The following document contains the results of FindBugs
FindBugs Version is 3.0.1
Threshold is medium
Effort is min
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Should com.github.celldynamics.quimp.BOAState$BOAp be a _static_ inner class? | PERFORMANCE | SIC_INNER_SHOULD_BE_STATIC | 509-937 | Medium |
Unread field: com.github.celldynamics.quimp.BOAState$BOAp.callCount | PERFORMANCE | URF_UNREAD_FIELD | 736 | Medium |
Unread field: com.github.celldynamics.quimp.BOAState$BOAp.savedOne | PERFORMANCE | URF_UNREAD_FIELD | 719 | Medium |
Unread field: com.github.celldynamics.quimp.BOAState$BOAp.stopOnPluginError | PERFORMANCE | URF_UNREAD_FIELD | 767 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Should com.github.celldynamics.quimp.BOAState$SegParam be a _static_ inner class? | PERFORMANCE | SIC_INNER_SHOULD_BE_STATIC | 145-485 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.BOA_.tightenSnake(Snake) uses the same code for two branches | STYLE | DB_DUPLICATE_BRANCHES | 2620 | Medium |
Comparison of String parameter using == or != in com.github.celldynamics.quimp.BOA_.instanceSnakePlugin(String, int, boolean) | BAD_PRACTICE | ES_COMPARING_PARAMETER_STRING_WITH_EQ | 2390 | Medium |
com.github.celldynamics.quimp.BOA_.qState isn't final and can't be protected from malicious code | MALICIOUS_CODE | MS_CANNOT_BE_FINAL | 203 | Medium |
com.github.celldynamics.quimp.BOA_.quimpInfo should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.BOA_.viewUpdater should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
Write to static field com.github.celldynamics.quimp.BOA_.logCount from instance method new com.github.celldynamics.quimp.BOA_() | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 214 | Medium |
Write to static field com.github.celldynamics.quimp.BOA_.qState from instance method new com.github.celldynamics.quimp.BOA_() | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 213 | Medium |
Write to static field com.github.celldynamics.quimp.BOA_.isBoaRunning from instance method com.github.celldynamics.quimp.BOA_.run(String) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 230 | Medium |
Write to static field com.github.celldynamics.quimp.BOA_.qState from instance method com.github.celldynamics.quimp.BOA_.run(String) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 264 | Medium |
Write to static field com.github.celldynamics.quimp.BOA_.quimpInfo from instance method com.github.celldynamics.quimp.BOA_.run(String) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 237 | Medium |
Write to static field com.github.celldynamics.quimp.BOA_.viewUpdater from instance method com.github.celldynamics.quimp.BOA_.run(String) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 235 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Possible null pointer dereference in com.github.celldynamics.quimp.BOA_$CustomStackWindow.loadQconfConfiguration(Path) due to return value of called method | STYLE | NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE | 2027 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Unread field: com.github.celldynamics.quimp.CellStatsEval.frameInterval | PERFORMANCE | URF_UNREAD_FIELD | 94 | Medium |
Unread field: com.github.celldynamics.quimp.CellStatsEval.iproc | PERFORMANCE | URF_UNREAD_FIELD | 92 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Hard coded reference to an absolute pathname in com.github.celldynamics.quimp.Constrictor.constrictWrite(Snake, ImageProcessor) | STYLE | DMI_HARDCODED_ABSOLUTE_FILENAME | 118 | Medium |
Found reliance on default encoding in com.github.celldynamics.quimp.Constrictor.constrictWrite(Snake, ImageProcessor): new java.io.FileWriter(String) | I18N | DM_DEFAULT_ENCODING | 118 | High |
Integral division result cast to double or float in com.github.celldynamics.quimp.Constrictor.imageForce(Node, ImageProcessor) | STYLE | ICAST_IDIV_CAST_TO_DOUBLE | 244 | Medium |
Exception is caught when Exception is not thrown in com.github.celldynamics.quimp.Constrictor.constrictWrite(Snake, ImageProcessor) | STYLE | REC_CATCH_EXCEPTION | 187 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Found reliance on default encoding in com.github.celldynamics.quimp.FrameStatistics.read(File): new java.io.FileReader(File) | I18N | DM_DEFAULT_ENCODING | 203 | High |
Found reliance on default encoding in com.github.celldynamics.quimp.FrameStatistics.write(FrameStatistics[], File, double, double): new java.io.FileWriter(File) | I18N | DM_DEFAULT_ENCODING | 153 | High |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Return value of ij.gui.ImageCanvas.getMagnification() ignored, but method has no side effect | STYLE | RV_RETURN_VALUE_IGNORED_NO_SIDE_EFFECT | 3144 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Write to static field com.github.celldynamics.quimp.EXp.frame from instance method com.github.celldynamics.quimp.ImageManager.setSlice(int) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 291 | High |
Unread field: com.github.celldynamics.quimp.ImageManager.xMap | PERFORMANCE | URF_UNREAD_FIELD | 254 | Medium |
Unread field: com.github.celldynamics.quimp.ImageManager.yMap | PERFORMANCE | URF_UNREAD_FIELD | 255 | Medium |
Unused field: com.github.celldynamics.quimp.ImageManager.mapCoord | PERFORMANCE | UUF_UNUSED_FIELD | Not available | Medium |
Unused field: com.github.celldynamics.quimp.ImageManager.movCoord | PERFORMANCE | UUF_UNUSED_FIELD | Not available | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Unread public/protected field: com.github.celldynamics.quimp.LogEntry.action | STYLE | URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD | 222 | Medium |
Unread public/protected field: com.github.celldynamics.quimp.LogEntry.fileName | STYLE | URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD | 225 | Medium |
Unread public/protected field: com.github.celldynamics.quimp.LogEntry.frame | STYLE | URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD | 223 | Medium |
Unread public/protected field: com.github.celldynamics.quimp.LogEntry.id | STYLE | URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD | 221 | Medium |
Unread public/protected field: com.github.celldynamics.quimp.LogEntry.segParam | STYLE | URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD | 224 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Rough value of Math.PI/2 found: 1.5708 | BAD_PRACTICE | CNT_ROUGH_CONSTANT_VALUE | 1073 | Medium |
com.github.celldynamics.quimp.Outline.clone() does not call super.clone() | BAD_PRACTICE | CN_IDIOM_NO_SUPER_CALL | 802-833 | Medium |
Dead store to intersect in com.github.celldynamics.quimp.Outline.cutSelfIntersects() | STYLE | DLS_DEAD_LOCAL_STORE | 667 | Medium |
Dead store to other in com.github.celldynamics.quimp.Outline.equals(Object) | STYLE | DLS_DEAD_LOCAL_STORE | 1120 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Found reliance on default encoding in com.github.celldynamics.quimp.OutlineHandler.readOutlines(File): new java.io.FileReader(File) | I18N | DM_DEFAULT_ENCODING | 268 | High |
Found reliance on default encoding in com.github.celldynamics.quimp.OutlineHandler.writeOutlines(File, boolean): new java.io.FileWriter(File) | I18N | DM_DEFAULT_ENCODING | 521 | High |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Write to static field com.github.celldynamics.quimp.PointsList.clockwise from instance method com.github.celldynamics.quimp.PointsList.updateNormale(boolean) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 409 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Found reliance on default encoding in com.github.celldynamics.quimp.PropertyReader.readProperty(Class, String, String, String): new java.io.InputStreamReader(InputStream) | I18N | DM_DEFAULT_ENCODING | 102 | High |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.QColor.colourMaps is a mutable array | MALICIOUS_CODE | MS_MUTABLE_ARRAY | 17 | High |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Hard coded reference to an absolute pathname in new com.github.celldynamics.quimp.QParams(File) | STYLE | DMI_HARDCODED_ABSOLUTE_FILENAME | 179 | Medium |
Found reliance on default encoding in com.github.celldynamics.quimp.QParams.readParams(): new java.io.FileReader(File) | I18N | DM_DEFAULT_ENCODING | 568 | High |
Found reliance on default encoding in com.github.celldynamics.quimp.QParams.verifyEcmminpsnQP(): new java.io.FileReader(File) | I18N | DM_DEFAULT_ENCODING | 807 | High |
Found reliance on default encoding in com.github.celldynamics.quimp.QParams.writeParams(): new java.io.FileWriter(File) | I18N | DM_DEFAULT_ENCODING | 675 | High |
com.github.celldynamics.quimp.QParams.getFluFiles() may expose internal representation by returning QParams.fluFiles | MALICIOUS_CODE | EI_EXPOSE_REP | 408 | Medium |
Exceptional return value of java.io.File.delete() ignored in com.github.celldynamics.quimp.QParams.writeParams() | BAD_PRACTICE | RV_RETURN_VALUE_IGNORED_BAD_PRACTICE | 668 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Write to static field com.github.celldynamics.quimp.BOA_.qState from instance method com.github.celldynamics.quimp.QParamsQconf.readParams() | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 136 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Write to static field com.github.celldynamics.quimp.EXp.frame from instance method com.github.celldynamics.quimp.Q_Explorer.buildWindows() | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 215 | Medium |
Write to static field com.github.celldynamics.quimp.EXp.qp from instance method com.github.celldynamics.quimp.Q_Explorer.run(String) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 73 | Medium |
Unread field: com.github.celldynamics.quimp.Q_Explorer.explorerWindow | PERFORMANCE | URF_UNREAD_FIELD | 211 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Write to static field com.github.celldynamics.quimp.EXp.frame from instance method com.github.celldynamics.quimp.Q_Explorer$ExplorerStackWindow.updateSliceSelector() | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 183 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Should com.github.celldynamics.quimp.Q_Explorer$MovCanvas be a _static_ inner class? | PERFORMANCE | SIC_INNER_SHOULD_BE_STATIC | 124-136 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Found reliance on default encoding in com.github.celldynamics.quimp.Serializer.jsonDump(Object, File, boolean): new java.io.PrintWriter(File) | I18N | DM_DEFAULT_ENCODING | 427 | High |
Found reliance on default encoding in com.github.celldynamics.quimp.Serializer.load(File): new java.io.FileReader(File) | I18N | DM_DEFAULT_ENCODING | 226 | High |
Found reliance on default encoding in com.github.celldynamics.quimp.Serializer.save(String): new java.io.PrintWriter(File) | I18N | DM_DEFAULT_ENCODING | 183 | High |
com.github.celldynamics.quimp.Serializer.load(File) may fail to clean up java.io.Reader | EXPERIMENTAL | OBL_UNSATISFIED_OBLIGATION | 230 | Medium |
com.github.celldynamics.quimp.Serializer.getQconfVersion(Reader) ignores result of java.io.Reader.read(char[]) | BAD_PRACTICE | RR_NOT_CHECKED | 458 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Integral division result cast to double or float in new com.github.celldynamics.quimp.Snake(List, int) | STYLE | ICAST_IDIV_CAST_TO_DOUBLE | 177 | Medium |
Integral division result cast to double or float in new com.github.celldynamics.quimp.Snake(double[], double[], int) | STYLE | ICAST_IDIV_CAST_TO_DOUBLE | 199 | Medium |
Integral division result cast to double or float in com.github.celldynamics.quimp.Snake.intializeOval(int, int, int, int, int, double) | STYLE | ICAST_IDIV_CAST_TO_DOUBLE | 312 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Found reliance on default encoding in com.github.celldynamics.quimp.SnakeHandler.snakeReader(File): new java.io.FileReader(File) | I18N | DM_DEFAULT_ENCODING | 432 | High |
Found reliance on default encoding in com.github.celldynamics.quimp.SnakeHandler.writeOldFormats(): new java.io.FileWriter(File) | I18N | DM_DEFAULT_ENCODING | 283 | High |
Found reliance on default encoding in com.github.celldynamics.quimp.SnakeHandler.writeSnakes(): new java.io.FileWriter(String) | I18N | DM_DEFAULT_ENCODING | 233 | High |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Hard coded reference to an absolute pathname in com.github.celldynamics.quimp.Test_QuimP.testQparams() | STYLE | DMI_HARDCODED_ABSOLUTE_FILENAME | 113 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.filesystem.DataContainer.getQState() may expose internal representation by returning DataContainer.QState | MALICIOUS_CODE | EI_EXPOSE_REP | 123 | Medium |
The field name com.github.celldynamics.quimp.filesystem.DataContainer.Stats doesn't start with a lower case letter | BAD_PRACTICE | NM_FIELD_NAMING_CONVENTION | Not available | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Should com.github.celldynamics.quimp.filesystem.FileDialogEx$QuimpConfigFilefilter be a _static_ inner class? | PERFORMANCE | SIC_INNER_SHOULD_BE_STATIC | 163-216 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Possible null pointer dereference in com.github.celldynamics.quimp.filesystem.QconfLoader.getImage() due to return value of called method | STYLE | NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE | 199 | Medium |
Possible null pointer dereference in com.github.celldynamics.quimp.filesystem.QconfLoader.loader(File, String) due to return value of called method | STYLE | NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE | 141 | Medium |
Possible null pointer dereference in com.github.celldynamics.quimp.filesystem.QconfLoader.loader(File, String) due to return value of called method | STYLE | NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE | 145 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.filesystem.converter.FormatConverter.headerEcmmOutline should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | 127 | Medium |
com.github.celldynamics.quimp.filesystem.converter.FormatConverter.logger isn't final but should be | MALICIOUS_CODE | MS_SHOULD_BE_FINAL | 119 | High |
Exception is caught when Exception is not thrown in com.github.celldynamics.quimp.filesystem.converter.FormatConverter.generateNewDataFiles() | STYLE | REC_CATCH_EXCEPTION | 442 | Medium |
Write to static field com.github.celldynamics.quimp.plugin.qanalysis.STmap.LOGGER from instance method com.github.celldynamics.quimp.filesystem.converter.FormatConverter.saveMaps(int) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 532 | High |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.filesystem.converter.FormatConverterModel.clone() does not call super.clone() | BAD_PRACTICE | CN_IDIOM_NO_SUPER_CALL | 63-67 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Should com.github.celldynamics.quimp.geom.MapTracker$PredicateBadIndex be a _static_ inner class? | PERFORMANCE | SIC_INNER_SHOULD_BE_STATIC | 382-389 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.geom.SegmentedShapeRoi doesn't override ij.gui.Roi.equals(Object) | STYLE | EQ_DOESNT_OVERRIDE_EQUALS | 1 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Dead store to shCont in com.github.celldynamics.quimp.geom.filters.HatSnakeFilter.calculateRank(List, ImageProcessor) | STYLE | DLS_DEAD_LOCAL_STORE | 400 | Medium |
Found reliance on default encoding in com.github.celldynamics.quimp.geom.filters.HatSnakeFilter.calculateRank(List, ImageProcessor): new java.io.FileWriter(File) | I18N | DM_DEFAULT_ENCODING | 415 | High |
Found reliance on default encoding in com.github.celldynamics.quimp.geom.filters.HatSnakeFilter.debugSaveList(Path, List): new java.io.FileWriter(File) | I18N | DM_DEFAULT_ENCODING | 501 | High |
com.github.celldynamics.quimp.geom.filters.HatSnakeFilter.calculateRank(List, ImageProcessor) may fail to close stream | BAD_PRACTICE | OS_OPEN_STREAM | 415 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Should com.github.celldynamics.quimp.geom.filters.HatSnakeFilter$WindowIndRange be a _static_ inner class? | PERFORMANCE | SIC_INNER_SHOULD_BE_STATIC | 660-775 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Possible null pointer dereference in com.github.celldynamics.quimp.omero.OmeroBrowser.upload(String, String, DatasetData) due to return value of called method | STYLE | NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE | 384 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Possible null pointer dereference in com.github.celldynamics.quimp.omero.OmeroClient_.upload() due to return value of called method | STYLE | NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE | 396 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Found reliance on default encoding in com.github.celldynamics.quimp.omero.OmeroClient_$Xor.decrypt(String, String): new String(byte[]) | I18N | DM_DEFAULT_ENCODING | 337 | High |
Found reliance on default encoding in com.github.celldynamics.quimp.omero.OmeroClient_$Xor.decrypt(String, String): String.getBytes() | I18N | DM_DEFAULT_ENCODING | 337 | High |
Found reliance on default encoding in com.github.celldynamics.quimp.omero.OmeroClient_$Xor.encrypt(String, String): String.getBytes() | I18N | DM_DEFAULT_ENCODING | 325 | High |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Primitive value is boxed then unboxed to perform primitive coercion in com.github.celldynamics.quimp.plugin.ParamList.getIntValue(String) | PERFORMANCE | BX_BOXING_IMMEDIATELY_UNBOXED_TO_PERFORM_COERCION | 90 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Hard coded reference to an absolute pathname in com.github.celldynamics.quimp.plugin.ana.ANA_.resetFluo() | STYLE | DMI_HARDCODED_ABSOLUTE_FILENAME | 531 | Medium |
Exceptional return value of java.io.File.delete() ignored in com.github.celldynamics.quimp.plugin.ana.ANA_.runFromPaqp() | BAD_PRACTICE | RV_RETURN_VALUE_IGNORED_BAD_PRACTICE | 369 | Medium |
Write to static field com.github.celldynamics.quimp.plugin.ecmm.ECMp.plot from instance method new com.github.celldynamics.quimp.plugin.ana.ANA_() | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 103 | Medium |
Write to static field ij.Prefs.interpolateScaledImages from instance method com.github.celldynamics.quimp.plugin.ana.ANA_.run(String) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 127 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Hard coded reference to an absolute pathname in new com.github.celldynamics.quimp.plugin.ana.ANAp() | STYLE | DMI_HARDCODED_ABSOLUTE_FILENAME | 118 | Medium |
Unread field: com.github.celldynamics.quimp.plugin.ana.ANAp.angleTh; should this field be static? | PERFORMANCE | SS_SHOULD_BE_STATIC | 58 | Medium |
Unread field: com.github.celldynamics.quimp.plugin.ana.ANAp.freezeTh; should this field be static? | PERFORMANCE | SS_SHOULD_BE_STATIC | 52 | Medium |
Unread field: com.github.celldynamics.quimp.plugin.ana.ANAp.oneFrameRes; should this field be static? | PERFORMANCE | SS_SHOULD_BE_STATIC | 64 | Medium |
Unread field: com.github.celldynamics.quimp.plugin.ana.ANAp.stepRes; should this field be static? | PERFORMANCE | SS_SHOULD_BE_STATIC | 48 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.plugin.ana.AnaOptions.clone() does not call super.clone() | BAD_PRACTICE | CN_IDIOM_NO_SUPER_CALL | 65-75 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Found reliance on default encoding in com.github.celldynamics.quimp.plugin.bar.QuimP_Bar.actionPerformed(ActionEvent): new java.io.InputStreamReader(InputStream) | I18N | DM_DEFAULT_ENCODING | 458 | High |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentationOptions.clone() does not call super.clone() | BAD_PRACTICE | CN_IDIOM_NO_SUPER_CALL | 47-51 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Redundant nullcheck of maskFile, which is known to be non-null in com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentation_.runPlugin() | STYLE | RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE | 220 | High |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping.plot should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
Exceptional return value of java.io.File.delete() ignored in com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping.runFromPaqp() | BAD_PRACTICE | RV_RETURN_VALUE_IGNORED_BAD_PRACTICE | 550 | Medium |
Write to static field com.github.celldynamics.quimp.plugin.ecmm.ECMp.image from instance method com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping.runByANA(OutlineHandler, ImageProcessor, double) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 254 | High |
Write to static field com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping.plot from instance method new com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping(int) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 112 | Medium |
Write to static field com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping.plot from instance method com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping.runByANA(OutlineHandler, ImageProcessor, double) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 265 | Medium |
Write to static field com.github.celldynamics.quimp.plugin.ecmm.ECMp.ANA from instance method com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping.runByANA(OutlineHandler, ImageProcessor, double) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 259 | Medium |
Write to static field com.github.celldynamics.quimp.plugin.ecmm.ECMp.anaMigDist from instance method com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping.runByANA(OutlineHandler, ImageProcessor, double) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 260 | Medium |
Write to static field com.github.celldynamics.quimp.plugin.ecmm.ECMp.chargeDensity from instance method com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping.runByANA(OutlineHandler, ImageProcessor, double) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 272 | Medium |
Write to static field com.github.celldynamics.quimp.plugin.ecmm.ECMp.d from instance method com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping.runByANA(OutlineHandler, ImageProcessor, double) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 273 | Medium |
Write to static field com.github.celldynamics.quimp.plugin.ecmm.ECMp.endFrame from instance method com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping.runByANA(OutlineHandler, ImageProcessor, double) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 257 | Medium |
Write to static field com.github.celldynamics.quimp.plugin.ecmm.ECMp.h from instance method com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping.runByANA(OutlineHandler, ImageProcessor, double) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 271 | Medium |
Write to static field com.github.celldynamics.quimp.plugin.ecmm.ECMp.maxVertF from instance method com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping.runByANA(OutlineHandler, ImageProcessor, double) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 274 | Medium |
Write to static field com.github.celldynamics.quimp.plugin.ecmm.ECMp.migQ from instance method com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping.runByANA(OutlineHandler, ImageProcessor, double) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 261 | Medium |
Write to static field com.github.celldynamics.quimp.plugin.ecmm.ECMp.plot from instance method com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping.runByANA(OutlineHandler, ImageProcessor, double) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 258 | Medium |
Write to static field com.github.celldynamics.quimp.plugin.ecmm.ECMp.startFrame from instance method com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping.runByANA(OutlineHandler, ImageProcessor, double) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 256 | Medium |
Write to static field com.github.celldynamics.quimp.plugin.ecmm.ECMp.tarQ from instance method com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping.runByANA(OutlineHandler, ImageProcessor, double) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 262 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.plugin.ecmm.ECMp.plot isn't final and can't be protected from malicious code | MALICIOUS_CODE | MS_CANNOT_BE_FINAL | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.ANA should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.INFILE should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.OUTFILE should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.anaMigDist should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.chargeDensity should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.d should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.disableDensityCorrections should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.forceBackwardMapping should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.forceForwardMapping should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.forceNoSectors should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.frameInterval should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.h should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.image should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.its should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.k should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.lineCharges should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.markerRes should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.maxCellSize should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.maxIter should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.maxVertF should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.migPower should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.migQ should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.mobileQ should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.numINTS should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.scale should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.startFrame should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.tarPower should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.tarQ should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.unSnapped should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.visualRes should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
com.github.celldynamics.quimp.plugin.ecmm.ECMp.w should be package protected | MALICIOUS_CODE | MS_PKGPROTECT | Not available | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Integral division result cast to double or float in com.github.celldynamics.quimp.plugin.ecmm.ECMplot.relocate(ExtendedVector2d) | STYLE | ICAST_IDIV_CAST_TO_DOUBLE | 139 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.plugin.ecmm.EcmmOptions.clone() does not call super.clone() | BAD_PRACTICE | CN_IDIOM_NO_SUPER_CALL | 42-44 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Integral division result cast to double or float in com.github.celldynamics.quimp.plugin.ecmm.Mapping.rebuildInts() | STYLE | ICAST_IDIV_CAST_TO_DOUBLE | 301 | Medium |
Write to static field com.github.celldynamics.quimp.plugin.ecmm.ECMp.numINTS from instance method new com.github.celldynamics.quimp.plugin.ecmm.Mapping(Outline, Outline) | STYLE | ST_WRITE_TO_STATIC_FROM_INSTANCE_METHOD | 24 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Hard coded reference to an absolute pathname in new com.github.celldynamics.quimp.plugin.engine.PluginFactory(Path) | STYLE | DMI_HARDCODED_ABSOLUTE_FILENAME | 268 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.plugin.generatemask.GenerateMaskOptions.clone() does not call super.clone() | BAD_PRACTICE | CN_IDIOM_NO_SUPER_CALL | 27-30 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Found reliance on default encoding in com.github.celldynamics.quimp.plugin.protanalysis.ActionSaveTracks.actionPerformed(ActionEvent): new java.io.FileWriter(File) | I18N | DM_DEFAULT_ENCODING | 63 | High |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Integral division result cast to double or float in com.github.celldynamics.quimp.plugin.protanalysis.CustomCanvas.paint(Graphics) | STYLE | ICAST_IDIV_CAST_TO_DOUBLE | 694 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions.pointColor isn't final but should be | MALICIOUS_CODE | MS_SHOULD_BE_FINAL | 24 | High |
com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions.staticPointColor isn't final but should be | MALICIOUS_CODE | MS_SHOULD_BE_FINAL | 28 | High |
com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions.pointSize isn't final but should be | MALICIOUS_CODE | MS_SHOULD_BE_FINAL | 36 | Medium |
com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions.staticPointSize isn't final but should be | MALICIOUS_CODE | MS_SHOULD_BE_FINAL | 32 | Medium |
Unread public/protected field: com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions.chbMeanCtfPlot | STYLE | URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD | 177 | Medium |
Unread public/protected field: com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions.dropValue | STYLE | URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD | 226 | Medium |
Unread public/protected field: com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions.noiseTolerance | STYLE | URF_UNREAD_PUBLIC_OR_PROTECTED_FIELD | 222 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Should com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions$OutlinesToImage be a _static_ inner class? | PERFORMANCE | SIC_INNER_SHOULD_BE_STATIC | 310-344 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Found reliance on default encoding in com.github.celldynamics.quimp.plugin.protanalysis.Prot_Analysis.writeStats(int, STmap, MaximaFinder, TrackCollection): new java.io.PrintWriter(File) | I18N | DM_DEFAULT_ENCODING | 433 | High |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Dead store to ret in com.github.celldynamics.quimp.plugin.protanalysis.TrackMapAnalyser.getIntersectionPoints(Polygon, Polygon) | STYLE | DLS_DEAD_LOCAL_STORE | 237 | Medium |
com.github.celldynamics.quimp.plugin.protanalysis.TrackMapAnalyser.removeSelfRepeatings(List, List) makes inefficient use of keySet iterator instead of entrySet iterator | PERFORMANCE | WMI_WRONG_MAP_ITERATOR | 305 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation.color should be both final and package protected | MALICIOUS_CODE | MS_FINAL_PKGPROTECT | 70 | Medium |
com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation.MAXIMA_COLOR isn't final but should be | MALICIOUS_CODE | MS_SHOULD_BE_FINAL | 58 | High |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Check for oddness that won't work for negative numbers in com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation$Stack.addTrackingLinesToImage(STmap, TrackCollection) | STYLE | IM_BAD_CHECK_FOR_ODD | 688 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Should com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation$Stack$ListPoint2iComparator be a _static_ inner class? | PERFORMANCE | SIC_INNER_SHOULD_BE_STATIC | 899-914 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.plugin.qanalysis.FluoMap.getColours() may expose internal representation by returning FluoMap.fluColor | MALICIOUS_CODE | EI_EXPOSE_REP | 142 | Medium |
com.github.celldynamics.quimp.plugin.qanalysis.FluoMap.getMap() may expose internal representation by returning FluoMap.map | MALICIOUS_CODE | EI_EXPOSE_REP | 151 | Medium |
com.github.celldynamics.quimp.plugin.qanalysis.FluoMap.setMap(double[][]) may expose internal representation by storing an externally mutable object into FluoMap.map | MALICIOUS_CODE | EI_EXPOSE_REP2 | 169 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.plugin.qanalysis.Qp.clone() does not call super.clone() | BAD_PRACTICE | CN_IDIOM_NO_SUPER_CALL | 148-175 | Medium |
Unread field: com.github.celldynamics.quimp.plugin.qanalysis.Qp.Build3D; should this field be static? | PERFORMANCE | SS_SHOULD_BE_STATIC | 87 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
new com.github.celldynamics.quimp.plugin.qanalysis.STMap3D(double[][], double[][], int[]) may expose internal representation by storing an externally mutable object into STMap3D.colors | MALICIOUS_CODE | EI_EXPOSE_REP2 | 68 | Medium |
new com.github.celldynamics.quimp.plugin.qanalysis.STMap3D(double[][], double[][], int[]) may expose internal representation by storing an externally mutable object into STMap3D.xMap | MALICIOUS_CODE | EI_EXPOSE_REP2 | 66 | Medium |
new com.github.celldynamics.quimp.plugin.qanalysis.STMap3D(double[][], double[][], int[]) may expose internal representation by storing an externally mutable object into STMap3D.yMap | MALICIOUS_CODE | EI_EXPOSE_REP2 | 67 | Medium |
Exceptional return value of java.io.File.delete() ignored in com.github.celldynamics.quimp.plugin.qanalysis.STMap3D.write(File) | BAD_PRACTICE | RV_RETURN_VALUE_IGNORED_BAD_PRACTICE | 156 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.plugin.qanalysis.STmap.getConvMap() may expose internal representation by returning STmap.convMap | MALICIOUS_CODE | EI_EXPOSE_REP | 1146 | Medium |
com.github.celldynamics.quimp.plugin.qanalysis.STmap.getCoordMap() may expose internal representation by returning STmap.coordMap | MALICIOUS_CODE | EI_EXPOSE_REP | 1078 | Medium |
com.github.celldynamics.quimp.plugin.qanalysis.STmap.getFluMaps() may expose internal representation by returning STmap.fluoMaps | MALICIOUS_CODE | EI_EXPOSE_REP | 1155 | Medium |
com.github.celldynamics.quimp.plugin.qanalysis.STmap.getMotMap() may expose internal representation by returning STmap.motMap | MALICIOUS_CODE | EI_EXPOSE_REP | 1123 | Medium |
com.github.celldynamics.quimp.plugin.qanalysis.STmap.getOriginMap() may expose internal representation by returning STmap.originMap | MALICIOUS_CODE | EI_EXPOSE_REP | 1100 | Medium |
com.github.celldynamics.quimp.plugin.qanalysis.STmap.getxMap() may expose internal representation by returning STmap.xMap | MALICIOUS_CODE | EI_EXPOSE_REP | 1034 | Medium |
com.github.celldynamics.quimp.plugin.qanalysis.STmap.getyMap() may expose internal representation by returning STmap.yMap | MALICIOUS_CODE | EI_EXPOSE_REP | 1056 | Medium |
com.github.celldynamics.quimp.plugin.qanalysis.STmap.setConvMap(double[][]) may expose internal representation by storing an externally mutable object into STmap.convMap | MALICIOUS_CODE | EI_EXPOSE_REP2 | 1166 | Medium |
com.github.celldynamics.quimp.plugin.qanalysis.STmap.setCoordMap(double[][]) may expose internal representation by storing an externally mutable object into STmap.coordMap | MALICIOUS_CODE | EI_EXPOSE_REP2 | 1089 | Medium |
com.github.celldynamics.quimp.plugin.qanalysis.STmap.setMotMap(double[][]) may expose internal representation by storing an externally mutable object into STmap.motMap | MALICIOUS_CODE | EI_EXPOSE_REP2 | 1135 | Medium |
com.github.celldynamics.quimp.plugin.qanalysis.STmap.setOriginMap(double[][]) may expose internal representation by storing an externally mutable object into STmap.originMap | MALICIOUS_CODE | EI_EXPOSE_REP2 | 1112 | Medium |
com.github.celldynamics.quimp.plugin.qanalysis.STmap.setxMap(double[][]) may expose internal representation by storing an externally mutable object into STmap.xMap | MALICIOUS_CODE | EI_EXPOSE_REP2 | 1045 | Medium |
com.github.celldynamics.quimp.plugin.qanalysis.STmap.setyMap(double[][]) may expose internal representation by storing an externally mutable object into STmap.yMap | MALICIOUS_CODE | EI_EXPOSE_REP2 | 1067 | Medium |
com.github.celldynamics.quimp.plugin.qanalysis.STmap.LOGGER isn't final and can't be protected from malicious code | MALICIOUS_CODE | MS_CANNOT_BE_FINAL | 42 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds$Contour$1.compare(Pair, Pair) invokes inefficient new Integer(int) constructor; use Integer.valueOf(int) instead | PERFORMANCE | DM_NUMBER_CTOR | 581 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Load of known null value in com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel.setQconfFile(String) | STYLE | NP_LOAD_OF_KNOWN_NULL_VALUE | 252 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Possible null pointer dereference of seedImage in com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_.runPlugin() | CORRECTNESS | NP_NULL_ON_SOME_PATH | 940 | Medium |
Redundant nullcheck of seedImage, which is known to be non-null in com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_.runPlugin() | STYLE | RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE | 897 | Medium |
Switch statement found in com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_.runPlugin() where one case falls through to the next case | STYLE | SF_SWITCH_FALLTHROUGH | 925-928 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Should com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_$HelpBtnController be a _static_ inner class? | PERFORMANCE | SIC_INNER_SHOULD_BE_STATIC | 516-531 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Possible null pointer dereference in com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_$QconfShowSeedImageController.actionPerformed(ActionEvent) due to return value of called method | STYLE | NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE | 801 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.plugin.randomwalk.SeedProcessor.decodeSeedsfromGrayscaleImage(ImageProcessor) invokes inefficient new Integer(int) constructor; use Integer.valueOf(int) instead | PERFORMANCE | DM_NUMBER_CTOR | 314 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Should com.github.celldynamics.quimp.plugin.utils.ImageProcessorPlus$GenerateKernel be a _static_ inner class? | PERFORMANCE | SIC_INNER_SHOULD_BE_STATIC | 168-240 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Should com.github.celldynamics.quimp.plugin.utils.QWindowBuilder$ComponentList be a _static_ inner class? | PERFORMANCE | SIC_INNER_SHOULD_BE_STATIC | 765 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter.getX() may expose internal representation by returning QuimpDataConverter.xc | MALICIOUS_CODE | EI_EXPOSE_REP | 166 | Medium |
com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter.getY() may expose internal representation by returning QuimpDataConverter.yc | MALICIOUS_CODE | EI_EXPOSE_REP | 175 | Medium |
new com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter(double[], double[]) may expose internal representation by storing an externally mutable object into QuimpDataConverter.xc | MALICIOUS_CODE | EI_EXPOSE_REP2 | 84 | Medium |
new com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter(double[], double[]) may expose internal representation by storing an externally mutable object into QuimpDataConverter.yc | MALICIOUS_CODE | EI_EXPOSE_REP2 | 85 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Found reliance on default encoding in new com.github.celldynamics.quimp.utils.CsvWritter(): new java.io.FileWriter(File) | I18N | DM_DEFAULT_ENCODING | 37 | High |
Found reliance on default encoding in new com.github.celldynamics.quimp.utils.CsvWritter(Path, String[]): new java.io.FileWriter(File) | I18N | DM_DEFAULT_ENCODING | 50 | High |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.utils.IJTools.WAIT_TIME isn't final but should be | MALICIOUS_CODE | MS_SHOULD_BE_FINAL | 26 | High |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Found reliance on default encoding in com.github.celldynamics.quimp.utils.QuimPArrayUtils.arrayToFile(double[][], String, File): new java.io.FileWriter(File) | I18N | DM_DEFAULT_ENCODING | 273 | High |
Found reliance on default encoding in com.github.celldynamics.quimp.utils.QuimPArrayUtils.file2Array(String, File): new java.io.FileReader(File) | I18N | DM_DEFAULT_ENCODING | 317 | High |
Found reliance on default encoding in com.github.celldynamics.quimp.utils.QuimPArrayUtils.getNumberOfLinesinFile(File): new java.io.FileReader(File) | I18N | DM_DEFAULT_ENCODING | 342 | High |
com.github.celldynamics.quimp.utils.QuimPArrayUtils.getNumberOfLinesinFile(File) ignores result of java.io.LineNumberReader.skip(long) | BAD_PRACTICE | SR_NOT_CHECKED | 343 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.utils.QuimpToolsCollection.getQuimPBuildInfo() might ignore java.lang.Exception | BAD_PRACTICE | DE_MIGHT_IGNORE | 115 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
com.github.celldynamics.quimp.utils.UiTools.toolTipLength isn't final but should be | MALICIOUS_CODE | MS_SHOULD_BE_FINAL | 20 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Found reliance on default encoding in com.github.celldynamics.quimp.utils.graphics.PolarPlot.polarPlotPoints(String, double[], double[], double[]): new java.io.PrintWriter(OutputStream, boolean) | I18N | DM_DEFAULT_ENCODING | 259 | High |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Found reliance on default encoding in com.github.celldynamics.quimp.utils.graphics.svg.SVGplotter.plotTrack(String, int): new java.io.PrintWriter(OutputStream) | I18N | DM_DEFAULT_ENCODING | 209 | High |
Found reliance on default encoding in com.github.celldynamics.quimp.utils.graphics.svg.SVGplotter.plotTrackAnim(): new java.io.PrintWriter(OutputStream) | I18N | DM_DEFAULT_ENCODING | 156 | High |
Found reliance on default encoding in com.github.celldynamics.quimp.utils.graphics.svg.SVGplotter.plotTrackER(String): new java.io.PrintWriter(OutputStream) | I18N | DM_DEFAULT_ENCODING | 105 | High |
Unread field: com.github.celldynamics.quimp.utils.graphics.svg.SVGplotter.deltaT | PERFORMANCE | URF_UNREAD_FIELD | 73 | Medium |
Bug | Category | Details | Line | Priority |
---|---|---|---|---|
Found reliance on default encoding in com.github.celldynamics.quimp.utils.graphics.vrml.VRMLobject.write(File): new java.io.FileWriter(File) | I18N | DM_DEFAULT_ENCODING | 73 | High |
new com.github.celldynamics.quimp.utils.graphics.vrml.VRMLobject(Point3f[], Color3f[], int[]) may expose internal representation by storing an externally mutable object into VRMLobject.colorsF | MALICIOUS_CODE | EI_EXPOSE_REP2 | 36 | Medium |
new com.github.celldynamics.quimp.utils.graphics.vrml.VRMLobject(Point3f[], Color3f[], int[]) may expose internal representation by storing an externally mutable object into VRMLobject.coordIndices | MALICIOUS_CODE | EI_EXPOSE_REP2 | 37 | Medium |
new com.github.celldynamics.quimp.utils.graphics.vrml.VRMLobject(Point3f[], Color3f[], int[]) may expose internal representation by storing an externally mutable object into VRMLobject.coords | MALICIOUS_CODE | EI_EXPOSE_REP2 | 35 | Medium |
Exception is caught when Exception is not thrown in com.github.celldynamics.quimp.utils.graphics.vrml.VRMLobject.write(File) | STYLE | REC_CATCH_EXCEPTION | 126 | Medium |