FindBugs Bug Detector Report

The following document contains the results of FindBugs

FindBugs Version is 3.0.1

Threshold is medium

Effort is min

Summary

Classes Bugs Errors Missing Classes
338 233 0 0

Files

Class Bugs
com.github.celldynamics.quimp.BOAState$BOAp 4
com.github.celldynamics.quimp.BOAState$SegParam 1
com.github.celldynamics.quimp.BOA_ 11
com.github.celldynamics.quimp.BOA_$CustomStackWindow 1
com.github.celldynamics.quimp.CellStatsEval 2
com.github.celldynamics.quimp.Constrictor 4
com.github.celldynamics.quimp.FrameStatistics 2
com.github.celldynamics.quimp.ImageGroup 1
com.github.celldynamics.quimp.ImageManager 5
com.github.celldynamics.quimp.LogEntry 5
com.github.celldynamics.quimp.Outline 4
com.github.celldynamics.quimp.OutlineHandler 2
com.github.celldynamics.quimp.PointsList 1
com.github.celldynamics.quimp.PropertyReader 1
com.github.celldynamics.quimp.QColor 1
com.github.celldynamics.quimp.QParams 6
com.github.celldynamics.quimp.QParamsQconf 1
com.github.celldynamics.quimp.Q_Explorer 3
com.github.celldynamics.quimp.Q_Explorer$ExplorerStackWindow 1
com.github.celldynamics.quimp.Q_Explorer$MovCanvas 1
com.github.celldynamics.quimp.Serializer 5
com.github.celldynamics.quimp.Snake 3
com.github.celldynamics.quimp.SnakeHandler 3
com.github.celldynamics.quimp.Test_QuimP 1
com.github.celldynamics.quimp.filesystem.DataContainer 2
com.github.celldynamics.quimp.filesystem.FileDialogEx$QuimpConfigFilefilter 1
com.github.celldynamics.quimp.filesystem.QconfLoader 3
com.github.celldynamics.quimp.filesystem.converter.FormatConverter 4
com.github.celldynamics.quimp.filesystem.converter.FormatConverterModel 1
com.github.celldynamics.quimp.geom.MapTracker$PredicateBadIndex 1
com.github.celldynamics.quimp.geom.SegmentedShapeRoi 1
com.github.celldynamics.quimp.geom.filters.HatSnakeFilter 4
com.github.celldynamics.quimp.geom.filters.HatSnakeFilter$WindowIndRange 1
com.github.celldynamics.quimp.omero.OmeroBrowser 1
com.github.celldynamics.quimp.omero.OmeroClient_ 1
com.github.celldynamics.quimp.omero.OmeroClient_$Xor 3
com.github.celldynamics.quimp.plugin.ParamList 1
com.github.celldynamics.quimp.plugin.ana.ANA_ 4
com.github.celldynamics.quimp.plugin.ana.ANAp 5
com.github.celldynamics.quimp.plugin.ana.AnaOptions 1
com.github.celldynamics.quimp.plugin.bar.QuimP_Bar 1
com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentationOptions 1
com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentation_ 1
com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping 16
com.github.celldynamics.quimp.plugin.ecmm.ECMp 32
com.github.celldynamics.quimp.plugin.ecmm.ECMplot 1
com.github.celldynamics.quimp.plugin.ecmm.EcmmOptions 1
com.github.celldynamics.quimp.plugin.ecmm.Mapping 2
com.github.celldynamics.quimp.plugin.engine.PluginFactory 1
com.github.celldynamics.quimp.plugin.generatemask.GenerateMaskOptions 1
com.github.celldynamics.quimp.plugin.protanalysis.ActionSaveTracks 1
com.github.celldynamics.quimp.plugin.protanalysis.CustomCanvas 1
com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions 7
com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions$OutlinesToImage 1
com.github.celldynamics.quimp.plugin.protanalysis.Prot_Analysis 1
com.github.celldynamics.quimp.plugin.protanalysis.TrackMapAnalyser 2
com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation 2
com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation$Stack 1
com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation$Stack$ListPoint2iComparator 1
com.github.celldynamics.quimp.plugin.qanalysis.FluoMap 3
com.github.celldynamics.quimp.plugin.qanalysis.Qp 2
com.github.celldynamics.quimp.plugin.qanalysis.STMap3D 4
com.github.celldynamics.quimp.plugin.qanalysis.STmap 14
com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds$Contour$1 1
com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel 1
com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_ 3
com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_$HelpBtnController 1
com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_$QconfShowSeedImageController 1
com.github.celldynamics.quimp.plugin.randomwalk.SeedProcessor 1
com.github.celldynamics.quimp.plugin.utils.ImageProcessorPlus$GenerateKernel 1
com.github.celldynamics.quimp.plugin.utils.QWindowBuilder$ComponentList 1
com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter 4
com.github.celldynamics.quimp.utils.CsvWritter 2
com.github.celldynamics.quimp.utils.IJTools 1
com.github.celldynamics.quimp.utils.QuimPArrayUtils 4
com.github.celldynamics.quimp.utils.QuimpToolsCollection 1
com.github.celldynamics.quimp.utils.UiTools 1
com.github.celldynamics.quimp.utils.graphics.PolarPlot 1
com.github.celldynamics.quimp.utils.graphics.svg.SVGplotter 4
com.github.celldynamics.quimp.utils.graphics.vrml.VRMLobject 5

com.github.celldynamics.quimp.BOAState$BOAp

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

com.github.celldynamics.quimp.BOAState$SegParam

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

com.github.celldynamics.quimp.BOA_

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

com.github.celldynamics.quimp.BOA_$CustomStackWindow

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

com.github.celldynamics.quimp.CellStatsEval

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

com.github.celldynamics.quimp.Constrictor

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

com.github.celldynamics.quimp.FrameStatistics

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

com.github.celldynamics.quimp.ImageGroup

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

com.github.celldynamics.quimp.ImageManager

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

com.github.celldynamics.quimp.LogEntry

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

com.github.celldynamics.quimp.Outline

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

com.github.celldynamics.quimp.OutlineHandler

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

com.github.celldynamics.quimp.PointsList

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

com.github.celldynamics.quimp.PropertyReader

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

com.github.celldynamics.quimp.QColor

Bug Category Details Line Priority
com.github.celldynamics.quimp.QColor.colourMaps is a mutable array MALICIOUS_CODE MS_MUTABLE_ARRAY 17 High

com.github.celldynamics.quimp.QParams

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

com.github.celldynamics.quimp.QParamsQconf

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

com.github.celldynamics.quimp.Q_Explorer

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

com.github.celldynamics.quimp.Q_Explorer$ExplorerStackWindow

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

com.github.celldynamics.quimp.Q_Explorer$MovCanvas

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

com.github.celldynamics.quimp.Serializer

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

com.github.celldynamics.quimp.Snake

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

com.github.celldynamics.quimp.SnakeHandler

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

com.github.celldynamics.quimp.Test_QuimP

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

com.github.celldynamics.quimp.filesystem.DataContainer

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

com.github.celldynamics.quimp.filesystem.FileDialogEx$QuimpConfigFilefilter

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

com.github.celldynamics.quimp.filesystem.QconfLoader

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

com.github.celldynamics.quimp.filesystem.converter.FormatConverter

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

com.github.celldynamics.quimp.filesystem.converter.FormatConverterModel

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

com.github.celldynamics.quimp.geom.MapTracker$PredicateBadIndex

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

com.github.celldynamics.quimp.geom.SegmentedShapeRoi

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

com.github.celldynamics.quimp.geom.filters.HatSnakeFilter

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

com.github.celldynamics.quimp.geom.filters.HatSnakeFilter$WindowIndRange

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

com.github.celldynamics.quimp.omero.OmeroBrowser

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

com.github.celldynamics.quimp.omero.OmeroClient_

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

com.github.celldynamics.quimp.omero.OmeroClient_$Xor

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

com.github.celldynamics.quimp.plugin.ParamList

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

com.github.celldynamics.quimp.plugin.ana.ANA_

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

com.github.celldynamics.quimp.plugin.ana.ANAp

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

com.github.celldynamics.quimp.plugin.ana.AnaOptions

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

com.github.celldynamics.quimp.plugin.bar.QuimP_Bar

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

com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentationOptions

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

com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentation_

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

com.github.celldynamics.quimp.plugin.ecmm.ECMM_Mapping

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

com.github.celldynamics.quimp.plugin.ecmm.ECMp

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

com.github.celldynamics.quimp.plugin.ecmm.ECMplot

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

com.github.celldynamics.quimp.plugin.ecmm.EcmmOptions

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

com.github.celldynamics.quimp.plugin.ecmm.Mapping

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

com.github.celldynamics.quimp.plugin.engine.PluginFactory

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

com.github.celldynamics.quimp.plugin.generatemask.GenerateMaskOptions

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

com.github.celldynamics.quimp.plugin.protanalysis.ActionSaveTracks

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

com.github.celldynamics.quimp.plugin.protanalysis.CustomCanvas

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

com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions

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

com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisOptions$OutlinesToImage

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

com.github.celldynamics.quimp.plugin.protanalysis.Prot_Analysis

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

com.github.celldynamics.quimp.plugin.protanalysis.TrackMapAnalyser

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

com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation

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

com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation$Stack

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

com.github.celldynamics.quimp.plugin.protanalysis.TrackVisualisation$Stack$ListPoint2iComparator

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

com.github.celldynamics.quimp.plugin.qanalysis.FluoMap

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

com.github.celldynamics.quimp.plugin.qanalysis.Qp

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

com.github.celldynamics.quimp.plugin.qanalysis.STMap3D

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

com.github.celldynamics.quimp.plugin.qanalysis.STmap

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

com.github.celldynamics.quimp.plugin.randomwalk.PropagateSeeds$Contour$1

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

com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkModel

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

com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_

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

com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_$HelpBtnController

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

com.github.celldynamics.quimp.plugin.randomwalk.RandomWalkSegmentationPlugin_$QconfShowSeedImageController

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

com.github.celldynamics.quimp.plugin.randomwalk.SeedProcessor

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

com.github.celldynamics.quimp.plugin.utils.ImageProcessorPlus$GenerateKernel

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

com.github.celldynamics.quimp.plugin.utils.QWindowBuilder$ComponentList

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

com.github.celldynamics.quimp.plugin.utils.QuimpDataConverter

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

com.github.celldynamics.quimp.utils.CsvWritter

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

com.github.celldynamics.quimp.utils.IJTools

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

com.github.celldynamics.quimp.utils.QuimPArrayUtils

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

com.github.celldynamics.quimp.utils.QuimpToolsCollection

Bug Category Details Line Priority
com.github.celldynamics.quimp.utils.QuimpToolsCollection.getQuimPBuildInfo() might ignore java.lang.Exception BAD_PRACTICE DE_MIGHT_IGNORE 115 Medium

com.github.celldynamics.quimp.utils.UiTools

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

com.github.celldynamics.quimp.utils.graphics.PolarPlot

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

com.github.celldynamics.quimp.utils.graphics.svg.SVGplotter

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

com.github.celldynamics.quimp.utils.graphics.vrml.VRMLobject

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