PMD Results
The following document contains the results of PMD 7.14.0.
Violations By Priority
Priority 2
ubic/basecode/io/reader/AbstractMatrixReader.java
| Rule | Violation | Line |
|---|---|---|
| AvoidBranchingStatementAsLastInLoop | Avoid using a branching statement as the last in a loop. | 66 |
ubic/basecode/math/DescriptiveWithMissing.java
| Rule | Violation | Line |
|---|---|---|
| AvoidBranchingStatementAsLastInLoop | Avoid using a branching statement as the last in a loop. | 228 |
ubic/basecode/util/StringUtil.java
| Rule | Violation | Line |
|---|---|---|
| AvoidBranchingStatementAsLastInLoop | Avoid using a branching statement as the last in a loop. | 149 |
Priority 3
ubic/basecode/dataStructure/graph/DirectedGraph.java
| Rule | Violation | Line |
|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Integer(...)`, prefer `Integer.valueOf(...)` | 278 |
ubic/basecode/dataStructure/graph/Graph.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'addNode': the method is declared in an interface type | 27 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'containsKey': the method is declared in an interface type | 29 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'get': the method is declared in an interface type | 31 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getNodeContents': the method is declared in an interface type | 33 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'unmarkAll': the method is declared in an interface type | 35 |
ubic/basecode/dataStructure/graph/GraphNode.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getGraph': the method is declared in an interface type | 30 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getItem': the method is declared in an interface type | 35 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getKey': the method is declared in an interface type | 40 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setItem': the method is declared in an interface type | 47 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setValue': the method is declared in an interface type | 55 |
ubic/basecode/dataStructure/matrix/CompressedSparseDoubleMatrix.java
| Rule | Violation | Line |
|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 137 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 181 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 228 |
ubic/basecode/dataStructure/matrix/DenseDouble3dMatrix.java
| Rule | Violation | Line |
|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 91 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 108 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 128 |
ubic/basecode/dataStructure/matrix/DenseDoubleMatrix.java
| Rule | Violation | Line |
|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 123 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 182 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 221 |
ubic/basecode/dataStructure/matrix/FastRowAccessDoubleMatrix.java
| Rule | Violation | Line |
|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 122 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 172 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 194 |
ubic/basecode/dataStructure/matrix/Matrix2D.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'abstract' on interface 'Matrix2D': interface types are implicitly abstract | 31 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'addColumnName': the method is declared in an interface type | 38 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'asDoubles': the method is declared in an interface type | 49 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type | 56 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'columns': the method is declared in an interface type | 63 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'containsColumnName': the method is declared in an interface type | 69 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'containsRowName': the method is declared in an interface type | 75 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getByKeys': the method is declared in an interface type | 81 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getColIndexByName': the method is declared in an interface type | 89 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getColName': the method is declared in an interface type | 97 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getColNames': the method is declared in an interface type | 102 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getEntry': the method is declared in an interface type | 109 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRowIndexByName': the method is declared in an interface type | 117 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRowName': the method is declared in an interface type | 125 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRowNameMapIterator': the method is declared in an interface type | 130 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRowNames': the method is declared in an interface type | 135 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'hasColNames': the method is declared in an interface type | 142 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'hasRow': the method is declared in an interface type | 148 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'hasRowNames': the method is declared in an interface type | 153 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'isMissing': the method is declared in an interface type | 162 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'numMissing': the method is declared in an interface type | 169 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'rows': the method is declared in an interface type | 176 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'set': the method is declared in an interface type | 183 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setByKeys': the method is declared in an interface type | 190 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setColumnName': the method is declared in an interface type | 198 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setColumnNames': the method is declared in an interface type | 203 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setRowName': the method is declared in an interface type | 211 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setRowNames': the method is declared in an interface type | 216 |
ubic/basecode/dataStructure/matrix/Matrix3D.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'addColumnName': the method is declared in an interface type | 35 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'addRowName': the method is declared in an interface type | 43 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'addSliceName': the method is declared in an interface type | 51 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'columns': the method is declared in an interface type | 58 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'containsColumnName': the method is declared in an interface type | 66 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'containsRowName': the method is declared in an interface type | 74 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'containsSliceName': the method is declared in an interface type | 82 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getColIndexByName': the method is declared in an interface type | 90 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getColName': the method is declared in an interface type | 98 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getColNameIterator': the method is declared in an interface type | 100 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getColNames': the method is declared in an interface type | 105 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getObject': the method is declared in an interface type | 107 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRowIndexByName': the method is declared in an interface type | 115 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRowName': the method is declared in an interface type | 123 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRowNameIterator': the method is declared in an interface type | 128 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRowNames': the method is declared in an interface type | 133 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getSliceIndexByName': the method is declared in an interface type | 141 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getSliceName': the method is declared in an interface type | 149 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getSliceNameIterator': the method is declared in an interface type | 151 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getSliceNames': the method is declared in an interface type | 153 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'hasColNames': the method is declared in an interface type | 160 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'hasRow': the method is declared in an interface type | 166 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'hasRowNames': the method is declared in an interface type | 171 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'hasSliceNames': the method is declared in an interface type | 173 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'isMissing': the method is declared in an interface type | 183 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'numMissing': the method is declared in an interface type | 190 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'rows': the method is declared in an interface type | 197 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setColumnNames': the method is declared in an interface type | 202 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setRowNames': the method is declared in an interface type | 207 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setSliceNames': the method is declared in an interface type | 209 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'slices': the method is declared in an interface type | 211 |
ubic/basecode/dataStructure/matrix/ObjectMatrix.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'get': the method is declared in an interface type | 29 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getColumn': the method is declared in an interface type | 31 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRow': the method is declared in an interface type | 33 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'subset': the method is declared in an interface type | 42 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'subsetColumns': the method is declared in an interface type | 48 |
ubic/basecode/dataStructure/matrix/PrimitiveMatrix.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getColObj': the method is declared in an interface type | 33 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getObject': the method is declared in an interface type | 40 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRowObj': the method is declared in an interface type | 46 |
ubic/basecode/dataStructure/matrix/RCDoubleMatrix1D.java
| Rule | Violation | Line |
|---|---|---|
| UnusedFormalParameter | Avoid unused constructor parameters such as 'length'. | 53 |
ubic/basecode/dataStructure/matrix/SparseDoubleMatrix.java
| Rule | Violation | Line |
|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 129 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 173 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 210 |
ubic/basecode/dataStructure/matrix/SparseRaggedDoubleMatrix.java
| Rule | Violation | Line |
|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 206 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 251 |
ubic/basecode/datafilter/Filter.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'filter': the method is declared in an interface type | 39 |
ubic/basecode/graphics/ColorMatrix.java
| Rule | Violation | Line |
|---|---|---|
| EmptyCatchBlock | Avoid empty catch blocks | 88–89 |
ubic/basecode/io/excel/CreateSpreadSheet.java
| Rule | Violation | Line |
|---|---|---|
| EmptyControlStatement | Empty if statement | 45–47 |
ubic/basecode/io/reader/AbstractMatrixReader.java
| Rule | Violation | Line |
|---|---|---|
| EmptyControlStatement | Empty if statement | 103–108 |
| EmptyControlStatement | Empty else statement | 109–111 |
ubic/basecode/io/reader/DoubleMatrixReader.java
| Rule | Violation | Line |
|---|---|---|
| EmptyControlStatement | Empty if statement | 85–87 |
| EmptyControlStatement | Empty if statement | 311–330 |
ubic/basecode/io/reader/SparseDoubleMatrixReader.java
| Rule | Violation | Line |
|---|---|---|
| EmptyControlStatement | Empty else statement | 78–80 |
| EmptyControlStatement | Empty else statement | 91–93 |
| UnnecessaryConversionTemporary | Avoid unnecessary temporaries when converting primitives to Strings | 183 |
| PrimitiveWrapperInstantiation | Do not use `new Integer(...)`, prefer `Integer.valueOf(...)` | 183 |
| UnnecessaryConversionTemporary | Avoid unnecessary temporaries when converting primitives to Strings | 184 |
| PrimitiveWrapperInstantiation | Do not use `new Integer(...)`, prefer `Integer.valueOf(...)` | 184 |
ubic/basecode/io/reader/StringMatrixReader.java
| Rule | Violation | Line |
|---|---|---|
| EmptyControlStatement | Empty if statement | 101–107 |
ubic/basecode/math/MatrixStats.java
| Rule | Violation | Line |
|---|---|---|
| EmptyControlStatement | Empty if statement | 186–188 |
| EmptyControlStatement | Empty if statement | 196–198 |
| EmptyControlStatement | Empty if statement | 206–208 |
| EmptyControlStatement | Empty if statement | 216–218 |
ubic/basecode/math/ROC.java
| Rule | Violation | Line |
|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Long(...)`, prefer `Long.valueOf(...)` | 48 |
ubic/basecode/math/SpecFunc.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'final' on method 'apply': an anonymous class cannot be extended | 187 |
ubic/basecode/math/Wilcoxon.java
| Rule | Violation | Line |
|---|---|---|
| CollapsibleIfStatements | This if statement could be combined with its parent | 135–138 |
ubic/basecode/math/distribution/DensityGenerator.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'density': the method is declared in an interface type | 33 |
ubic/basecode/math/distribution/ProbabilityComputer.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'probability': the method is declared in an interface type | 35 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'probability': the method is declared in an interface type | 44 |
ubic/basecode/math/linalg/Blas.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryReturn | Unnecessary return statement | 178 |
| UnnecessaryReturn | Unnecessary return statement | 419 |
| UnnecessaryReturn | Unnecessary return statement | 468 |
| UnnecessaryReturn | Unnecessary return statement | 522 |
| UnnecessaryReturn | Unnecessary return statement | 576 |
| UnnecessaryReturn | Unnecessary return statement | 685 |
| UnnecessaryReturn | Unnecessary return statement | 759 |
| UnnecessaryReturn | Unnecessary return statement | 833 |
| UnnecessaryReturn | Unnecessary return statement | 883 |
| UnnecessaryReturn | Unnecessary return statement | 1159 |
| UnnecessaryReturn | Unnecessary return statement | 1222 |
| UnnecessaryReturn | Unnecessary return statement | 1270 |
| UnnecessaryReturn | Unnecessary return statement | 1353 |
ubic/basecode/math/linalg/Dqrsl.java
| Rule | Violation | Line |
|---|---|---|
| CollapsibleIfStatements | This if statement could be combined with its parent | 358–377 |
| UnnecessaryReturn | Unnecessary return statement | 390 |
ubic/basecode/math/linalg/QRDecomposition.java
| Rule | Violation | Line |
|---|---|---|
| UnusedPrivateField | Avoid unused private fields such as 'effects'. | 93 |
ubic/basecode/math/linearmodels/DesignMatrix.java
| Rule | Violation | Line |
|---|---|---|
| CollapsibleIfStatements | This if statement could be combined with its parent | 552–555 |
ubic/basecode/math/linearmodels/LeastSquaresFit.java
| Rule | Violation | Line |
|---|---|---|
| UnusedFormalParameter | Avoid unused method parameters such as 'ypsize'. | 1071 |
ubic/basecode/math/linearmodels/MeanVarianceEstimator.java
| Rule | Violation | Line |
|---|---|---|
| TooManyStaticImports | Too many static imports may lead to messy code | 15–337 |
ubic/basecode/math/linearmodels/ModeratedTstat.java
| Rule | Violation | Line |
|---|---|---|
| UnusedPrivateField | Avoid unused private fields such as 'trigammainverse'. | 54 |
| UnnecessaryModifier | Unnecessary modifier 'final' on method 'okVars': private methods cannot be overridden | 99 |
| UnnecessaryModifier | Unnecessary modifier 'final' on method 'okDfs': private methods cannot be overridden | 109 |
ubic/basecode/ontology/jena/OntologyTermImpl.java
| Rule | Violation | Line |
|---|---|---|
| EmptyCatchBlock | Avoid empty catch blocks | 183–185 |
ubic/basecode/ontology/model/DatatypeProperty.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getType': the method is declared in an interface type | 23 |
ubic/basecode/ontology/model/ObjectProperty.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRange': the method is declared in an interface type | 29 |
ubic/basecode/ontology/model/OntologyCardinalityRestriction.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on enum 'CardinalityType': the enum is declared in an interface type | 27 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getCardinality': the method is declared in an interface type | 31 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getCardinalityType': the method is declared in an interface type | 33 |
ubic/basecode/ontology/model/OntologyClassRestriction.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRestrictedTo': the method is declared in an interface type | 27 |
ubic/basecode/ontology/model/OntologyDatatypeRestriction.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRestrictedTo': the method is declared in an interface type | 27 |
ubic/basecode/ontology/model/OntologyIndividual.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getInstanceOf': the method is declared in an interface type | 34 |
ubic/basecode/ontology/model/OntologyProperty.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'isFunctional': the method is declared in an interface type | 30 |
ubic/basecode/ontology/model/OntologyRestriction.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRestrictionOn': the method is declared in an interface type | 29 |
ubic/basecode/ontology/ncbo/AnnotatorClient.java
| Rule | Violation | Line |
|---|---|---|
| EmptyCatchBlock | Avoid empty catch blocks | 83–85 |
| PrimitiveWrapperInstantiation | Do not use `new Integer(...)`, prefer `Integer.valueOf(...)` | 118 |
| PrimitiveWrapperInstantiation | Do not use `new Integer(...)`, prefer `Integer.valueOf(...)` | 119 |
| EmptyCatchBlock | Avoid empty catch blocks | 201–202 |
ubic/basecode/ontology/ncbo/AnnotatorResponse.java
| Rule | Violation | Line |
|---|---|---|
| CollapsibleIfStatements | This if statement could be combined with its parent | 87–89 |
ubic/basecode/ontology/ncbo/OmimAnnotatorClient.java
| Rule | Violation | Line |
|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Long(...)`, prefer `Long.valueOf(...)` | 86 |
| PrimitiveWrapperInstantiation | Do not use `new Long(...)`, prefer `Long.valueOf(...)` | 87 |
ubic/basecode/util/FileTools.java
| Rule | Violation | Line |
|---|---|---|
| CollapsibleIfStatements | This if statement could be combined with its parent | 567–569 |
ubic/basecode/util/PrettyPrinter.java
| Rule | Violation | Line |
|---|---|---|
| EmptyCatchBlock | Avoid empty catch blocks | 69–71 |
ubic/basecode/util/RegressionTesting.java
| Rule | Violation | Line |
|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 185 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 186 |
ubic/basecode/util/SQLUtils.java
| Rule | Violation | Line |
|---|---|---|
| UnusedPrivateField | Avoid unused private fields such as 'bac'. | 33 |
ubic/basecode/util/StatusViewer.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifiers 'public abstract' on method 'clear': the method is declared in an interface type | 33 |
| UnnecessaryModifier | Unnecessary modifiers 'public abstract' on method 'showError': the method is declared in an interface type | 40 |
| UnnecessaryModifier | Unnecessary modifiers 'public abstract' on method 'showError': the method is declared in an interface type | 45 |
| UnnecessaryModifier | Unnecessary modifiers 'public abstract' on method 'showError': the method is declared in an interface type | 50 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'showProgress': the method is declared in an interface type | 52 |
| UnnecessaryModifier | Unnecessary modifiers 'public abstract' on method 'showStatus': the method is declared in an interface type | 59 |
| UnnecessaryModifier | Unnecessary modifiers 'public abstract' on method 'showStatus': the method is declared in an interface type | 65 |
| UnnecessaryModifier | Unnecessary modifiers 'public abstract' on method 'showWarning': the method is declared in an interface type | 70 |
ubic/basecode/util/StringUtil.java
| Rule | Violation | Line |
|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Long(...)`, prefer `Long.valueOf(...)` | 303 |
| PrimitiveWrapperInstantiation | Do not use `new Long(...)`, prefer `Long.valueOf(...)` | 305 |
ubic/basecode/util/r/AbstractRClient.java
| Rule | Violation | Line |
|---|---|---|
| EmptyControlStatement | Empty if statement | 584–586 |
ubic/basecode/util/r/HTest.java
| Rule | Violation | Line |
|---|---|---|
| EmptyControlStatement | Empty if statement | 41–45 |
ubic/basecode/util/r/RClient.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type | 44 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type | 51 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type | 58 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type | 60 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assignFactor': the method is declared in an interface type | 66 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assignFactor': the method is declared in an interface type | 73 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assignMatrix': the method is declared in an interface type | 81 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assignMatrix': the method is declared in an interface type | 89 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assignMatrix': the method is declared in an interface type | 98 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assignStringList': the method is declared in an interface type | 106 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'booleanDoubleArrayEval': the method is declared in an interface type | 116 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'dataFrame': the method is declared in an interface type | 125 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'dataFrameEval': the method is declared in an interface type | 133 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'doubleArrayDoubleArrayEval': the method is declared in an interface type | 143 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'doubleArrayEval': the method is declared in an interface type | 151 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'doubleArrayTwoDoubleArrayEval': the method is declared in an interface type | 163 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'doubleTwoDoubleArrayEval': the method is declared in an interface type | 176 |
| UnnecessaryModifier | Unnecessary modifiers 'public abstract' on method 'eval': the method is declared in an interface type | 184 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getLastError': the method is declared in an interface type | 191 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'intArrayEval': the method is declared in an interface type | 193 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'isConnected': the method is declared in an interface type | 195 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'linearModel': the method is declared in an interface type | 204 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'linearModel': the method is declared in an interface type | 213 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'listEval': the method is declared in an interface type | 221 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'loadLibrary': the method is declared in an interface type | 223 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'oneWayAnova': the method is declared in an interface type | 232 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'oneWayAnovaEval': the method is declared in an interface type | 234 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'remove': the method is declared in an interface type | 241 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'retrieveMatrix': the method is declared in an interface type | 250 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'rowApplyLinearModel': the method is declared in an interface type | 261 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'stringEval': the method is declared in an interface type | 270 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'stringListEval': the method is declared in an interface type | 272 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'twoWayAnova': the method is declared in an interface type | 283 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'twoWayAnovaEval': the method is declared in an interface type | 300 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'voidEval': the method is declared in an interface type | 302 |
ubic/basecode/util/r/RConnectionFactory.java
| Rule | Violation | Line |
|---|---|---|
| EmptyCatchBlock | Avoid empty catch blocks | 54–56 |
Priority 4
ubic/basecode/dataStructure/CountingMap.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.util.Map': 'Entry' is already in scope because it is inherited by an enclosing type | 133 |
ubic/basecode/dataStructure/matrix/CompressedBitMatrix.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'CompressedBitMatrix': 'BITS_PER_ELEMENT' is already in scope because it is declared in an enclosing type | 121 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'CompressedBitMatrix': 'BITS_PER_ELEMENT' is already in scope because it is declared in an enclosing type | 122 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'CompressedBitMatrix': 'BIT1' is already in scope because it is declared in an enclosing type | 124 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'CompressedBitMatrix': 'BIT1' is already in scope because it is declared in an enclosing type | 303 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'CompressedBitMatrix': 'BIT1' is already in scope because it is declared in an enclosing type | 445 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'CompressedBitMatrix': 'BIT1' is already in scope because it is declared in an enclosing type | 448 |
ubic/basecode/dataStructure/matrix/MatrixUtil.java
| Rule | Violation | Line |
|---|---|---|
| UselessParentheses | Useless parentheses. | 287 |
ubic/basecode/graphics/ColorMatrix.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'cern.colt.list': 'DoubleArrayList' is already in scope because it is imported in this file | 331 |
ubic/basecode/graphics/MatrixDisplay.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.io': 'IOException' is already in scope because it is imported in this file | 229 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.io': 'IOException' is already in scope because it is imported in this file | 275 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.io': 'IOException' is already in scope because it is imported in this file | 284 |
ubic/basecode/io/excel/ExcelUtil.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'ExcelUtil': 'getValue' is already in scope | 136 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'ExcelUtil': 'setFormula' is already in scope | 151 |
ubic/basecode/math/CorrelationStats.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'CorrelationStats': 'fisherTransform' is already in scope | 244 |
ubic/basecode/math/Distance.java
| Rule | Violation | Line |
|---|---|---|
| UselessParentheses | Useless parentheses. | 105 |
| UselessParentheses | Useless parentheses. | 156 |
ubic/basecode/math/Smooth.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryImport | Unused import 'ubic.basecode.math.linearmodels.MeanVarianceEstimator' | 32 |
ubic/basecode/math/SpecFunc.java
| Rule | Violation | Line |
|---|---|---|
| UselessParentheses | Useless parentheses. | 98 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'abs' is already in scope | 236 |
| UselessParentheses | Useless parentheses. | 245 |
| UselessParentheses | Useless parentheses. | 250 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'log' is already in scope | 250 |
| UselessParentheses | Useless parentheses. | 279 |
| UselessParentheses | Useless parentheses. | 280 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'log' is already in scope | 284 |
| UselessParentheses | Useless parentheses. | 285 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'exp' is already in scope | 285 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'log' is already in scope | 288 |
| UselessParentheses | Useless parentheses. | 289 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'exp' is already in scope | 289 |
| UselessParentheses | Useless parentheses. | 291 |
| UselessParentheses | Useless parentheses. | 294 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'PI' is already in scope because it is imported in this file | 294 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'exp' is already in scope | 296 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'sqrt' is already in scope | 296 |
| UselessParentheses | Useless parentheses. | 397 |
| UselessParentheses | Useless parentheses. | 398 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'log' is already in scope | 398 |
| UselessParentheses | Useless parentheses. | 402 |
| UselessParentheses | Useless parentheses. | 403 |
| UselessParentheses | Useless parentheses. | 404 |
| UselessParentheses | Useless parentheses. | 406 |
ubic/basecode/math/StringDistance.java
| Rule | Violation | Line |
|---|---|---|
| UselessParentheses | Useless parentheses. | 153 |
ubic/basecode/math/linalg/Blas.java
| Rule | Violation | Line |
|---|---|---|
| ExtendsObject | No need to explicitly extend Object. | 127 |
ubic/basecode/math/linalg/Dqrsl.java
| Rule | Violation | Line |
|---|---|---|
| ExtendsObject | No need to explicitly extend Object. | 95 |
| UselessParentheses | Useless parentheses. | 612 |
| UselessParentheses | Useless parentheses. | 613 |
ubic/basecode/math/linalg/QRDecomposition.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'ubic.basecode.math.linalg': 'Dqrsl' is already in scope because it is declared in the same package | 245 |
ubic/basecode/math/linearmodels/DesignMatrix.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryImport | Unused import 'java.util.Collections' | 20 |
| UselessParentheses | Useless parentheses. | 549 |
ubic/basecode/math/linearmodels/LinearModelSummaryImpl.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'LinearModelSummary': 'INTERCEPT_COEFFICIENT_NAME' is already in scope because it is inherited by an enclosing type | 190 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'LinearModelSummary': 'INTERCEPT_COEFFICIENT_NAME' is already in scope because it is inherited by an enclosing type | 191 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'LinearModelSummary': 'INTERCEPT_COEFFICIENT_NAME' is already in scope because it is inherited by an enclosing type | 207 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'LinearModelSummary': 'INTERCEPT_COEFFICIENT_NAME' is already in scope because it is inherited by an enclosing type | 208 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'LinearModelSummary': 'INTERCEPT_COEFFICIENT_NAME' is already in scope because it is inherited by an enclosing type | 224 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'LinearModelSummary': 'INTERCEPT_COEFFICIENT_NAME' is already in scope because it is inherited by an enclosing type | 225 |
ubic/basecode/math/linearmodels/MeanVarianceEstimator.java
| Rule | Violation | Line |
|---|---|---|
| UselessParentheses | Useless parentheses. | 293 |
ubic/basecode/ontology/jena/AbstractOntologyService.java
| Rule | Violation | Line |
|---|---|---|
| UselessParentheses | Useless parentheses. | 424 |
| UselessParentheses | Useless parentheses. | 472 |
ubic/basecode/ontology/jena/JenaUtils.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'JenaUtils': 'getChildrenInternal' is already in scope | 110 |
ubic/basecode/ontology/jena/ObjectPropertyImpl.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'com.hp.hpl.jena.ontology': 'ObjectProperty' is already in scope because it is imported in this file | 37 |
ubic/basecode/ontology/jena/OntologyLoader.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryImport | Unused import 'com.hp.hpl.jena.tdb.TDBFactory' | 28 |
ubic/basecode/ontology/jena/PropertyFactory.java
| Rule | Violation | Line |
|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.lang': 'String' is already in scope because it is declared in java.lang | 52 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.lang': 'String' is already in scope because it is declared in java.lang | 59 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.lang': 'String' is already in scope because it is declared in java.lang | 61 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.lang': 'Boolean' is already in scope because it is declared in java.lang | 63 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.lang': 'Double' is already in scope because it is declared in java.lang | 65 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.lang': 'Double' is already in scope because it is declared in java.lang | 67 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.lang': 'Integer' is already in scope because it is declared in java.lang | 69 |
ubic/basecode/util/DateUtil.java
| Rule | Violation | Line |
|---|---|---|
| UselessParentheses | Useless parentheses. | 77 |
ubic/basecode/util/FileTools.java
| Rule | Violation | Line |
|---|---|---|
| UselessParentheses | Useless parentheses. | 79–80 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'DEFAULT_DATA_EXTENSION' is already in scope because it is declared in an enclosing type | 79 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'DEFAULT_DATA_EXTENSION' is already in scope because it is declared in an enclosing type | 80 |
| UselessParentheses | Useless parentheses. | 88–89 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'DEFAULT_IMAGE_EXTENSION' is already in scope because it is declared in an enclosing type | 88 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'DEFAULT_IMAGE_EXTENSION' is already in scope because it is declared in an enclosing type | 89 |
| UselessParentheses | Useless parentheses. | 100 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'getInputStreamFromPlainOrCompressedFile' is already in scope | 187 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'testFile' is already in scope | 303 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'isZipped' is already in scope | 307 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'isGZipped' is already in scope | 322 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'getLines' is already in scope | 372 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'IMAGE_EXTENSIONS' is already in scope because it is declared in an enclosing type | 390 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'IMAGE_EXTENSIONS' is already in scope because it is declared in an enclosing type | 391 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'XML_EXTENSIONS' is already in scope because it is declared in an enclosing type | 404 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'XML_EXTENSIONS' is already in scope because it is declared in an enclosing type | 405 |
ubic/basecode/util/r/AbstractRClient.java
| Rule | Violation | Line |
|---|---|---|
| UselessParentheses | Useless parentheses. | 177 |
ubic/basecode/util/r/LinearModelSummaryImpl.java
| Rule | Violation | Line |
|---|---|---|
| UselessParentheses | Useless parentheses. | 116 |
Files
ubic/basecode/dataStructure/CountingMap.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.util.Map': 'Entry' is already in scope because it is inherited by an enclosing type | 4 | 133 |
ubic/basecode/dataStructure/graph/DirectedGraph.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Integer(...)`, prefer `Integer.valueOf(...)` | 3 | 278 |
ubic/basecode/dataStructure/graph/Graph.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'addNode': the method is declared in an interface type | 3 | 27 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'containsKey': the method is declared in an interface type | 3 | 29 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'get': the method is declared in an interface type | 3 | 31 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getNodeContents': the method is declared in an interface type | 3 | 33 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'unmarkAll': the method is declared in an interface type | 3 | 35 |
ubic/basecode/dataStructure/graph/GraphNode.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getGraph': the method is declared in an interface type | 3 | 30 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getItem': the method is declared in an interface type | 3 | 35 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getKey': the method is declared in an interface type | 3 | 40 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setItem': the method is declared in an interface type | 3 | 47 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setValue': the method is declared in an interface type | 3 | 55 |
ubic/basecode/dataStructure/matrix/CompressedBitMatrix.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'CompressedBitMatrix': 'BITS_PER_ELEMENT' is already in scope because it is declared in an enclosing type | 4 | 121 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'CompressedBitMatrix': 'BITS_PER_ELEMENT' is already in scope because it is declared in an enclosing type | 4 | 122 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'CompressedBitMatrix': 'BIT1' is already in scope because it is declared in an enclosing type | 4 | 124 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'CompressedBitMatrix': 'BIT1' is already in scope because it is declared in an enclosing type | 4 | 303 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'CompressedBitMatrix': 'BIT1' is already in scope because it is declared in an enclosing type | 4 | 445 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'CompressedBitMatrix': 'BIT1' is already in scope because it is declared in an enclosing type | 4 | 448 |
ubic/basecode/dataStructure/matrix/CompressedSparseDoubleMatrix.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 3 | 137 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 3 | 181 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 3 | 228 |
ubic/basecode/dataStructure/matrix/DenseDouble3dMatrix.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 3 | 91 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 3 | 108 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 3 | 128 |
ubic/basecode/dataStructure/matrix/DenseDoubleMatrix.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 3 | 123 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 3 | 182 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 3 | 221 |
ubic/basecode/dataStructure/matrix/FastRowAccessDoubleMatrix.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 3 | 122 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 3 | 172 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 3 | 194 |
ubic/basecode/dataStructure/matrix/Matrix2D.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'abstract' on interface 'Matrix2D': interface types are implicitly abstract | 3 | 31 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'addColumnName': the method is declared in an interface type | 3 | 38 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'asDoubles': the method is declared in an interface type | 3 | 49 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type | 3 | 56 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'columns': the method is declared in an interface type | 3 | 63 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'containsColumnName': the method is declared in an interface type | 3 | 69 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'containsRowName': the method is declared in an interface type | 3 | 75 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getByKeys': the method is declared in an interface type | 3 | 81 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getColIndexByName': the method is declared in an interface type | 3 | 89 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getColName': the method is declared in an interface type | 3 | 97 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getColNames': the method is declared in an interface type | 3 | 102 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getEntry': the method is declared in an interface type | 3 | 109 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRowIndexByName': the method is declared in an interface type | 3 | 117 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRowName': the method is declared in an interface type | 3 | 125 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRowNameMapIterator': the method is declared in an interface type | 3 | 130 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRowNames': the method is declared in an interface type | 3 | 135 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'hasColNames': the method is declared in an interface type | 3 | 142 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'hasRow': the method is declared in an interface type | 3 | 148 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'hasRowNames': the method is declared in an interface type | 3 | 153 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'isMissing': the method is declared in an interface type | 3 | 162 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'numMissing': the method is declared in an interface type | 3 | 169 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'rows': the method is declared in an interface type | 3 | 176 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'set': the method is declared in an interface type | 3 | 183 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setByKeys': the method is declared in an interface type | 3 | 190 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setColumnName': the method is declared in an interface type | 3 | 198 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setColumnNames': the method is declared in an interface type | 3 | 203 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setRowName': the method is declared in an interface type | 3 | 211 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setRowNames': the method is declared in an interface type | 3 | 216 |
ubic/basecode/dataStructure/matrix/Matrix3D.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'addColumnName': the method is declared in an interface type | 3 | 35 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'addRowName': the method is declared in an interface type | 3 | 43 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'addSliceName': the method is declared in an interface type | 3 | 51 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'columns': the method is declared in an interface type | 3 | 58 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'containsColumnName': the method is declared in an interface type | 3 | 66 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'containsRowName': the method is declared in an interface type | 3 | 74 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'containsSliceName': the method is declared in an interface type | 3 | 82 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getColIndexByName': the method is declared in an interface type | 3 | 90 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getColName': the method is declared in an interface type | 3 | 98 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getColNameIterator': the method is declared in an interface type | 3 | 100 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getColNames': the method is declared in an interface type | 3 | 105 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getObject': the method is declared in an interface type | 3 | 107 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRowIndexByName': the method is declared in an interface type | 3 | 115 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRowName': the method is declared in an interface type | 3 | 123 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRowNameIterator': the method is declared in an interface type | 3 | 128 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRowNames': the method is declared in an interface type | 3 | 133 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getSliceIndexByName': the method is declared in an interface type | 3 | 141 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getSliceName': the method is declared in an interface type | 3 | 149 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getSliceNameIterator': the method is declared in an interface type | 3 | 151 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getSliceNames': the method is declared in an interface type | 3 | 153 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'hasColNames': the method is declared in an interface type | 3 | 160 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'hasRow': the method is declared in an interface type | 3 | 166 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'hasRowNames': the method is declared in an interface type | 3 | 171 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'hasSliceNames': the method is declared in an interface type | 3 | 173 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'isMissing': the method is declared in an interface type | 3 | 183 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'numMissing': the method is declared in an interface type | 3 | 190 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'rows': the method is declared in an interface type | 3 | 197 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setColumnNames': the method is declared in an interface type | 3 | 202 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setRowNames': the method is declared in an interface type | 3 | 207 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'setSliceNames': the method is declared in an interface type | 3 | 209 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'slices': the method is declared in an interface type | 3 | 211 |
ubic/basecode/dataStructure/matrix/MatrixUtil.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UselessParentheses | Useless parentheses. | 4 | 287 |
ubic/basecode/dataStructure/matrix/ObjectMatrix.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'get': the method is declared in an interface type | 3 | 29 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getColumn': the method is declared in an interface type | 3 | 31 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRow': the method is declared in an interface type | 3 | 33 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'subset': the method is declared in an interface type | 3 | 42 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'subsetColumns': the method is declared in an interface type | 3 | 48 |
ubic/basecode/dataStructure/matrix/PrimitiveMatrix.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getColObj': the method is declared in an interface type | 3 | 33 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getObject': the method is declared in an interface type | 3 | 40 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRowObj': the method is declared in an interface type | 3 | 46 |
ubic/basecode/dataStructure/matrix/RCDoubleMatrix1D.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnusedFormalParameter | Avoid unused constructor parameters such as 'length'. | 3 | 53 |
ubic/basecode/dataStructure/matrix/SparseDoubleMatrix.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 3 | 129 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 3 | 173 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 3 | 210 |
ubic/basecode/dataStructure/matrix/SparseRaggedDoubleMatrix.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 3 | 206 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 3 | 251 |
ubic/basecode/datafilter/Filter.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'filter': the method is declared in an interface type | 3 | 39 |
ubic/basecode/graphics/ColorMatrix.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| EmptyCatchBlock | Avoid empty catch blocks | 3 | 88–89 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'cern.colt.list': 'DoubleArrayList' is already in scope because it is imported in this file | 4 | 331 |
ubic/basecode/graphics/MatrixDisplay.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.io': 'IOException' is already in scope because it is imported in this file | 4 | 229 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.io': 'IOException' is already in scope because it is imported in this file | 4 | 275 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.io': 'IOException' is already in scope because it is imported in this file | 4 | 284 |
ubic/basecode/io/excel/CreateSpreadSheet.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| EmptyControlStatement | Empty if statement | 3 | 45–47 |
ubic/basecode/io/excel/ExcelUtil.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'ExcelUtil': 'getValue' is already in scope | 4 | 136 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'ExcelUtil': 'setFormula' is already in scope | 4 | 151 |
ubic/basecode/io/reader/AbstractMatrixReader.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| AvoidBranchingStatementAsLastInLoop | Avoid using a branching statement as the last in a loop. | 2 | 66 |
| EmptyControlStatement | Empty if statement | 3 | 103–108 |
| EmptyControlStatement | Empty else statement | 3 | 109–111 |
ubic/basecode/io/reader/DoubleMatrixReader.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| EmptyControlStatement | Empty if statement | 3 | 85–87 |
| EmptyControlStatement | Empty if statement | 3 | 311–330 |
ubic/basecode/io/reader/SparseDoubleMatrixReader.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| EmptyControlStatement | Empty else statement | 3 | 78–80 |
| EmptyControlStatement | Empty else statement | 3 | 91–93 |
| UnnecessaryConversionTemporary | Avoid unnecessary temporaries when converting primitives to Strings | 3 | 183 |
| PrimitiveWrapperInstantiation | Do not use `new Integer(...)`, prefer `Integer.valueOf(...)` | 3 | 183 |
| UnnecessaryConversionTemporary | Avoid unnecessary temporaries when converting primitives to Strings | 3 | 184 |
| PrimitiveWrapperInstantiation | Do not use `new Integer(...)`, prefer `Integer.valueOf(...)` | 3 | 184 |
ubic/basecode/io/reader/StringMatrixReader.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| EmptyControlStatement | Empty if statement | 3 | 101–107 |
ubic/basecode/math/CorrelationStats.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'CorrelationStats': 'fisherTransform' is already in scope | 4 | 244 |
ubic/basecode/math/DescriptiveWithMissing.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| AvoidBranchingStatementAsLastInLoop | Avoid using a branching statement as the last in a loop. | 2 | 228 |
ubic/basecode/math/Distance.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UselessParentheses | Useless parentheses. | 4 | 105 |
| UselessParentheses | Useless parentheses. | 4 | 156 |
ubic/basecode/math/MatrixStats.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| EmptyControlStatement | Empty if statement | 3 | 186–188 |
| EmptyControlStatement | Empty if statement | 3 | 196–198 |
| EmptyControlStatement | Empty if statement | 3 | 206–208 |
| EmptyControlStatement | Empty if statement | 3 | 216–218 |
ubic/basecode/math/ROC.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Long(...)`, prefer `Long.valueOf(...)` | 3 | 48 |
ubic/basecode/math/Smooth.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryImport | Unused import 'ubic.basecode.math.linearmodels.MeanVarianceEstimator' | 4 | 32 |
ubic/basecode/math/SpecFunc.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UselessParentheses | Useless parentheses. | 4 | 98 |
| UnnecessaryModifier | Unnecessary modifier 'final' on method 'apply': an anonymous class cannot be extended | 3 | 187 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'abs' is already in scope | 4 | 236 |
| UselessParentheses | Useless parentheses. | 4 | 245 |
| UselessParentheses | Useless parentheses. | 4 | 250 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'log' is already in scope | 4 | 250 |
| UselessParentheses | Useless parentheses. | 4 | 279 |
| UselessParentheses | Useless parentheses. | 4 | 280 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'log' is already in scope | 4 | 284 |
| UselessParentheses | Useless parentheses. | 4 | 285 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'exp' is already in scope | 4 | 285 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'log' is already in scope | 4 | 288 |
| UselessParentheses | Useless parentheses. | 4 | 289 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'exp' is already in scope | 4 | 289 |
| UselessParentheses | Useless parentheses. | 4 | 291 |
| UselessParentheses | Useless parentheses. | 4 | 294 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'PI' is already in scope because it is imported in this file | 4 | 294 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'exp' is already in scope | 4 | 296 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'sqrt' is already in scope | 4 | 296 |
| UselessParentheses | Useless parentheses. | 4 | 397 |
| UselessParentheses | Useless parentheses. | 4 | 398 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'Math': 'log' is already in scope | 4 | 398 |
| UselessParentheses | Useless parentheses. | 4 | 402 |
| UselessParentheses | Useless parentheses. | 4 | 403 |
| UselessParentheses | Useless parentheses. | 4 | 404 |
| UselessParentheses | Useless parentheses. | 4 | 406 |
ubic/basecode/math/StringDistance.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UselessParentheses | Useless parentheses. | 4 | 153 |
ubic/basecode/math/Wilcoxon.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| CollapsibleIfStatements | This if statement could be combined with its parent | 3 | 135–138 |
ubic/basecode/math/distribution/DensityGenerator.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'density': the method is declared in an interface type | 3 | 33 |
ubic/basecode/math/distribution/ProbabilityComputer.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'probability': the method is declared in an interface type | 3 | 35 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'probability': the method is declared in an interface type | 3 | 44 |
ubic/basecode/math/linalg/Blas.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| ExtendsObject | No need to explicitly extend Object. | 4 | 127 |
| UnnecessaryReturn | Unnecessary return statement | 3 | 178 |
| UnnecessaryReturn | Unnecessary return statement | 3 | 419 |
| UnnecessaryReturn | Unnecessary return statement | 3 | 468 |
| UnnecessaryReturn | Unnecessary return statement | 3 | 522 |
| UnnecessaryReturn | Unnecessary return statement | 3 | 576 |
| UnnecessaryReturn | Unnecessary return statement | 3 | 685 |
| UnnecessaryReturn | Unnecessary return statement | 3 | 759 |
| UnnecessaryReturn | Unnecessary return statement | 3 | 833 |
| UnnecessaryReturn | Unnecessary return statement | 3 | 883 |
| UnnecessaryReturn | Unnecessary return statement | 3 | 1159 |
| UnnecessaryReturn | Unnecessary return statement | 3 | 1222 |
| UnnecessaryReturn | Unnecessary return statement | 3 | 1270 |
| UnnecessaryReturn | Unnecessary return statement | 3 | 1353 |
ubic/basecode/math/linalg/Dqrsl.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| ExtendsObject | No need to explicitly extend Object. | 4 | 95 |
| CollapsibleIfStatements | This if statement could be combined with its parent | 3 | 358–377 |
| UnnecessaryReturn | Unnecessary return statement | 3 | 390 |
| UselessParentheses | Useless parentheses. | 4 | 612 |
| UselessParentheses | Useless parentheses. | 4 | 613 |
ubic/basecode/math/linalg/QRDecomposition.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnusedPrivateField | Avoid unused private fields such as 'effects'. | 3 | 93 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'ubic.basecode.math.linalg': 'Dqrsl' is already in scope because it is declared in the same package | 4 | 245 |
ubic/basecode/math/linearmodels/DesignMatrix.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryImport | Unused import 'java.util.Collections' | 4 | 20 |
| UselessParentheses | Useless parentheses. | 4 | 549 |
| CollapsibleIfStatements | This if statement could be combined with its parent | 3 | 552–555 |
ubic/basecode/math/linearmodels/LeastSquaresFit.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnusedFormalParameter | Avoid unused method parameters such as 'ypsize'. | 3 | 1071 |
ubic/basecode/math/linearmodels/LinearModelSummaryImpl.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'LinearModelSummary': 'INTERCEPT_COEFFICIENT_NAME' is already in scope because it is inherited by an enclosing type | 4 | 190 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'LinearModelSummary': 'INTERCEPT_COEFFICIENT_NAME' is already in scope because it is inherited by an enclosing type | 4 | 191 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'LinearModelSummary': 'INTERCEPT_COEFFICIENT_NAME' is already in scope because it is inherited by an enclosing type | 4 | 207 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'LinearModelSummary': 'INTERCEPT_COEFFICIENT_NAME' is already in scope because it is inherited by an enclosing type | 4 | 208 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'LinearModelSummary': 'INTERCEPT_COEFFICIENT_NAME' is already in scope because it is inherited by an enclosing type | 4 | 224 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'LinearModelSummary': 'INTERCEPT_COEFFICIENT_NAME' is already in scope because it is inherited by an enclosing type | 4 | 225 |
ubic/basecode/math/linearmodels/MeanVarianceEstimator.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| TooManyStaticImports | Too many static imports may lead to messy code | 3 | 15–337 |
| UselessParentheses | Useless parentheses. | 4 | 293 |
ubic/basecode/math/linearmodels/ModeratedTstat.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnusedPrivateField | Avoid unused private fields such as 'trigammainverse'. | 3 | 54 |
| UnnecessaryModifier | Unnecessary modifier 'final' on method 'okVars': private methods cannot be overridden | 3 | 99 |
| UnnecessaryModifier | Unnecessary modifier 'final' on method 'okDfs': private methods cannot be overridden | 3 | 109 |
ubic/basecode/ontology/jena/AbstractOntologyService.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UselessParentheses | Useless parentheses. | 4 | 424 |
| UselessParentheses | Useless parentheses. | 4 | 472 |
ubic/basecode/ontology/jena/JenaUtils.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'JenaUtils': 'getChildrenInternal' is already in scope | 4 | 110 |
ubic/basecode/ontology/jena/ObjectPropertyImpl.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'com.hp.hpl.jena.ontology': 'ObjectProperty' is already in scope because it is imported in this file | 4 | 37 |
ubic/basecode/ontology/jena/OntologyLoader.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryImport | Unused import 'com.hp.hpl.jena.tdb.TDBFactory' | 4 | 28 |
ubic/basecode/ontology/jena/OntologyTermImpl.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| EmptyCatchBlock | Avoid empty catch blocks | 3 | 183–185 |
ubic/basecode/ontology/jena/PropertyFactory.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.lang': 'String' is already in scope because it is declared in java.lang | 4 | 52 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.lang': 'String' is already in scope because it is declared in java.lang | 4 | 59 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.lang': 'String' is already in scope because it is declared in java.lang | 4 | 61 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.lang': 'Boolean' is already in scope because it is declared in java.lang | 4 | 63 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.lang': 'Double' is already in scope because it is declared in java.lang | 4 | 65 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.lang': 'Double' is already in scope because it is declared in java.lang | 4 | 67 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'java.lang': 'Integer' is already in scope because it is declared in java.lang | 4 | 69 |
ubic/basecode/ontology/model/DatatypeProperty.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getType': the method is declared in an interface type | 3 | 23 |
ubic/basecode/ontology/model/ObjectProperty.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRange': the method is declared in an interface type | 3 | 29 |
ubic/basecode/ontology/model/OntologyCardinalityRestriction.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on enum 'CardinalityType': the enum is declared in an interface type | 3 | 27 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getCardinality': the method is declared in an interface type | 3 | 31 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getCardinalityType': the method is declared in an interface type | 3 | 33 |
ubic/basecode/ontology/model/OntologyClassRestriction.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRestrictedTo': the method is declared in an interface type | 3 | 27 |
ubic/basecode/ontology/model/OntologyDatatypeRestriction.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRestrictedTo': the method is declared in an interface type | 3 | 27 |
ubic/basecode/ontology/model/OntologyIndividual.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getInstanceOf': the method is declared in an interface type | 3 | 34 |
ubic/basecode/ontology/model/OntologyProperty.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'isFunctional': the method is declared in an interface type | 3 | 30 |
ubic/basecode/ontology/model/OntologyRestriction.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getRestrictionOn': the method is declared in an interface type | 3 | 29 |
ubic/basecode/ontology/ncbo/AnnotatorClient.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| EmptyCatchBlock | Avoid empty catch blocks | 3 | 83–85 |
| PrimitiveWrapperInstantiation | Do not use `new Integer(...)`, prefer `Integer.valueOf(...)` | 3 | 118 |
| PrimitiveWrapperInstantiation | Do not use `new Integer(...)`, prefer `Integer.valueOf(...)` | 3 | 119 |
| EmptyCatchBlock | Avoid empty catch blocks | 3 | 201–202 |
ubic/basecode/ontology/ncbo/AnnotatorResponse.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| CollapsibleIfStatements | This if statement could be combined with its parent | 3 | 87–89 |
ubic/basecode/ontology/ncbo/OmimAnnotatorClient.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Long(...)`, prefer `Long.valueOf(...)` | 3 | 86 |
| PrimitiveWrapperInstantiation | Do not use `new Long(...)`, prefer `Long.valueOf(...)` | 3 | 87 |
ubic/basecode/util/DateUtil.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UselessParentheses | Useless parentheses. | 4 | 77 |
ubic/basecode/util/FileTools.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UselessParentheses | Useless parentheses. | 4 | 79–80 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'DEFAULT_DATA_EXTENSION' is already in scope because it is declared in an enclosing type | 4 | 79 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'DEFAULT_DATA_EXTENSION' is already in scope because it is declared in an enclosing type | 4 | 80 |
| UselessParentheses | Useless parentheses. | 4 | 88–89 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'DEFAULT_IMAGE_EXTENSION' is already in scope because it is declared in an enclosing type | 4 | 88 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'DEFAULT_IMAGE_EXTENSION' is already in scope because it is declared in an enclosing type | 4 | 89 |
| UselessParentheses | Useless parentheses. | 4 | 100 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'getInputStreamFromPlainOrCompressedFile' is already in scope | 4 | 187 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'testFile' is already in scope | 4 | 303 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'isZipped' is already in scope | 4 | 307 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'isGZipped' is already in scope | 4 | 322 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'getLines' is already in scope | 4 | 372 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'IMAGE_EXTENSIONS' is already in scope because it is declared in an enclosing type | 4 | 390 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'IMAGE_EXTENSIONS' is already in scope because it is declared in an enclosing type | 4 | 391 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'XML_EXTENSIONS' is already in scope because it is declared in an enclosing type | 4 | 404 |
| UnnecessaryFullyQualifiedName | Unnecessary qualifier 'FileTools': 'XML_EXTENSIONS' is already in scope because it is declared in an enclosing type | 4 | 405 |
| CollapsibleIfStatements | This if statement could be combined with its parent | 3 | 567–569 |
ubic/basecode/util/PrettyPrinter.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| EmptyCatchBlock | Avoid empty catch blocks | 3 | 69–71 |
ubic/basecode/util/RegressionTesting.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 3 | 185 |
| PrimitiveWrapperInstantiation | Do not use `new Double(...)`, prefer `Double.valueOf(...)` | 3 | 186 |
ubic/basecode/util/SQLUtils.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnusedPrivateField | Avoid unused private fields such as 'bac'. | 3 | 33 |
ubic/basecode/util/StatusViewer.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryModifier | Unnecessary modifiers 'public abstract' on method 'clear': the method is declared in an interface type | 3 | 33 |
| UnnecessaryModifier | Unnecessary modifiers 'public abstract' on method 'showError': the method is declared in an interface type | 3 | 40 |
| UnnecessaryModifier | Unnecessary modifiers 'public abstract' on method 'showError': the method is declared in an interface type | 3 | 45 |
| UnnecessaryModifier | Unnecessary modifiers 'public abstract' on method 'showError': the method is declared in an interface type | 3 | 50 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'showProgress': the method is declared in an interface type | 3 | 52 |
| UnnecessaryModifier | Unnecessary modifiers 'public abstract' on method 'showStatus': the method is declared in an interface type | 3 | 59 |
| UnnecessaryModifier | Unnecessary modifiers 'public abstract' on method 'showStatus': the method is declared in an interface type | 3 | 65 |
| UnnecessaryModifier | Unnecessary modifiers 'public abstract' on method 'showWarning': the method is declared in an interface type | 3 | 70 |
ubic/basecode/util/StringUtil.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| AvoidBranchingStatementAsLastInLoop | Avoid using a branching statement as the last in a loop. | 2 | 149 |
| PrimitiveWrapperInstantiation | Do not use `new Long(...)`, prefer `Long.valueOf(...)` | 3 | 303 |
| PrimitiveWrapperInstantiation | Do not use `new Long(...)`, prefer `Long.valueOf(...)` | 3 | 305 |
ubic/basecode/util/r/AbstractRClient.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UselessParentheses | Useless parentheses. | 4 | 177 |
| EmptyControlStatement | Empty if statement | 3 | 584–586 |
ubic/basecode/util/r/HTest.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| EmptyControlStatement | Empty if statement | 3 | 41–45 |
ubic/basecode/util/r/LinearModelSummaryImpl.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UselessParentheses | Useless parentheses. | 4 | 116 |
ubic/basecode/util/r/RClient.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type | 3 | 44 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type | 3 | 51 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type | 3 | 58 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assign': the method is declared in an interface type | 3 | 60 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assignFactor': the method is declared in an interface type | 3 | 66 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assignFactor': the method is declared in an interface type | 3 | 73 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assignMatrix': the method is declared in an interface type | 3 | 81 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assignMatrix': the method is declared in an interface type | 3 | 89 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assignMatrix': the method is declared in an interface type | 3 | 98 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'assignStringList': the method is declared in an interface type | 3 | 106 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'booleanDoubleArrayEval': the method is declared in an interface type | 3 | 116 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'dataFrame': the method is declared in an interface type | 3 | 125 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'dataFrameEval': the method is declared in an interface type | 3 | 133 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'doubleArrayDoubleArrayEval': the method is declared in an interface type | 3 | 143 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'doubleArrayEval': the method is declared in an interface type | 3 | 151 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'doubleArrayTwoDoubleArrayEval': the method is declared in an interface type | 3 | 163 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'doubleTwoDoubleArrayEval': the method is declared in an interface type | 3 | 176 |
| UnnecessaryModifier | Unnecessary modifiers 'public abstract' on method 'eval': the method is declared in an interface type | 3 | 184 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'getLastError': the method is declared in an interface type | 3 | 191 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'intArrayEval': the method is declared in an interface type | 3 | 193 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'isConnected': the method is declared in an interface type | 3 | 195 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'linearModel': the method is declared in an interface type | 3 | 204 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'linearModel': the method is declared in an interface type | 3 | 213 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'listEval': the method is declared in an interface type | 3 | 221 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'loadLibrary': the method is declared in an interface type | 3 | 223 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'oneWayAnova': the method is declared in an interface type | 3 | 232 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'oneWayAnovaEval': the method is declared in an interface type | 3 | 234 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'remove': the method is declared in an interface type | 3 | 241 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'retrieveMatrix': the method is declared in an interface type | 3 | 250 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'rowApplyLinearModel': the method is declared in an interface type | 3 | 261 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'stringEval': the method is declared in an interface type | 3 | 270 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'stringListEval': the method is declared in an interface type | 3 | 272 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'twoWayAnova': the method is declared in an interface type | 3 | 283 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'twoWayAnovaEval': the method is declared in an interface type | 3 | 300 |
| UnnecessaryModifier | Unnecessary modifier 'public' on method 'voidEval': the method is declared in an interface type | 3 | 302 |
ubic/basecode/util/r/RConnectionFactory.java
| Rule | Violation | Priority | Line |
|---|---|---|---|
| EmptyCatchBlock | Avoid empty catch blocks | 3 | 54–56 |