.java
                StrTabSection ss = file.getSectionHeaderStringTable();
                if (ss == null) throw new IOException();
                this.name = ss.getString(s.sectionNameIndex);
            }
            this.stringTable = (StrTabSection)file.getSection(s.link);
            file.set_position(s.offset);
            int n = s.size / this.getEntSize();
            if (s.size % this.getEntSize() != 0) throw new IOException();
            this.localSymbols = new LinkedList(); // size is s.info
            this.globalSymbols = new LinkedList(); // size is n - s.info
            while (--n >= 0) {
                SymbolTableEntry e = SymbolTableEntry.read(file, this.stringTable);
                this.addSymbol(e);
            }
            if (this.getInfo() != s.info) throw new IOException();
        }

    }
    
=====================================================================
Found a 18 line (156 tokens) duplication in the following files: 
Starting at line 631 of /home/tom/data/pmd/pmd-web/src/joeq/Bootstrap/BootImage.java
Starting at line 670 of /home/tom/data/pmd/pmd-web/src/joeq/Bootstrap/BootImage.java
            type = DT_ARY;
        } else if (t.isReferenceType()) {
            type = DT_PTR;
        }
        if (t.isPrimitiveType()) {
            if (t == jq_Primitive.INT) type |= T_LONG;
            else if (t == jq_Primitive.LONG) type |= T_LNGDBL;
            else if (t == jq_Primitive.FLOAT) type |= T_FLOAT;
            else if (t == jq_Primitive.DOUBLE) type |= T_DOUBLE;
            else if (t == jq_Primitive.BYTE) type |= T_CHAR;
            else if (t == jq_Primitive.BOOLEAN) type |= T_UCHAR;
            else if (t == jq_Primitive.SHORT) type |= T_SHORT;
            else if (t == jq_Primitive.CHAR) type |= T_USHORT;
            else Assert.UNREACHABLE();
        } else {
            type |= T_STRUCT;
        }
        out.writeUShort(type); // e_type
=====================================================================
Found a 28 line (149 tokens) duplication in the following files: 
Starting at line 31 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/ibm13_win32/java/lang/System.java
Starting at line 32 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/sun13_win32/java/lang/System.java
        props.setProperty("java.vm.vendor", "joeq");
        props.setProperty("java.vm.version", "1.3.0");
        
        props.setProperty("os.arch", "x86");
        props.setProperty("os.name", "Windows 2000");
        props.setProperty("os.version", "5.0");
        
        props.setProperty("file.encoding", "Cp1252");
        props.setProperty("file.encoding.pkg", "sun.io");
        props.setProperty("file.separator", "\\");
        
        props.setProperty("line.separator", "\r\n");
        
        props.setProperty("path.separator", ";");
        
        props.setProperty("user.dir", "C:\\joeq");
        props.setProperty("user.home", "C:\\Documents and Settings\\John Whaley");
        props.setProperty("user.language", "en");
        props.setProperty("user.name", "jwhaley");
        props.setProperty("user.region", "US");
        props.setProperty("user.timezone", "");

        // must be at end: classpathToString() uses some properties from above.
        props.setProperty("java.class.path", PrimordialClassLoader.loader.classpathToString());

        return props;
    }

=====================================================================
Found a 18 line (148 tokens) duplication in the following files: 
Starting at line 4320 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Analysis/FlowInsensitive/MethodSummary.java
Starting at line 157 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Analysis/IPA/ClassInvariantAnalysis.java
                FieldNode n2;
                if (o instanceof FieldNode) {
                    n2 = (FieldNode)o;
                } else {
                    Set s = (Set)NodeSet.FACTORY.makeSet((Set)o);
                    if (s.size() == 0) {
                        i.remove();
                        continue;
                    }
                    if (s.size() == 1) {
                        n2 = (FieldNode)s.iterator().next();
                        e.setValue(n2);
                        continue;
                    }
                    if (TRACE_INTRA) out.println("Node "+n+" has duplicate access path edges on field "+f+": "+s);
                    n2 = FieldNode.unify(f, s);
                    for (Iterator j=s.iterator(); j.hasNext(); ) {
                        FieldNode n3 = (FieldNode)j.next();
=====================================================================
Found a 18 line (147 tokens) duplication in the following files: 
Starting at line 199 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Quad/MethodInline.java
Starting at line 310 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Quad/MethodInline.java
        if (TRACE) out.println("Code to inline:");
        if (TRACE) out.println(callee.fullDump());
        if (TRACE) out.println(callee.getRegisterFactory().fullDump());

        // copy the callee's control flow graph, renumbering the basic blocks,
        // registers and quads, and add the exception handlers.
        callee = caller.merge(callee);
        if (TRACE) out.println("After renumbering:");
        if (TRACE) out.println(callee.fullDump());
        if (TRACE) out.println(callee.getRegisterFactory().fullDump());
        callee.appendExceptionHandlers(bb.getExceptionHandlers());

        if (TRACE) out.println("Original basic block containing invoke:");
        if (TRACE) out.println(bb.fullDump());

        // split the basic block containing the invoke, and start splicing
        // in the callee's control flow graph.
=====================================================================
Found a 20 line (147 tokens) duplication in the following files: 
Starting at line 77 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Analysis/IPSSA/Apps/FindOwnership.java
Starting at line 279 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Analysis/IPSSA/Apps/FindCollectionImplementations.java
                        list.add(s);
                    }
                    i = new AppendIterator(list.iterator(), i);
                }catch(IOException e) {
                    e.printStackTrace();
                    System.exit(2);
                }
                
            } else
            if (args[x].endsWith("*")) {
                i = new AppendIterator(PrimordialClassLoader.loader.listPackage(args[x].substring(0, args[x].length()-1)), i);
            } else 
            if(args[x].charAt(0) == '-'){
                System.exit(2);                    
            }else {
                String classname = args[x];
                i = new AppendIterator(Collections.singleton(classname).iterator(), i);
            }
        }

=====================================================================
Found a 18 line (147 tokens) duplication in the following files: 
Starting at line 1024 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Analysis/IPA/PAResults.java
Starting at line 1451 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Analysis/IPA/PAResults.java
            // A: v2=v1;
            BDD b = r.A.relprod(vPrelation, r.V1set); // V2
            // L: v2=v1.f;
            vPrelation.replaceWith(r.V1toV2); // V2
            BDD c = r.L.relprod(vPrelation, r.V2set); // V1xF
            vPrelation.free();
            BDD d = r.vP.relprod(c, r.V1set); // H1xF
            c.free();
            BDD e = r.hP.relprod(d, r.H1Fset); // H2
            d.free();
            e.replaceWith(r.H2toH1);
            BDD f = r.vP.relprod(e, r.H1set); // V1
            e.free();
            vPrelation = b;
            vPrelation.replaceWith(r.V2toV1);
            vPrelation.orWith(f);
            vPrelation.applyWith(visited.id(), BDDFactory.diff);
        }
=====================================================================
Found a 14 line (144 tokens) duplication in the following files: 
Starting at line 377 of /home/tom/data/pmd/pmd-web/src/joeq/Clazz/jq_ClassFileConstants.java
Starting at line 377 of /home/tom/data/pmd/pmd-web/src/joeq/Clazz/jq_ClassFileConstants.java
      0/*istore_3*/, 0/*lstore_0*/, 0/*lstore_1*/, 0/*lstore_2*/,
      0/*lstore_3*/, 0/*fstore_0*/, 0/*fstore_1*/, 0/*fstore_2*/,
      0/*fstore_3*/, 0/*dstore_0*/, 0/*dstore_1*/, 0/*dstore_2*/,
      0/*dstore_3*/, 0/*astore_0*/, 0/*astore_1*/, 0/*astore_2*/,
      0/*astore_3*/, 0/*iastore*/, 0/*lastore*/, 0/*fastore*/,
      0/*dastore*/, 0/*aastore*/, 0/*bastore*/, 0/*castore*/,
      0/*sastore*/, 0/*pop*/, 0/*pop2*/, 0/*dup*/, 0/*dup_x1*/,
      0/*dup_x2*/, 0/*dup2*/, 0/*dup2_x1*/, 0/*dup2_x2*/, 0/*swap*/,
      0/*iadd*/, 0/*ladd*/, 0/*fadd*/, 0/*dadd*/, 0/*isub*/,
      0/*lsub*/, 0/*fsub*/, 0/*dsub*/, 0/*imul*/, 0/*lmul*/,
      0/*fmul*/, 0/*dmul*/, 0/*idiv*/, 0/*ldiv*/, 0/*fdiv*/,
      0/*ddiv*/, 0/*irem*/, 0/*lrem*/, 0/*frem*/, 0/*drem*/,
      0/*ineg*/, 0/*lneg*/, 0/*fneg*/, 0/*dneg*/, 0/*ishl*/,
      0/*lshl*/, 0/*ishr*/, 0/*lshr*/, 0/*iushr*/, 0/*lushr*/,
=====================================================================
Found a 17 line (141 tokens) duplication in the following files: 
Starting at line 499 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/BytecodeAnalysis/LiveRefAnalysis.java
Starting at line 822 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/BytecodeAnalysis/LiveRefAnalysis.java
            if (stackDepth > 0) {
                sb.append(Strings.lineSep);
                sb.append("Stack: {");
                for (int i=0; i<stackDepth; ++i) {
                    sb.append(i);
                    sb.append('=');
                    sb.append(stack[i]==null?"null":stack[i].toString());
                    if (i < stackDepth-1) sb.append(',');
                }
                sb.append(" }");
            }
            return sb.toString();
        }
        public String toString() {
            if (liveness != null) return toString_live();
            StringBuffer sb = new StringBuffer("Locals: { ");
            for (int i=0; i<locals.length; ++i) {
=====================================================================
Found a 15 line (135 tokens) duplication in the following files: 
Starting at line 60 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/sun14_win32/Interface.java
Starting at line 59 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/sun14_linux/Interface.java
            k = (jq_Class)PrimordialClassLoader.loader.getOrCreateBSType("Ljava/lang/reflect/Field;");
            nullInstanceFields.add(k.getOrCreateInstanceField("fieldAccessor", "Lsun/reflect/FieldAccessor;"));
            k = (jq_Class)PrimordialClassLoader.loader.getOrCreateBSType("Ljava/lang/reflect/Method;");
            nullInstanceFields.add(k.getOrCreateInstanceField("methodAccessor", "Lsun/reflect/MethodAccessor;"));
            k = (Clazz.jq_Class)PrimordialClassLoader.loader.getOrCreateBSType("Ljava/lang/reflect/Constructor;");
            nullInstanceFields.add(k.getOrCreateInstanceField("constructorAccessor", "Lsun/reflect/ConstructorAccessor;"));
            
            if (IGNORE_THREAD_LOCALS) {
                // for some reason, thread local gets created during bootstrapping. (SoftReference)
                // for now, just kill all thread locals.
                k = (Clazz.jq_Class)PrimordialClassLoader.loader.getOrCreateBSType("Ljava/lang/Thread;");
                nullInstanceFields.add(k.getOrCreateInstanceField("threadLocals", "Ljava/lang/ThreadLocal$ThreadLocalMap;"));
                nullInstanceFields.add(k.getOrCreateInstanceField("inheritableThreadLocals", "Ljava/lang/ThreadLocal$ThreadLocalMap;"));
            }
            
=====================================================================
Found a 14 line (132 tokens) duplication in the following files: 
Starting at line 78 of /home/tom/data/pmd/pmd-web/src/joeq/Run_Time/ArrayCopy.java
Starting at line 61 of /home/tom/data/pmd/pmd-web/src/joeq/Run_Time/ArrayCopy.java
        if ((src_position < 0) || (dst_position < 0) || (length < 0) ||
            (src_position+length > src.length) || (dst_position+length > dst.length))
            throw new ArrayIndexOutOfBoundsException();
        if ((src == dst) && (src_position < dst_position) && (src_position+length > dst_position)) {
            // overlapping case
            for (int i=length-1; i>=0; --i) {
                dst[dst_position+i] = src[src_position+i];
            }
            return;
        }
        for (int i=0; i<length; ++i) {
            dst[dst_position+i] = src[src_position+i];
        }
    }
=====================================================================
Found a 22 line (132 tokens) duplication in the following files: 
Starting at line 71 of /home/tom/data/pmd/pmd-web/src/joeq/Memory/HeapAddress.java
Starting at line 32 of /home/tom/data/pmd/pmd-web/src/joeq/Memory/CodeAddress.java
    public native byte    peek1();
    public native short   peek2();
    public native int     peek4();
    public native long    peek8();
    
    public native void poke(Address v);
    public native void poke1(byte v);
    public native void poke2(short v);
    public native void poke4(int v);
    public native void poke8(long v);
    
    public native Address offset(int offset);
    public native Address align(int shift);
    public native int difference(Address v);
    public native boolean isNull();
    
    public native int to32BitValue();
    public native String stringRep();
    
    public static final jq_Class _class;
    public static final jq_StaticField _FACTORY;
    static {
=====================================================================
Found a 9 line (129 tokens) duplication in the following files: 
Starting at line 2718 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Quad/BytecodeToQuad.java
Starting at line 8350 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/BytecodeAnalysis/Bytecodes.java
            this.returnTarget = returnTarget;
        }
        public boolean isAddressType() { return false; }
        public String getJDKName() { return desc.toString(); }
        public String getJDKDesc() { return getJDKName(); }
        public Clazz.jq_Class[] getInterfaces() { Assert.UNREACHABLE(); return null; }
        public Clazz.jq_Class getInterface(Utf8 desc) { Assert.UNREACHABLE(); return null; }
        public boolean implementsInterface(Clazz.jq_Class k) { Assert.UNREACHABLE(); return false; }
        public Clazz.jq_InstanceMethod getVirtualMethod(Clazz.jq_NameAndDesc nd) { Assert.UNREACHABLE(); return null; }
=====================================================================
Found a -1 line (126 tokens) duplication in the following files: 
Starting at line 153 of /home/tom/data/pmd/pmd-web/src/joeq/Util/BitString.java
Starting at line 153 of /home/tom/data/pmd/pmd-web/src/joeq/Util/BitString.java

=====================================================================
Found a 28 line (121 tokens) duplication in the following files: 
Starting at line 27 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/pa/java/security/AccessController.java
Starting at line 27 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/Common/java/security/AccessController.java
        } catch (RuntimeException x) {
            throw x;
        } catch (Exception x) {
            throw new java.security.PrivilegedActionException(x);
        }
    }
    public static Object doPrivileged(java.security.PrivilegedExceptionAction action,
                                      java.security.AccessControlContext context)
        throws java.security.PrivilegedActionException {
        // TODO: set privilege level
        try {
            return action.run();
        } catch (RuntimeException x) {
            throw x;
        } catch (Exception x) {
            throw new java.security.PrivilegedActionException(x);
        }
    }
    private static java.security.AccessControlContext getStackAccessControlContext() {
        // TODO
        return null;
    }
    static java.security.AccessControlContext getInheritedAccessControlContext() {
        // TODO
        return null;
    }

    //public static final jq_Class _class = (jq_Class)PrimordialClassLoader.loader.getOrCreateBSType("Ljava/security/AccessController;");
=====================================================================
Found a 10 line (120 tokens) duplication in the following files: 
Starting at line 318 of /home/tom/data/pmd/pmd-web/src/joeq/Run_Time/SystemInterface.java
Starting at line 283 of /home/tom/data/pmd/pmd-web/src/joeq/Run_Time/SystemInterface.java
            System.err.println(msg);
            return;
        }
        HeapAddress value = (HeapAddress)HeapAddress.addressOf(msg).offset(_string_value.getOffset()).peek();
        int offset = HeapAddress.addressOf(msg).offset(_string_offset.getOffset()).peek4();
        int count = HeapAddress.addressOf(msg).offset(_string_count.getOffset()).peek4();
        Unsafe.pushArg(count);
        Unsafe.pushArgA(value.offset(offset*2));
        try {
            Unsafe.getThreadBlock().disableThreadSwitch();
=====================================================================
Found a 9 line (120 tokens) duplication in the following files: 
Starting at line 2828 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Quad/Operator.java
Starting at line 2842 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Quad/Operator.java
                s.handleException(result.getThrown());
            else if (getDest(q) != null) {
                Object r = result.getReturnValue();
                if (f.getReturnType() == jq_Primitive.BOOLEAN && r instanceof Boolean) r = new Integer(((Boolean)r).booleanValue()?1:0);
                else if (f.getReturnType() == jq_Primitive.CHAR && r instanceof Character) r = new Integer(((Character)r).charValue());
                s.putReg(getDest(q).getRegister(), r);
            }
        }

=====================================================================
Found a 12 line (120 tokens) duplication in the following files: 
Starting at line 16 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/sun14_win32/java/lang/Thread.java
Starting at line 18 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/sun14_linux/java/lang/Thread.java
        this.init(g, target, name, 0L);
    }
    private native void init(java.lang.ThreadGroup g, java.lang.Runnable target, java.lang.String name, long stackSize);
    
    public Thread(java.lang.ThreadGroup group, java.lang.Runnable target, java.lang.String name, long stackSize) {
        java.lang.Object o = this;
        jq_Thread t = new jq_Thread((java.lang.Thread)o);
        this.jq_thread = t;
        this.init(group, target, name, stackSize);
        t.init();
    }
    
=====================================================================
Found a 17 line (116 tokens) duplication in the following files: 
Starting at line 47 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/sun14_win32/java/lang/Throwable.java
Starting at line 47 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/sun14_linux/java/lang/Throwable.java
                    Utf8 fn = m.getDeclaringClass().getSourceFile();
                    if (fn != null) fileName = fn.toString();
                    int bc_index = cc.getBytecodeIndex(ip);
                    lineNumber = m.getLineNumber(bc_index);
                }
            }
        }
        return new StackTraceElement(declaringClass, methodName, fileName, lineNumber);
    }

    public java.lang.Throwable fillInStackTrace() {
        this.backtrace = ExceptionDeliverer.getStackTrace();
        java.lang.Object o = this;
        return (java.lang.Throwable)o;
    }

    public java.lang.Object getBacktraceObject() { return this.backtrace; }
=====================================================================
Found a 15 line (116 tokens) duplication in the following files: 
Starting at line 566 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/Common/java/lang/reflect/Field.java
Starting at line 508 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/Common/java/lang/reflect/Field.java
            }
            else if (t == jq_Primitive.DOUBLE) {
                Reflection.putstatic_D(sf, (double)val);
            }
            else Assert.UNREACHABLE();
        } else {
            jq_Reference obj_t = jq_Reference.getTypeOf(obj);
            if (!TypeCheck.isAssignable(obj_t, jq_f.getDeclaringClass())) {
                throw new IllegalArgumentException();
            }
            if (!this.isAccessible()) ClassUtils.checkCallerAccess(jq_f, 2);
            if (!jq_f.isFinal()) {
                throw new IllegalAccessException();
            }
            jq_InstanceField f = (jq_InstanceField)jq_f;
=====================================================================
Found a 20 line (115 tokens) duplication in the following files: 
Starting at line 50 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/sun13_win32/Interface.java
Starting at line 43 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/apple13_osx/Interface.java
                    String fieldName = f.getName().toString();
                    if (fieldName.equals("threadLocals") || fieldName.equals("inheritableThreadLocals")) {
                        // 1.3.1_05 and greater uses the 1.4 implementation of thread locals.
                        // see Sun BugParade id#4667411.
                        // we check the type of the field and return the appropriate object.
                        if (f.getType().getDesc() == Utf8.get("Ljava/util/Map;")) {
                            return java.util.Collections.EMPTY_MAP;
                        } else if (f.getType().getDesc() == Utf8.get("Ljava/lang/ThreadLocal$ThreadLocalMap;")) {
                            return null;
                        } else {
                            SystemInterface.debugwriteln("Unknown type for field "+f);
                            return null;
                        }
                    }
                }
            }
            return super.mapInstanceField(o, f);
        }
    }
    
=====================================================================
Found a 17 line (112 tokens) duplication in the following files: 
Starting at line 23 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/sun14_linux/java/io/RandomAccessFile.java
Starting at line 23 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/sun14_win32/java/io/RandomAccessFile.java
    throws java.io.FileNotFoundException {
        int flags = SystemInterface._O_BINARY;
        if ((mode & O_RDONLY) != 0) flags |= SystemInterface._O_RDONLY;
        if ((mode & O_RDWR) != 0) flags |= SystemInterface._O_RDWR | SystemInterface._O_CREAT;
        if ((mode & O_SYNC) != 0) {
            // todo: require that every update to the file's content or metadata be
            //       written synchronously to the underlying storage device
        }
        if ((mode & O_DSYNC) != 0) {
            // todo: require that every update to the file's content be written
            //       synchronously to the underlying storage device.
        }
        int fdnum = SystemInterface.file_open(name, flags, 0);
        if (fdnum == -1) throw new java.io.FileNotFoundException(name);
        this.fd.fd = fdnum;
    }

=====================================================================
Found a 12 line (110 tokens) duplication in the following files: 
Starting at line 434 of /home/tom/data/pmd/pmd-web/src/joeq/Scheduler/jq_NativeThread.java
Starting at line 482 of /home/tom/data/pmd/pmd-web/src/joeq/Scheduler/jq_NativeThread.java
        if (t1.isThreadSwitchEnabled()) {
            SystemInterface.debugwriteln("Java thread " + t1 + " has thread switching enabled on threadSwitch entry!");
            SystemInterface.die(-1);
        }
        Assert._assert(t1 != this.schedulerThread);

        // simulate a return in the current register state, so when the thread gets swapped back
        // in, it will continue where it left off.
        jq_RegisterState state = t1.getRegisterState();
        state.Eip = (CodeAddress) state.getEsp().peek();
        state.Esp = (StackAddress) state.getEsp().offset(StackAddress.size() + CodeAddress.size());

=====================================================================
Found a 14 line (109 tokens) duplication in the following files: 
Starting at line 274 of /home/tom/data/pmd/pmd-web/src/joeq/Interpreter/ReflectiveInterpreter.java
Starting at line 373 of /home/tom/data/pmd/pmd-web/src/joeq/Interpreter/DirectInterpreter.java
        c.cls_initialize();

        jq_StaticMethod rootm = null;
        Utf8 rootm_name = Utf8.get(rootMethodName);
        for(Iterator it = Arrays.asList(c.getDeclaredStaticMethods()).iterator();
            it.hasNext(); ) {
            jq_StaticMethod m = (jq_StaticMethod)it.next();
            if (m.getName() == rootm_name) {
                rootm = m;
                break;
            }
        }
        if (rootm == null)
            Assert.UNREACHABLE("root method not found: "+rootMethodClassName+"."+rootMethodName);
=====================================================================
Found a 12 line (108 tokens) duplication in the following files: 
Starting at line 1885 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/BytecodeAnalysis/TypeAnalysis.java
Starting at line 1833 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/BytecodeAnalysis/TypeAnalysis.java
                                (((StaticFieldLocation)pl).field != e.getKey())) {
                                necessary.add(pl);
                            }
                            necessaryHelper(necessary, pl, visited);
                        } else while (j.hasNext()) {
                            ProgramLocation pl = (ProgramLocation)j.next();
                            necessary.add(pl);
                            necessaryHelper(necessary, pl, visited);
                        }
                    }
                    if (TRACE_TRIM) out_ta.println("Necessary set: "+necessary);
                    visited = new HashSet();
=====================================================================
Found a 11 line (108 tokens) duplication in the following files: 
Starting at line 72 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Dataflow/WorklistSolver.java
Starting at line 94 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Dataflow/IterativeSolver.java
                             getSuccessors(c).iterator();
                Object p = j.next();
                Fact in = (Fact) dataflowValues.get(p);
                while (j.hasNext()) {
                    p = j.next();
                    Fact in2 = (Fact) dataflowValues.get(p);
                    in = problem.merge(in, in2);
                }
                TransferFunction tf = problem.getTransferFunction(c);
                Fact out = problem.apply(tf, in);
                Fact old = (Fact) dataflowValues.put(c, out);
=====================================================================
Found a 14 line (106 tokens) duplication in the following files: 
Starting at line 15 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/sun142_win32/java/lang/ClassLoader.java
Starting at line 15 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/sun142_linux/java/lang/ClassLoader.java
        if (getClassLoaderPerm == null) {
            try {
                java.lang.Class c = java.lang.Class.forName("sun.security.util.SecurityConstants");
                java.lang.reflect.Field f = c.getField("GET_CLASSLOADER_PERMISSION");
                getClassLoaderPerm = (java.lang.RuntimePermission) f.get(null);
            } catch (java.lang.ClassNotFoundException x) {
            } catch (java.lang.NoSuchFieldException x) {
            } catch (java.lang.IllegalAccessException x) {
            } catch (java.lang.ClassCastException x) {
            }
        }
        return getClassLoaderPerm;
    }
    
=====================================================================
Found a 14 line (106 tokens) duplication in the following files: 
Starting at line 278 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Quad/Operand.java
Starting at line 306 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Quad/Operand.java
        public int size() { return table.length; }
        public String toString() {
            StringBuffer sb = new StringBuffer("{ ");
            if (table.length > 0) {
                sb.append(table[0]);
                for (int i=1; i<table.length; ++i) {
                    sb.append(", ");
                    sb.append(table[i]);
                }
            }
            sb.append(" }");
            return sb.toString();
        }
        public Operand copy() {
=====================================================================
Found a 12 line (106 tokens) duplication in the following files: 
Starting at line 32 of /home/tom/data/pmd/pmd-web/src/joeq/Clazz/jq_Initializer.java
Starting at line 39 of /home/tom/data/pmd/pmd-web/src/joeq/Clazz/jq_InstanceMethod.java
        // get them for real
        param_types = new jq_Type[num];
        param_types[0] = clazz;
        i = nd.getDesc().getParamDescriptors();
        for (int j=1; j<num; ++j) {
            Utf8 pd = i.nextUtf8();
            param_types[j] = PrimordialClassLoader.getOrCreateType(clazz.getClassLoader(), pd);
            ++words;
            if ((param_types[j] == jq_Primitive.LONG) ||
                (param_types[j] == jq_Primitive.DOUBLE)) ++words;
        }
        param_words = words;
=====================================================================
Found a 33 line (105 tokens) duplication in the following files: 
Starting at line 320 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/CompilationState.java
Starting at line 238 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/CompilationState.java
            return TypeCheck.isAssignable_noload(t1, t2);
        }

        /* (non-Javadoc)
         * @see Compil3r.CompilationState#findCommonSuperclass(Clazz.jq_Type, Clazz.jq_Type)
         */
        public jq_Type findCommonSuperclass(jq_Type t1, jq_Type t2) {
            return TypeCheck.findCommonSuperclass(t1, t2, false);
        }

        /* (non-Javadoc)
         * @see Compil3r.CompilationState#declaresInterface(Clazz.jq_Class, java.util.Collection)
         */
        public byte declaresInterface(jq_Class klass, Collection interfaces) {
            return TypeCheck.declaresInterface(klass, interfaces, false);
        }

        /* (non-Javadoc)
         * @see Compil3r.CompilationState#implementsInterface(Clazz.jq_Class, Clazz.jq_Class)
         */
        public byte implementsInterface(jq_Class klass, jq_Class inter) {
            return TypeCheck.implementsInterface_noload(klass, inter);
        }

        /* (non-Javadoc)
         * @see Compil3r.CompilationState#getOrCreateType(UTF.Utf8)
         */
        public jq_Type getOrCreateType(Utf8 desc) {
            return PrimordialClassLoader.loader.getOrCreateBSType(desc);
        }
        
    }
    
=====================================================================
Found a 9 line (104 tokens) duplication in the following files: 
Starting at line 47 of /home/tom/data/pmd/pmd-web/src/joeq/Memory/Manager/ScanStatics.java
Starting at line 104 of /home/tom/data/pmd/pmd-web/src/joeq/Memory/Manager/ScanStatics.java
        for (Iterator i=types.iterator(); i.hasNext(); ) {
            Object o = i.next();
            if (o instanceof jq_Class) {
                jq_Class c = (jq_Class) o;
                jq_StaticField[] sfs = c.getStaticFields();
                for (int j=0; j<sfs.length; ++j) {
                    jq_StaticField sf = sfs[j];
                    if (sf.getType().isReferenceType()) {
                        HeapAddress ref = (HeapAddress) sf.getAddress().peek();
=====================================================================
Found a 5 line (103 tokens) duplication in the following files: 
Starting at line 63 of /home/tom/data/pmd/pmd-web/src/joeq/Run_Time/MathSupport.java
Starting at line 185 of /home/tom/data/pmd/pmd-web/src/joeq/Run_Time/MathSupport.java
        result += ((long)r1)   ;
        r1 = a_2*b_1; if (r1 < 0) { result += ((long)Integer.MAX_VALUE)<<16; r1 -= Integer.MAX_VALUE; }
        result += ((long)r1)<<16;
        r1 = a_1*b_2; if (r1 < 0) { result += ((long)Integer.MAX_VALUE)<<16; r1 -= Integer.MAX_VALUE; }
        result += ((long)r1)<<16;
=====================================================================
Found a 7 line (103 tokens) duplication in the following files: 
Starting at line 1305 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Quad/AndersenPointerAnalysis.java
Starting at line 1288 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/Quad/AndersenPointerAnalysis.java
        if (TRACE) out.println("Node "+base+" corresponds to concrete nodes "+s);
        Set result = NodeSet.FACTORY.makeSet();
        for (Iterator j=s.iterator(); j.hasNext(); ) {
            Node n2 = (Node)j.next();
            n2.getAllEdges(f, result);
        }
        if (TRACE) out.println("Edges from "+base+((f==null)?"[]":("."+f.getName()))+" : "+result);
=====================================================================
Found a 10 line (103 tokens) duplication in the following files: 
Starting at line 217 of /home/tom/data/pmd/pmd-web/src/joeq/Clazz/jq_CompiledCode.java
Starting at line 361 of /home/tom/data/pmd/pmd-web/src/joeq/Clazz/jq_Array.java
            return (Delegate)c.newInstance();
        } catch (java.lang.ClassNotFoundException x) {
            System.err.println("Cannot find "+type+" "+s+": "+x);
        } catch (java.lang.InstantiationException x) {
            System.err.println("Cannot instantiate "+type+" "+s+": "+x);
        } catch (java.lang.IllegalAccessException x) {
            System.err.println("Cannot access "+type+" "+s+": "+x);
        }
        return null;
    }
=====================================================================
Found a 22 line (103 tokens) duplication in the following files: 
Starting at line 14 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/ibm13_linux/java/lang/Class.java
Starting at line 14 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/ibm13_win32/java/lang/Class.java
    private static native Class forName0(java.lang.String name, boolean initialize,
                                         java.lang.ClassLoader loader)
        throws ClassNotFoundException;
    private native java.lang.Object newInstance0()
        throws InstantiationException, IllegalAccessException;

    private static Class forName1(java.lang.String name)
        throws ClassNotFoundException
    {
        // TODO: is this the correct classloader to use?
        java.lang.ClassLoader loader = PrimordialClassLoader.loader;
        return forName0(name, true, loader);
    }
    
    private java.lang.Object newInstance2(java.lang.Class ccls)
        throws InstantiationException, IllegalAccessException
    {
        // TODO: what do we do with the extra ccls argument?
        return newInstance0();
    }
    
=====================================================================
Found a 10 line (101 tokens) duplication in the following files: 
Starting at line 137 of /home/tom/data/pmd/pmd-web/src/joeq/Main/ClassDump.java
Starting at line 152 of /home/tom/data/pmd/pmd-web/src/joeq/Main/ClassDump.java
                out.println("method attributes:");
                for(Iterator it2 = c.getAttributes().keySet().iterator();
                    it2.hasNext(); ) {
                    Utf8 key = (Utf8)it2.next();
                    out.print("\t"+key);
                    byte[] val = t.getAttribute(key);
                    out.println(": "+((val!=null)?"(length "+val.length+")\t":"\t")+val);
                }
            }
            out.println();
=====================================================================
Found a 10 line (101 tokens) duplication in the following files: 
Starting at line 86 of /home/tom/data/pmd/pmd-web/src/joeq/Clazz/jq_Field.java
Starting at line 439 of /home/tom/data/pmd/pmd-web/src/joeq/Run_Time/Reflection.java
            return (Delegate)c.newInstance();
        } catch (java.lang.ClassNotFoundException x) {
            System.err.println("Cannot find "+type+" "+s+": "+x);
        } catch (java.lang.InstantiationException x) {
            System.err.println("Cannot instantiate "+type+" "+s+": "+x);
        } catch (java.lang.IllegalAccessException x) {
            System.err.println("Cannot access "+type+" "+s+": "+x);
        }
        return null;
    }
=====================================================================
Found a 7 line (101 tokens) duplication in the following files: 
Starting at line 300 of /home/tom/data/pmd/pmd-web/src/joeq/Assembler/x86/x86Assembler.java
Starting at line 406 of /home/tom/data/pmd/pmd-web/src/joeq/Assembler/x86/x86Assembler.java
        if (base == ESP) {
            if (off == 0)
                ip += x.emit2_Reg_SIB_EA(mc, r1, ESP, ESP, SCALE_1);
            else if (fits_signed(off, 8))
                ip += x.emit2_Reg_SIB_DISP8(mc, r1, ESP, ESP, SCALE_1, (byte)off);
            else
                ip += x.emit2_Reg_SIB_DISP32(mc, r1, ESP, ESP, SCALE_1, off);
=====================================================================
Found a 36 line (100 tokens) duplication in the following files: 
Starting at line 17 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/sun14_win32/java/lang/System.java
Starting at line 19 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/sun14_linux/java/lang/System.java
    public static java.lang.String mapLibraryName(java.lang.String libname) {
        return libname; // TODO.
    }

    /***
    public static void initializeSystemClass() {
        props = new java.util.Properties();
        initProperties(props);
        sun.misc.Version.init();
        java.io.FileInputStream fdIn = new java.io.FileInputStream(java.io.FileDescriptor.in);
        java.io.FileOutputStream fdOut = new java.io.FileOutputStream(java.io.FileDescriptor.out);
        java.io.FileOutputStream fdErr = new java.io.FileOutputStream(java.io.FileDescriptor.err);
        setIn0(new java.io.BufferedInputStream(fdIn));
        setOut0(new java.io.PrintStream(new java.io.BufferedOutputStream(fdOut, 128), true));
        setErr0(new java.io.PrintStream(new java.io.BufferedOutputStream(fdErr, 128), true));

        //try {
        //    java.util.logging.LogManager.getLogManager().readConfiguration();
        //} catch (java.lang.Exception ex) {
        //}

        //loadLibrary("zip");

        //sun.misc.VM.booted();
    }
    ***/
    public static void loadLibrary(String libname) {
        if (libname.equals("zip")) return;
        Runtime.getRuntime().loadLibrary0(getCallerClass(), libname);
    }
    static native Class getCallerClass();

    private static java.util.Properties initProperties(java.util.Properties props) {
        // TODO: read these properties from environment.
        props.setProperty("java.class.version", "48.0");
=====================================================================
Found a 18 line (100 tokens) duplication in the following files: 
Starting at line 14 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/ibm13_win32/java/util/zip/ZipFile.java
Starting at line 14 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/ibm13_linux/java/util/zip/ZipFile.java
    
    public static void init_inflaters() {
        inflaters = new java.util.Vector();
    }
    
    private String name;
    private java.io.RandomAccessFile raf;
    private java.util.Hashtable entries;
    
    public void __init__(String name) throws java.io.IOException {
        this.name = name;
        java.io.RandomAccessFile raf = new java.io.RandomAccessFile(name, "r");
        this.raf = raf;
        //this.inflaters = new java.util.Vector();
        this.readCEN();
    }
    
    private native void readCEN() throws java.io.IOException;
=====================================================================
Found a 7 line (100 tokens) duplication in the following files: 
Starting at line 1325 of /home/tom/data/pmd/pmd-web/src/joeq/Assembler/x86/x86.java
Starting at line 1311 of /home/tom/data/pmd/pmd-web/src/joeq/Assembler/x86/x86.java
        Assert._assert(length == 2);
        Assert._assert((opcode & 0xC7) == 0);
        Assert._assert(base >= EAX && base <= EDI);
        Assert._assert(ind >= EAX && ind <= EDI);
        if (mc != null) {
            mc.add2(opcode | MOD_EA | RM_SIB);
            mc.add1((byte)(scale | (ind << 3) | base));
=====================================================================
Found a 16 line (100 tokens) duplication in the following files: 
Starting at line 96 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/BytecodeAnalysis/CallTargets.java
Starting at line 147 of /home/tom/data/pmd/pmd-web/src/joeq/Compil3r/BytecodeAnalysis/CallTargets.java
                        if (mtarget instanceof jq_StaticMethod) break;
                        target = (jq_InstanceMethod)mtarget;
                        if (target != null) {
                            if (VerifyAssertions)
                                Assert._assert(imethod.getNameAndDesc().equals(target.getNameAndDesc()), imethod+" != "+target);
                            if (!target.isAbstract())
                                c.add(target);
                            break;
                        }
                        rclass = rclass.getSuperclass();
                        if (rclass == null) {
                            // method doesn't exist in this class or any of its superclasses.
                            break;
                        }
                    }
                    continue;
=====================================================================
Found a 15 line (100 tokens) duplication in the following files: 
Starting at line 12 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/sun14_win32/java/util/zip/ZipFile.java
Starting at line 12 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/sun14_linux/java/util/zip/ZipFile.java
    private String name;
    private java.util.Vector inflaters;
    private java.io.RandomAccessFile raf;
    private java.util.Hashtable entries;
    
    public void __init__(String name) throws java.io.IOException {
        this.name = name;
        java.io.RandomAccessFile raf = new java.io.RandomAccessFile(name, "r");
        this.raf = raf;
        this.inflaters = new java.util.Vector();
        this.readCEN();
    }
    
    private native void readCEN() throws java.io.IOException;
=====================================================================
Found a 15 line (100 tokens) duplication in the following files: 
Starting at line 12 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/apple13_osx/java/util/zip/ZipFile.java
Starting at line 12 of /home/tom/data/pmd/pmd-web/src/joeq/ClassLib/sun13_win32/java/util/zip/ZipFile.java
    private String name;
    private java.util.Vector inflaters;
    private java.io.RandomAccessFile raf;
    private java.util.Hashtable entries;
    
    public void __init__(String name) throws java.io.IOException {
        this.name = name;
        java.io.RandomAccessFile raf = new java.io.RandomAccessFile(name, "r");
        this.raf = raf;
        this.inflaters = new java.util.Vector();
        this.readCEN();
    }
    
    private native void readCEN() throws java.io.IOException;

That took 17430 milliseconds