PMD report

Problems found

#FileLineProblem
1 openscience/cdk/applications/APIVersionTester.java 46 Avoid unused local variables such as 'b'
2 openscience/cdk/applications/FileConvertor.java 555 Avoid unused private methods such as 'write(ChemFile,String)'
3 openscience/cdk/applications/FileConvertor.java 579 Avoid unused private methods such as 'write(org.openscience.cdk.interfaces.ChemSequence,String)'
4 openscience/cdk/applications/FileConvertor.java 598 Avoid unused private methods such as 'write(org.openscience.cdk.interfaces.ChemModel,String)'
5 openscience/cdk/applications/FileConvertor.java 614 Avoid unused formal parameters such as 'outputFilename'
6 openscience/cdk/applications/FileConvertor.java 614 Avoid unused private methods such as 'write(org.openscience.cdk.interfaces.Crystal,String)'
7 openscience/cdk/applications/FileConvertor.java 622 Avoid unused private methods such as 'write(SetOfMolecules,String)'
8 openscience/cdk/applications/FileConvertor.java 657 Avoid unused formal parameters such as 'outputFilename'
9 openscience/cdk/applications/jchempaint/JCPLocalizationHandler.java 47 Avoid unused private fields such as 'logger'
10 openscience/cdk/applications/jchempaint/JCPPropertyHandler.java 58 Avoid unused private fields such as 'defaultPropsFile'
11 openscience/cdk/applications/jchempaint/JCPPropertyHandler.java 60 Avoid unused private fields such as 'userAtypeFile'
12 openscience/cdk/applications/jchempaint/JChemPaintModel.java 60 Avoid unused private fields such as 'status'
13 openscience/cdk/applications/jchempaint/JChemPaintPanel.java 138 Avoid unused private fields such as 'undoManager'
14 openscience/cdk/applications/jchempaint/JChemPaintPanel.java 139 Avoid unused private fields such as 'undoSupport'
15 openscience/cdk/applications/jchempaint/JChemPaintPanel.java 403 Avoid unused private methods such as 'setupWorkingDirectory()'
16 openscience/cdk/applications/jchempaint/JChemPaintViewerOnlyPanel.java 45 Avoid unused private fields such as 'logger'
17 openscience/cdk/applications/jchempaint/action/HelpAction.java 55 Avoid unused local variables such as 'jHD'
18 openscience/cdk/applications/jchempaint/action/HelpAction.java 59 Avoid unused local variables such as 'jHD'
19 openscience/cdk/applications/jchempaint/action/ModifyGeneralSettingsAction.java 45 Avoid unused local variables such as 'frame'
20 openscience/cdk/applications/jchempaint/action/OpenAction.java 62 Avoid unused private fields such as 'currentOpenFileFilter'
21 openscience/cdk/applications/jchempaint/action/OpenAction.java 63 Avoid unused private fields such as 'currentSaveFileFilter'
22 openscience/cdk/applications/jchempaint/applet/JChemPaintAbstractApplet.java 61 Avoid unused private fields such as 'localeString'
23 openscience/cdk/applications/jchempaint/applet/JChemPaintAbstractApplet.java 95 Avoid unused private methods such as 'getValue(String,int)'
24 openscience/cdk/applications/jchempaint/applet/JChemPaintAbstractApplet.java 107 Avoid unused private methods such as 'getValue(String,double)'
25 openscience/cdk/applications/jchempaint/application/JChemPaint.java 168 Avoid unused local variables such as 'jcp'
26 openscience/cdk/applications/jchempaint/dialogs/CreateCoordinatesForFileDialog.java 248 Avoid unused local variables such as 'jcpm'
27 openscience/cdk/applications/jchempaint/dialogs/JChemPaintModelPropsEditor.java 130 Avoid unused private fields such as 'prop'
28 openscience/cdk/applications/jchempaint/dialogs/LicenseDialog.java 86 Avoid unused local variables such as 'label1'
29 openscience/cdk/applications/jchempaint/dialogs/PTDialog.java 43 Avoid unused private fields such as 'logger'
30 openscience/cdk/applications/jchempaint/dialogs/TextViewDialog.java 53 Avoid unused private fields such as 'dimension'
31 openscience/cdk/applications/swing/GraphRenderer.java 88 Avoid unused local variables such as 'factorY'
32 openscience/cdk/applications/swing/GraphRenderer.java 100 Avoid unused local variables such as 'factorX'
33 openscience/cdk/applications/swing/GraphRenderer.java 117 Avoid unused local variables such as 'num'
34 openscience/cdk/applications/swing/PeriodicTablePanel.java 72 Avoid unused private fields such as 'label'
35 openscience/cdk/atomtype/MM2AtomTypeMatcher.java 72 Avoid unused private methods such as 'getSphericalMatcher(AtomType)'
36 openscience/cdk/atomtype/MMFF94AtomTypeMatcher.java 76 Avoid unused private methods such as 'getSphericalMatcher(AtomType)'
37 openscience/cdk/config/AtomTypeFactory.java 99 Avoid unused private fields such as 'builder'
38 openscience/cdk/controller/AbstractController2D.java 1414 Avoid unused private methods such as 'snapCartesian(int)'
39 openscience/cdk/database/DBAdmin.java 371 Avoid unused local variables such as 'st'
40 openscience/cdk/dict/DictionaryDatabase.java 79 Avoid unused private methods such as 'readDictionary(String,String)'
41 openscience/cdk/fingerprint/Fingerprinter.java 151 Avoid unused local variables such as 'isAromatic'
42 openscience/cdk/fingerprint/Fingerprinter.java 259 Avoid unused local variables such as 'tempAtom'
43 openscience/cdk/fingerprint/Fingerprinter.java 261 Avoid unused local variables such as 'symbol'
44 openscience/cdk/geometry/BondTools.java 281 Avoid unused local variables such as 'normal'
45 openscience/cdk/geometry/BondTools.java 347 Avoid unused local variables such as 'normal'
46 openscience/cdk/geometry/BondTools.java 503 Avoid unused local variables such as 'normal'
47 openscience/cdk/geometry/alignment/KabschAlignment.java 138 Avoid unused private methods such as 'getCenterOfGeometry(Point3d)'
48 openscience/cdk/geometry/alignment/KabschAlignment.java 150 Avoid unused private methods such as 'dump(double,int,int,String)'
49 openscience/cdk/geometry/surface/NumericalSurface.java 256 Avoid unused formal parameters such as 'point_density'
50 openscience/cdk/graph/ConnectivityChecker.java 69 Avoid unused local variables such as 'bond'
51 openscience/cdk/graph/MinimalPathIterator.java 178 Avoid unused private methods such as 'createShortestPathWeightedGraph()'
52 openscience/cdk/graph/invariant/ConjugatedPiSystemsDetector.java 98 Avoid unused local variables such as 'addAtom'
53 openscience/cdk/graph/invariant/ConjugatedPiSystemsDetector.java 169 Avoid unused local variables such as 'singleBondCount'
54 openscience/cdk/graph/invariant/ConjugatedPiSystemsDetector.java 172 Avoid unused local variables such as 'atom'
55 openscience/cdk/graph/invariant/HuLuIndexTool.java 136 Avoid unused local variables such as 'k'
56 openscience/cdk/graph/invariant/IChIGenerator.java 80 Avoid unused local variables such as 'fos'
57 openscience/cdk/graph/invariant/IChIGenerator.java 161 Avoid unused local variables such as 'command'
58 openscience/cdk/graph/rebond/RebondTool.java 121 Avoid unused formal parameters such as 'atomA'
59 openscience/cdk/graph/rebond/RebondTool.java 121 Avoid unused formal parameters such as 'atomB'
60 openscience/cdk/graph/rebond/RebondTool.java 121 Avoid unused private methods such as 'isBonded(Atom,double,Atom,double,double)'
61 openscience/cdk/io/CrystClustWriter.java 94 Avoid unused private methods such as 'write(ChemSequence)'
62 openscience/cdk/io/CrystClustWriter.java 122 Avoid unused private methods such as 'write(Crystal)'
63 openscience/cdk/io/Gaussian03Reader.java 141 Avoid unused local variables such as 'levelOfTheory'
64 openscience/cdk/io/Gaussian03Reader.java 320 Avoid unused formal parameters such as 'model'
65 openscience/cdk/io/Gaussian03Reader.java 384 Avoid unused formal parameters such as 'labelLine'
66 openscience/cdk/io/Gaussian03Reader.java 384 Avoid unused formal parameters such as 'model'
67 openscience/cdk/io/Gaussian98Reader.java 459 Avoid unused formal parameters such as 'model'
68 openscience/cdk/io/Gaussian98Reader.java 459 Avoid unused private methods such as 'readFrequencies(ChemModel)'
69 openscience/cdk/io/Gaussian98Reader.java 533 Avoid unused local variables such as 'label'
70 openscience/cdk/io/HINWriter.java 105 Avoid unused local variables such as 'na'
71 openscience/cdk/io/HINWriter.java 106 Avoid unused local variables such as 'info'
72 openscience/cdk/io/HINWriter.java 109 Avoid unused local variables such as 'writecharge'
73 openscience/cdk/io/INChIPlainTextReader.java 153 Avoid unused local variables such as 'version'
74 openscience/cdk/io/INChIPlainTextReader.java 156 Avoid unused local variables such as 'hydrogens'
75 openscience/cdk/io/MACiEReader.java 478 Avoid unused local variables such as 'dictionary'
76 openscience/cdk/io/MDLRXNReader.java 212 Avoid unused local variables such as 'announceMDLFileLine'
77 openscience/cdk/io/MDLRXNV3000Reader.java 159 Avoid unused local variables such as 'dummy'
78 openscience/cdk/io/MDLRXNV3000Reader.java 270 Avoid unused private methods such as 'customizeJob()'
79 openscience/cdk/io/MDLReader.java 210 Avoid unused local variables such as 'content'
80 openscience/cdk/io/MDLReader.java 287 Avoid unused local variables such as 'help'
81 openscience/cdk/io/MDLReader.java 522 Avoid unused local variables such as 'whatIsThisString'
82 openscience/cdk/io/MDLReader.java 548 Avoid unused local variables such as 'error'
83 openscience/cdk/io/MDLV3000Reader.java 387 Avoid unused local variables such as 'atomCount'
84 openscience/cdk/io/MDLV3000Reader.java 527 Avoid unused private methods such as 'customizeJob()'
85 openscience/cdk/io/MDLWriter.java 94 Avoid unused private fields such as 'writeAromatic'
86 openscience/cdk/io/MOPAC97Reader.java 58 Avoid unused private fields such as 'logger'
87 openscience/cdk/io/Mol2Writer.java 100 Avoid unused local variables such as 'st'
88 openscience/cdk/io/Mol2Writer.java 101 Avoid unused local variables such as 'writecharge'
89 openscience/cdk/io/PDBReader.java 380 Avoid unused local variables such as 'residue'
90 openscience/cdk/io/PDBWriter.java 109 Avoid unused local variables such as 'na'
91 openscience/cdk/io/PDBWriter.java 111 Avoid unused local variables such as 'info'
92 openscience/cdk/io/PDBWriter.java 112 Avoid unused local variables such as 'st'
93 openscience/cdk/io/PDBWriter.java 113 Avoid unused local variables such as 'tab'
94 openscience/cdk/io/PDBWriter.java 114 Avoid unused local variables such as 'writecharge'
95 openscience/cdk/io/PDBWriter.java 115 Avoid unused local variables such as 'writevect'
96 openscience/cdk/io/ShelXReader.java 186 Avoid unused local variables such as 'command_again'
97 openscience/cdk/io/ShelXReader.java 187 Avoid unused local variables such as 'wavelength'
98 openscience/cdk/io/ShelXReader.java 301 Avoid unused local variables such as 'command_again'
99 openscience/cdk/io/ShelXReader.java 314 Avoid unused local variables such as 'scatt_factor'
100 openscience/cdk/io/ShelXWriter.java 102 Avoid unused private methods such as 'write(Crystal)'
101 openscience/cdk/isomorphism/UniversalIsomorphismTester.java 588 Avoid unused local variables such as 'k'
102 openscience/cdk/iupac/generator/NumberingRule.java 42 Avoid unused private fields such as 'namingRule'
103 openscience/cdk/iupac/generator/sectiona/Rule2dot2.java 59 Avoid unused local variables such as 'ai'
104 openscience/cdk/iupac/generator/sectiona/Rule2dot2.java 67 Avoid unused private methods such as 'deleteNonCarbonAtoms(AtomContainer)'
105 openscience/cdk/layout/AtomPlacer.java 140 Avoid unused local variables such as 'smallestDistance'
106 openscience/cdk/layout/AtomPlacer.java 442 Avoid unused local variables such as 'atom'
107 openscience/cdk/layout/AtomPlacer.java 533 Avoid unused local variables such as 'endAtom'
108 openscience/cdk/layout/AtomPlacer.java 632 Avoid unused local variables such as 'path'
109 openscience/cdk/layout/HydrogenPlacer.java 83 Avoid unused local variables such as 'startAngle'
110 openscience/cdk/layout/HydrogenPlacer.java 84 Avoid unused local variables such as 'addAngle'
111 openscience/cdk/layout/HydrogenPlacer.java 87 Avoid unused local variables such as 'atomVector'
112 openscience/cdk/layout/OverlapResolver.java 269 Avoid unused local variables such as 'p1'
113 openscience/cdk/layout/OverlapResolver.java 269 Avoid unused local variables such as 'p2'
114 openscience/cdk/layout/OverlapResolver.java 269 Avoid unused local variables such as 'p3'
115 openscience/cdk/layout/OverlapResolver.java 269 Avoid unused local variables such as 'p4'
116 openscience/cdk/layout/RingPlacer.java 316 Avoid unused local variables such as 'centerX'
117 openscience/cdk/layout/RingPlacer.java 317 Avoid unused local variables such as 'centerY'
118 openscience/cdk/layout/RingPlacer.java 319 Avoid unused local variables such as 'direction'
119 openscience/cdk/layout/RingPlacer.java 629 Avoid unused local variables such as 'newRingCenter'
120 openscience/cdk/layout/RingPlacer.java 631 Avoid unused local variables such as 'bond'
121 openscience/cdk/layout/StructureDiagramGenerator.java 301 Avoid unused local variables such as 'ringSystemVector'
122 openscience/cdk/layout/StructureDiagramGenerator.java 302 Avoid unused local variables such as 'newRingSystemVector'
123 openscience/cdk/layout/StructureDiagramGenerator.java 452 Avoid unused local variables such as 'bond'
124 openscience/cdk/layout/StructureDiagramGenerator.java 454 Avoid unused local variables such as 'ringCenter'
125 openscience/cdk/layout/StructureDiagramGenerator.java 605 Avoid unused local variables such as 'angle'
126 openscience/cdk/layout/StructureDiagramGenerator.java 832 Avoid unused local variables such as 'point'
127 openscience/cdk/libio/cml/Convertor.java 83 Avoid unused private fields such as 'useCMLIDs'
128 openscience/cdk/libio/openbabel/OpenBabelConvert.java 99 Avoid unused private fields such as 'SYSTEM'
129 openscience/cdk/math/IMatrix.java 257 Avoid unused local variables such as 'k'
130 openscience/cdk/math/IVector.java 83 Avoid unused local variables such as 'j'
131 openscience/cdk/math/IVector.java 113 Avoid unused local variables such as 'j'
132 openscience/cdk/math/IVector.java 157 Avoid unused local variables such as 'j'
133 openscience/cdk/math/IVector.java 197 Avoid unused local variables such as 'j'
134 openscience/cdk/math/Matrix.java 195 Avoid unused local variables such as 'k'
135 openscience/cdk/math/Matrix.java 540 Avoid unused local variables such as 'sum'
136 openscience/cdk/math/Matrix.java 542 Avoid unused local variables such as 'c'
137 openscience/cdk/math/Vector.java 99 Avoid unused local variables such as 'j'
138 openscience/cdk/math/Vector.java 115 Avoid unused local variables such as 'j'
139 openscience/cdk/math/Vector.java 144 Avoid unused local variables such as 'j'
140 openscience/cdk/math/Vector.java 217 Avoid unused local variables such as 'j'
141 openscience/cdk/math/qm/ClosedShellJob.java 148 Avoid unused local variables such as 'p'
142 openscience/cdk/math/qm/ClosedShellJob.java 205 Avoid unused local variables such as 'value'
143 openscience/cdk/math/qm/ClosedShellJob.java 238 Avoid unused local variables such as 'value'
144 openscience/cdk/math/qm/OneElectronJob.java 153 Avoid unused local variables such as 'D'
145 openscience/cdk/math/qm/OneElectronJob.java 153 Avoid unused local variables such as 'F'
146 openscience/cdk/math/qm/OneElectronJob.java 153 Avoid unused local variables such as 'J'
147 openscience/cdk/math/qm/OneElectronJob.java 153 Avoid unused local variables such as 'K'
148 openscience/cdk/math/qm/OneElectronJob.java 155 Avoid unused local variables such as 'energy'
149 openscience/cdk/math/qm/OneElectronJob.java 158 Avoid unused local variables such as 'count_electrons'
150 openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java 123 Avoid unused private methods such as 'readFile(File)'
151 openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java 390 Avoid unused local variables such as 'b_tmp'
152 openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java 394 Avoid unused local variables such as 'configAtom'
153 openscience/cdk/modeling/builder3d/MMFF94BasedParameterSetReader.java 123 Avoid unused local variables such as 'pbci'
154 openscience/cdk/modeling/builder3d/MMFF94BasedParameterSetReader.java 173 Avoid unused local variables such as 'an'
155 openscience/cdk/modeling/builder3d/MMFF94BasedParameterSetReader.java 220 Avoid unused local variables such as 'scode'
156 openscience/cdk/modeling/builder3d/MMFF94BasedParameterSetReader.java 257 Avoid unused local variables such as 'scode'
157 openscience/cdk/modeling/builder3d/MMFF94BasedParameterSetReader.java 301 Avoid unused local variables such as 'scode'
158 openscience/cdk/modeling/builder3d/MMFF94BasedParameterSetReader.java 330 Avoid unused local variables such as 'scode'
159 openscience/cdk/modeling/builder3d/MMFF94ParametersCall.java 17 Avoid unused private fields such as 'DEFAULT_BOND_LENGTH'
160 openscience/cdk/modeling/builder3d/MMFF94ParametersCall.java 18 Avoid unused private fields such as 'DEFAULT_ANGLE'
161 openscience/cdk/modeling/builder3d/TemplateHandler3D.java 150 Avoid unused local variables such as 'mapped'

Suppressed warnings

FileLineRuleNOPMD or Annotation
openscience/cdk/dict/CDKDictionaryReferences.java 89 UnusedFormalParameter NOPMD