Project	Packages	Average Method Complexity	TOTAL Coverage
Clover database Wed Dec 3 2025 17:03:17 GMT Clover database Wed Dec 3 2025 17:03:17 GMT	135.0 135	2.778177 2.78	0.40891525 0.4089152540.9%

Package	Files	Average Method Complexity	TOTAL Coverage
darrylbu.util darrylbu.util	1.0 1	2.7222223 2.72	0.0 0.00%
ext.edu.ucsf.rbvi.strucviz2 ext.edu.ucsf.rbvi.strucviz2	9.0 9	2.56383 2.56	0.0 0.00%
ext.edu.ucsf.rbvi.strucviz2.port ext.edu.ucsf.rbvi.strucviz2.port	1.0 1	3.0769231 3.08	0.0 0.00%
jalview.api jalview.api	31.0 31	1.0 1	0.0 0.00%
jalview.api.structures jalview.api.structures	1.0 1	1.0 1	0.0 0.00%
jalview.appletgui jalview.appletgui	42.0 42	3.3590307 3.36	0.0 0.00%
jalview.appletgui.js jalview.appletgui.js	6.0 6	3.92 3.92	0.0 0.00%
jalview.bin.groovy jalview.bin.groovy	2.0 2	1.75 1.75	0.0 0.00%
jalview.exceptions jalview.exceptions	1.0 1	1.0 1	0.0 0.00%
jalview.ext.paradise jalview.ext.paradise	1.0 1	1.2 1.2	0.0 0.00%
jalview.ext.varna jalview.ext.varna	3.0 3	7.3333335 7.33	0.0 0.00%
jalview.fts.service.alphafold jalview.fts.service.alphafold	1.0 1	2.8333333 2.83	0.0 0.00%
jalview.fts.service.uniprot jalview.fts.service.uniprot	2.0 2	2.6585367 2.66	0.0 0.00%
jalview.httpserver jalview.httpserver	2.0 2	1.8125 1.81	0.0 0.00%
jalview.io.exceptions jalview.io.exceptions	1.0 1	1.0 1	0.0 0.00%
jalview.io.packed jalview.io.packed	4.0 4	2.6785715 2.68	0.0 0.00%
jalview.io.vamsas jalview.io.vamsas	9.0 9	3.4782608 3.48	0.0 0.00%
jalview.javascript.json jalview.javascript.json	1.0 1	1.0 1	0.0 0.00%
jalview.javascript.web jalview.javascript.web	3.0 3	1.75 1.75	0.0 0.00%
jalview.rest jalview.rest	1.0 1	1.25 1.25	0.0 0.00%
jalview.util.dialogrunner jalview.util.dialogrunner	2.0 2	1.0 1	0.0 0.00%
jalview.ws.io.mime jalview.ws.io.mime	3.0 3	1.2222222 1.22	0.0 0.00%
jalview.ws.jws2.dm jalview.ws.jws2.dm	5.0 5	1.4324324 1.43	0.0 0.00%
jalview.ws.slivkaws jalview.ws.slivkaws	7.0 7	2.2592592 2.26	0.0 0.00%
jalview.ws2.actions.api jalview.ws2.actions.api	4.0 4	1.125 1.12	0.0 0.00%
org.stackoverflowusers.file org.stackoverflowusers.file	1.0 1	1.8333334 1.83	0.0 0.00%
swingjs.api swingjs.api	3.0 3	3.5 3.5	0.0 0.00%
swingjs.api.js swingjs.api.js	12.0 12	1.7833333 1.78	0.0 0.00%
uk.ac.ebi.picr.model uk.ac.ebi.picr.model	4.0 4	1.62 1.62	0.0 0.00%
uk.ac.ebi.www uk.ac.ebi.www	7.0 7	1.8395061 1.84	0.0 0.00%
uk.ac.ebi.www.picr.AccessionMappingService uk.ac.ebi.www.picr.AccessionMappingService	4.0 4	2.2608695 2.26	0.0 0.00%
vamsas.objects.simple vamsas.objects.simple	22.0 22	1.6068965 1.61	0.0 0.00%
jalview.hmmer jalview.hmmer	8.0 8	3.1232877 3.12	0.0028248588 0.00282485880.3%
jalview.ws.gui jalview.ws.gui	5.0 5	2.828125 2.83	0.0031796503 0.00317965030.3%
jalview.xml.binding.sifts jalview.xml.binding.sifts	4.0 4	1.0746269 1.07	0.0032467532 0.00324675320.3%
ext.vamsas ext.vamsas	18.0 18	2.1666667 2.17	0.03849115 0.038491153.8%
javajs.async javajs.async	7.0 7	2.2307692 2.23	0.044132397 0.0441323974.4%
jalview.ws.jws1 jalview.ws.jws1	11.0 11	3.3615384 3.36	0.052247874 0.0522478745.2%
jalview.ws2.params jalview.ws2.params	4.0 4	1.44 1.44	0.06557377 0.065573776.6%
jalview.ws.params jalview.ws.params	9.0 9	1.5 1.5	0.075 0.0757.5%
jalview.xml.binding.uniprot jalview.xml.binding.uniprot	37.0 37	1.2043269 1.2	0.07514945 0.075149457.5%
jalview.ws.sifts jalview.ws.sifts	4.0 4	2.2 2.2	0.082442746 0.0824427468.2%
org.json.simple org.json.simple	6.0 6	2.5873015 2.59	0.10193322 0.1019332210.2%
com.stevesoft.pat.wrap com.stevesoft.pat.wrap	6.0 6	1.4166666 1.42	0.105882354 0.10588235410.6%
jalview.ws.jws2.jabaws2 jalview.ws.jws2.jabaws2	9.0 9	3.4074075 3.41	0.12083333 0.1208333312.1%
jalview.ws2.actions.hmmer jalview.ws2.actions.hmmer	2.0 2	1.5833334 1.58	0.14666666 0.1466666614.7%
jalview.ws jalview.ws	11.0 11	3.6607144 3.66	0.14796548 0.1479654814.8%
junit.extensions junit.extensions	2.0 2	2.3 2.3	0.15120275 0.1512027515.1%
com.stevesoft.pat com.stevesoft.pat	77.0 77	5.1231027 5.12	0.15742412 0.1574241215.7%
org.json org.json	20.0 20	3.975352 3.98	0.1601683 0.160168316%
jalview.xml.binding.embl jalview.xml.binding.embl	5.0 5	1.1132076 1.11	0.17994858 0.1799485818%
jalview.ext.ensembl jalview.ext.ensembl	18.0 18	2.0677083 2.07	0.19192635 0.1919263519.2%
mc_view mc_view	10.0 10	4.016 4.02	0.19545859 0.1954585919.5%
jalview.ws.seqfetcher jalview.ws.seqfetcher	3.0 3	2.7083333 2.71	0.21755725 0.2175572521.8%
jalview.ws2.gui jalview.ws2.gui	4.0 4	3.680851 3.68	0.25662482 0.2566248225.7%
jalview.ws.jws2 jalview.ws.jws2	15.0 15	3.265823 3.27	0.27703065 0.2770306527.7%
jalview.ws2.actions.annotation jalview.ws2.actions.annotation	6.0 6	2.2045455 2.2	0.3084112 0.308411230.8%
jalview.ext.rbvi.chimera jalview.ext.rbvi.chimera	7.0 7	1.8414634 1.84	0.32920355 0.3292035532.9%
jalview.gui jalview.gui	100.0 100	2.871872 2.87	0.33490387 0.3349038733.5%
jalview.bin jalview.bin	21.0 21	4.211581 4.21	0.34617114 0.3461711434.6%
jalview.ws.rest.params jalview.ws.rest.params	7.0 7	2.2444444 2.24	0.35805628 0.3580562835.8%
jalview.ws.rest jalview.ws.rest	9.0 9	2.9375 2.94	0.3650895 0.365089536.5%
jalview.ws2.helpers jalview.ws2.helpers	3.0 3	1.1428572 1.14	0.39130434 0.3913043439.1%
jalview.ws.params.simple jalview.ws.params.simple	8.0 8	1.45 1.45	0.39764705 0.3976470539.8%
jalview.ws.ebi jalview.ws.ebi	3.0 3	3.9565217 3.96	0.40519482 0.4051948240.5%
jalview.ws.dbsources jalview.ws.dbsources	18.0 18	2.5481927 2.55	0.41575342 0.4157534241.6%
jalview.math jalview.math	7.0 7	3.0204082 3.02	0.42201835 0.4220183542.2%
jalview.controller jalview.controller	3.0 3	4.9333334 4.93	0.42711863 0.4271186342.7%
jalview.ws2.client.jpred4 jalview.ws2.client.jpred4	2.0 2	1.7222222 1.72	0.43269232 0.4326923243.3%
jalview.ext.pymol jalview.ext.pymol	2.0 2	2.3333333 2.33	0.4471831 0.447183144.7%
jalview.ws.api jalview.ws.api	14.0 14	1.4324324 1.43	0.45378152 0.4537815245.4%
org.jibble.epsgraphics org.jibble.epsgraphics	3.0 3	1.6944444 1.69	0.4610028 0.461002846.1%
org.json.simple.parser org.json.simple.parser	6.0 6	4.5208335 4.52	0.46751592 0.4675159246.8%
jalview.ext.android jalview.ext.android	4.0 4	2.265625 2.27	0.47048903 0.4704890347%
jalview.api.analysis jalview.api.analysis	3.0 3	1.0 1	0.5 0.550%
jalview.testutils jalview.testutils	4.0 4	1.625 1.62	0.51428574 0.5142857451.4%
jalview.fts.service.threedbeacons jalview.fts.service.threedbeacons	3.0 3	2.2105262 2.21	0.5145631 0.514563151.5%
jalview.ws.uimodel jalview.ws.uimodel	1.0 1	1.0 1	0.52 0.5252%
jalview.util jalview.util	48.0 48	3.525641 3.53	0.5235923 0.523592352.4%
jalview.ws2.client.ebi jalview.ws2.client.ebi	3.0 3	4.173913 4.17	0.5248869 0.524886952.5%
jalview.fts.service.pdb jalview.fts.service.pdb	2.0 2	3.0666666 3.07	0.5483871 0.548387154.8%
jalview.jbgui jalview.jbgui	24.0 24	1.2620838 1.26	0.5609364 0.560936456.1%
jalview.log jalview.log	4.0 4	1.7446809 1.74	0.5613208 0.561320856.1%
jalview.ext.htsjdk jalview.ext.htsjdk	2.0 2	2.347826 2.35	0.5792683 0.579268357.9%
jalview.fts.core jalview.fts.core	6.0 6	2.0496895 2.05	0.57929724 0.5792972457.9%
jalview.structure jalview.structure	20.0 20	2.6493506 2.65	0.5830462 0.583046258.3%
jalview.workers jalview.workers	13.0 13	2.4454546 2.45	0.5832402 0.583240258.3%
jalview.datamodel.annotations jalview.datamodel.annotations	3.0 3	1.1904762 1.19	0.5882353 0.588235358.8%
jalview.ws2.client.slivka jalview.ws2.client.slivka	3.0 3	2.6944444 2.69	0.5911111 0.591111159.1%
jalview.io jalview.io	63.0 63	3.9988263 4	0.5950802 0.595080259.5%
jalview.commands jalview.commands	9.0 9	4.4492755 4.45	0.59764916 0.5976491659.8%
jalview.ws2.actions jalview.ws2.actions	7.0 7	1.4155844 1.42	0.6 0.660%
jalview.renderer.seqfeatures jalview.renderer.seqfeatures	2.0 2	7.0 7	0.6044304 0.604430460.4%
jalview.ext.jmol jalview.ext.jmol	4.0 4	3.0086956 3.01	0.6120034 0.612003461.2%
jalview.structures.models jalview.structures.models	2.0 2	3.0705884 3.07	0.625 0.62562.5%
jalview.bin.argparser jalview.bin.argparser	9.0 9	3.0786026 3.08	0.6356011 0.635601163.6%
jalview.ws2.api jalview.ws2.api	5.0 5	1.3888888 1.39	0.6397059 0.639705964%
jalview.analytics jalview.analytics	1.0 1	2.8064516 2.81	0.663522 0.66352266.4%
jalview.renderer jalview.renderer	11.0 11	6.336735 6.34	0.67469877 0.6746987767.5%
jalview.analysis jalview.analysis	34.0 34	4.5659575 4.57	0.6814683 0.681468368.1%
jalview.io.vcf jalview.io.vcf	1.0 1	4.3714285 4.37	0.6992 0.699269.9%
jalview.io.cache jalview.io.cache	2.0 2	2.1333334 2.13	0.7048458 0.704845870.5%
jalview.gui.structurechooser jalview.gui.structurechooser	4.0 4	3.4363637 3.44	0.72129035 0.7212903572.1%
jalview.json.binding.biojs jalview.json.binding.biojs	2.0 2	1.125 1.12	0.73333335 0.7333333573.3%
jalview.datamodel jalview.datamodel	89.0 89	2.7276294 2.73	0.7390244 0.739024473.9%
jalview.project jalview.project	1.0 1	6.730769 6.73	0.7496974 0.749697475%
jalview.ws.utils jalview.ws.utils	1.0 1	1.3333334 1.33	0.75 0.7575%
jalview.json.binding.biojson.v1 jalview.json.binding.biojson.v1	8.0 8	1.2300885 1.23	0.7526502 0.752650275.3%
jalview.ws2.actions.secstructpred jalview.ws2.actions.secstructpred	4.0 4	2.1578948 2.16	0.7554348 0.755434875.5%
jalview.viewmodel jalview.viewmodel	9.0 9	1.8345679 1.83	0.7568282 0.756828275.7%
jalview.analysis.scoremodels jalview.analysis.scoremodels	9.0 9	2.5444446 2.54	0.7827815 0.782781578.3%
jalview.ws.datamodel.alphafold jalview.ws.datamodel.alphafold	2.0 2	2.725 2.72	0.78409094 0.7840909478.4%
jalview.xml.binding.jalview jalview.xml.binding.jalview	27.0 27	1.1163683 1.12	0.78486264 0.7848626478.5%
jalview.ws2.client.api jalview.ws2.client.api	7.0 7	2.3076923 2.31	0.8055556 0.805555680.6%
jalview.ws2.actions.alignment jalview.ws2.actions.alignment	5.0 5	2.173913 2.17	0.8088235 0.808823580.9%
jalview.viewmodel.seqfeatures jalview.viewmodel.seqfeatures	4.0 4	2.9041095 2.9	0.8307906 0.830790683.1%
jalview.ext.so jalview.ext.so	1.0 1	2.6111112 2.61	0.85 0.8585%
jalview.schemes jalview.schemes	41.0 41	2.139881 2.14	0.8645081 0.864508186.5%
jalview.urls jalview.urls	7.0 7	1.8901099 1.89	0.88123924 0.8812392488.1%
jalview.io.gff jalview.io.gff	11.0 11	4.0 4	0.8865132 0.886513288.7%
jalview.util.imagemaker jalview.util.imagemaker	1.0 1	1.2727273 1.27	0.9354839 0.935483993.5%
jalview.datamodel.features jalview.datamodel.features	13.0 13	2.8446603 2.84	0.94223106 0.9422310694.2%
jalview.util.matcher jalview.util.matcher	3.0 3	2.8947368 2.89	0.96666664 0.9666666496.7%
net.meyfa.sha256 net.meyfa.sha256	1.0 1	1.8 1.8	0.98734176 0.9873417698.7%
jalview.urls.applet jalview.urls.applet	1.0 1	1.0 1	1.0 1.0100%
jalview.urls.desktop jalview.urls.desktop	1.0 1	1.0 1	1.0 1.0100%
jalview.viewmodel.annotationfilter jalview.viewmodel.annotationfilter	1.0 1	1.0 1	1.0 1.0100%
jalview.viewmodel.styles jalview.viewmodel.styles	1.0 1	1.020202 1.02	1.0 1.0100%
jalview.ws.rest.clientdefs jalview.ws.rest.clientdefs	1.0 1	1.0 1	1.0 1.0100%