Package	Files	Average Method Complexity	TOTAL Coverage
jalview.io jalview.io	59.0 59	4.0628204 4.06	0.5661594 0.566159456.6%

Class	Methods	Average Method Complexity	TOTAL Coverage
AlignmentProperties AlignmentProperties	5.0 5	3.2 3.2	0.0 0.00%
DBRefFile DBRefFile	2.0 2	1.0 1	0.0 0.00%
HtmlFile HtmlFile	15.0 15	1.4 1.4	0.0 0.00%
InputStreamParser InputStreamParser	2.0 2	1.0 1	0.0 0.00%
JPredFile JPredFile	11.0 11	4.0 4	0.0 0.00%
JSONFile.JSONExportSettings JSONFile.JSONExportSettings	10.0 10	1.0 1	0.0 0.00%
JnetAnnotationMaker JnetAnnotationMaker	2.0 2	21.0 21	0.0 0.00%
ModellerDescription.resCode ModellerDescription.resCode	2.0 2	1.0 1	0.0 0.00%
PContactPredictionFile PContactPredictionFile	8.0 8	1.5 1.5	0.0 0.00%
SimpleBlastFile SimpleBlastFile	6.0 6	8.0 8	0.0 0.00%
VamsasAppDatastore VamsasAppDatastore	51.0 51	7.2941175 7.29	0.0 0.00%
WSWUBlastClient WSWUBlastClient	3.0 3	5.0 5	0.0 0.00%
WSWUBlastClient.BlastThread WSWUBlastClient.BlastThread	3.0 3	2.3333333 2.33	0.0 0.00%
WSWUBlastClient.ImageTwirler WSWUBlastClient.ImageTwirler	2.0 2	3.5 3.5	0.0 0.00%
ModellerDescription ModellerDescription	14.0 14	4.785714 4.79	0.14553991 0.1455399114.6%
AMSAFile AMSAFile	4.0 4	3.5 3.5	0.18867925 0.1886792518.9%
JalviewFileChooser JalviewFileChooser	24.0 24	3.2083333 3.21	0.29520294 0.2952029429.5%
AppletFormatAdapter AppletFormatAdapter	19.0 19	4.5263157 4.53	0.3043478 0.304347830.4%
FormatAdapter FormatAdapter	17.0 17	1.7058823 1.71	0.46 0.4646%
FileParse FileParse	34.0 34	2.9705882 2.97	0.53203344 0.5320334453.2%
BioJsHTMLOutput BioJsHTMLOutput	14.0 14	2.5 2.5	0.576 0.57657.6%
FileFormat FileFormat	59.0 59	1.0169492 1.02	0.5813953 0.581395358.1%
HTMLOutput HTMLOutput	12.0 12	2.3333333 2.33	0.6 0.660%
IntKeyStringValueEntry IntKeyStringValueEntry	2.0 2	1.0 1	0.6 0.660%
NewickFile NewickFile	26.0 26	4.3076925 4.31	0.6096998 0.609699861%
FastaFile FastaFile	9.0 9	3.3333333 3.33	0.6216216 0.621621662.2%
FileLoader FileLoader	21.0 21	3.952381 3.95	0.638796 0.63879663.9%
JalviewFileView JalviewFileView	6.0 6	3.3333333 3.33	0.6506024 0.650602465.1%
BackupFilenameParts BackupFilenameParts	8.0 8	3.0 3	0.6621622 0.662162266.2%
BackupFiles BackupFiles	34.0 34	3.4117646 3.41	0.666 0.66666.6%
PIRFile PIRFile	5.0 5	4.8 4.8	0.6759259 0.675925967.6%
RnamlFile RnamlFile	9.0 9	2.7777777 2.78	0.6818182 0.681818268.2%
PDBFeatureSettings PDBFeatureSettings	4.0 4	2.25 2.25	0.71428573 0.7142857371.4%
FeaturesFile FeaturesFile	29.0 29	5.6551723 5.66	0.7195846 0.719584672%
TCoffeeScoreFile TCoffeeScoreFile	14.0 14	5.0 5	0.71984434 0.7198443472%
JalviewFileFilter JalviewFileFilter	14.0 14	2.5714285 2.57	0.7264151 0.726415172.6%
Jalview2xmlBase Jalview2xmlBase	5.0 5	2.2 2.2	0.73333335 0.7333333573.3%
StructureFile StructureFile	41.0 41	1.7073171 1.71	0.74883723 0.7488372374.9%
BLCFile BLCFile	6.0 6	5.6666665 5.67	0.7557252 0.755725275.6%
StockholmFile StockholmFile	17.0 17	10.411765 10.41	0.76336896 0.7633689676.3%
AnnotationFile AnnotationFile	26.0 26	11.461538 11.46	0.7713339 0.771333977.1%
IdentifyFile IdentifyFile	9.0 9	10.666667 10.67	0.7809524 0.780952478.1%
SequenceAnnotationReport SequenceAnnotationReport	13.0 13	7.0 7	0.78834355 0.7883435578.8%
HtmlSvgOutput HtmlSvgOutput	9.0 9	2.4444444 2.44	0.792 0.79279.2%
PhylipFile PhylipFile	7.0 7	3.7142856 3.71	0.8108108 0.810810881.1%
ClustalFile ClustalFile	6.0 6	6.1666665 6.17	0.821192 0.82119282.1%
EMBLLikeFlatFile EMBLLikeFlatFile	15.0 15	5.4 5.4	0.83286905 0.8328690583.3%
JSONFile JSONFile	25.0 25	4.4 4.4	0.8329718 0.832971883.3%
TCoffeeScoreFile.Header TCoffeeScoreFile.Header	2.0 2	1.5 1.5	0.8333333 0.833333383.3%
PfamFile PfamFile	6.0 6	4.1666665 4.17	0.83838385 0.8383838583.8%
AlignFile AlignFile	32.0 32	1.59375 1.59	0.84246576 0.8424657684.2%
JalviewFileChooser.recentlyOpenedCellRenderer JalviewFileChooser.recentlyOpenedCellRenderer	1.0 1	10.0 10	0.8695652 0.869565287%
GenBankFile GenBankFile	6.0 6	3.6666667 3.67	0.87341774 0.8734177487.3%
EmblFlatFile EmblFlatFile	6.0 6	4.0 4	0.8924731 0.892473189.2%
MSFfile MSFfile	6.0 6	8.166667 8.17	0.8967136 0.896713689.7%
BackupFilesPresetEntry BackupFilesPresetEntry	6.0 6	2.3333333 2.33	0.9117647 0.911764791.2%
PileUpfile PileUpfile	4.0 4	5.0 5	0.9222222 0.922222292.2%
BackupFilenameFilter BackupFilenameFilter	2.0 2	2.0 2	0.9285714 0.928571492.9%
JalviewFileChooser.RecentlyOpened JalviewFileChooser.RecentlyOpened	3.0 3	1.6666666 1.67	0.93333334 0.9333333493.3%
ScoreMatrixFile ScoreMatrixFile	9.0 9	5.7777777 5.78	0.959596 0.95959696%
FileFormats FileFormats	11.0 11	1.6363636 1.64	0.98 0.9898%
AnnotationFile.ViewDef AnnotationFile.ViewDef	1.0 1	1.0 1	1.0 1.0100%
DataSourceType DataSourceType	2.0 2	1.0 1	1.0 1.0100%
FileFormatException FileFormatException	1.0 1	1.0 1	1.0 1.0100%
TCoffeeScoreFile.Block TCoffeeScoreFile.Block	3.0 3	1.0 1	1.0 1.0100%