Suspect locations of potential for ConcurrentModificationException or similar: AAFrequency.java:484: for (SequenceI seq : alignment.getSequences()) AlignmentAnnotationUtils.java:84: for (AlignmentAnnotation aa : annotations) AlignmentAnnotationUtils.java:216: for (AlignmentAnnotation ann : annotations) AlignmentSorter.java:741: for (String label : labs) AlignmentUtils.java:121: for (SequenceI s : core.getSequences()) AlignmentUtils.java:225: for (SequenceI alSeq : al.getSequences()) AlignmentUtils.java:248: for (SequenceI seq : al.getSequences()) AlignmentUtils.java:324: for (SequenceI aaSeq : thisSeqs) AlignmentUtils.java:329: for (SequenceI cdnaSeq : cdnaAlignment.getSequences()) AlignmentUtils.java:390: for (AlignedCodonFrame acf : mappings) AlignmentUtils.java:600: for (AlignedCodonFrame mp : mappings) AlignmentUtils.java:896,907: for (SequenceI dnaSeq : dna.getSequences()) AlignmentUtils.java:943: for (AlignedCodonFrame mapping : dnaMappings) AlignmentUtils.java:1080: for (SequenceI dnaSeq : dna.getSequences()) AlignmentUtils.java:1082: for (AlignedCodonFrame mapping : mappings) AlignmentUtils.java:1127,1130: for (Entry> entry : alignedCodons AlignmentUtils.java:1211: for (SequenceI seq : protein.getSequences()) AlignmentUtils.java:1220: for (AlignedCodon codon : alignedCodons.keySet()) AlignmentUtils.java:1330,1332: for (SequenceI dnaSeq : dna.getSequences()) AlignmentUtils.java:1365: for (AlignedCodonFrame mapping : mappings) AlignmentUtils.java:1415: for (SequenceI seq : sequenceScope) AlignmentUtils.java:1428: for (AlignmentAnnotation dsann : datasetAnnotations) AlignmentUtils.java:1471,1473: for (SequenceI seq : annotations.keySet()) AlignmentUtils.java:1525: for (AlignmentAnnotation aa : anns) AlignmentUtils.java:1572: for (DBRefEntry xref : xrefs) AlignmentUtils.java:1989: for (DBRefEntry dbr : contig.getDBRefs()) AlignmentUtils.java:2077: for (SequenceFeature sf : sfs) AlignmentUtils.java:2214: for (SequenceFeature sf : sfs) AlignmentUtils.java:2550: for (SequenceFeature sf : dnaFeatures) AlignmentUtils.java:2661: for (SequenceI xref : xrefs) AlignmentUtils.java:2722: for (SequenceI seq : unaligned.getSequences()) AlignmentUtils.java:2790: for (SequenceI seq : aligned.getSequences()) AlignmentUtils.java:2804,2817: for (SequenceI seq : unaligned.getSequences()) AlignmentUtils.java:2860,2862: for (SequenceI seq : unaligned.getSequences()) AlignmentUtils.java:2974: for (SequenceI seq : alignment.getSequences()) AnnotationSorter.java:303: for (AlignmentAnnotation ann : alignmentAnnotations) CrossRef.java:486: for (SequenceI sq : dataset.getSequences()) CrossRef.java:625: for (SequenceFeature feat : sfs) CrossRef.java:741: for (SequenceI seq : dataset.getSequences()) CrossRef.java:1016: for (SequenceI nxt : ds) Dna.java:791: for (SequenceFeature sf : sfs) Grouping.java:61: for (SequenceGroup sg : list) Grouping.java:122: for (SequenceGroup sg : list) Grouping.java:138: for (Integer pos : cs.getSelected()) SequenceIdMatcher.java:55: for (SequenceI seq : seqs) appletgui/AlignFrame.java:927: for (AlignmentAnnotation aa : alignPanel.getAlignment() appletgui/AlignFrame.java:1896: for (int[] region : viewport.getColumnSelection().getHiddenColumns()) appletgui/AlignFrame.java:2326: for (SequenceGroup sg : viewport.getAlignment().getGroups()) appletgui/AlignmentPanel.java:921: for (SequenceI seq : seqs) appletgui/AnnotationColourChooser.java:82,513,546: for (SequenceGroup sg : ap.av.getAlignment().getGroups()) appletgui/AnnotationLabels.java:739: for (SequenceI sgs : aa[selectedRow].groupRef.getSequences()) appletgui/AnnotationPanel.java:166,188,212,272: for (int index : av.getColumnSelection().getSelected()) AppletJmol.java:382: for (String ch : chains) EditCommand.java:1218: for (Edit e : getEdits()) AlignViewController.java:116: for (SequenceI sq : gps[g].getSequences(null)) AlignViewController.java:238: for (SequenceI sq : seqs) AlignViewController.java:257: for (SequenceFeature sf : sfs) AlignedCodonFrame.java:many locations: for (SequenceToSequenceMapping ssm : mappings) AlignedCodonFrame.java:390,409: for (SequenceI sourceAligned : al.getSequences()) Alignment.java:791,1596,1626,1647: for (AlignmentAnnotation alan : getAlignmentAnnotation()) Alignment.java:1089: for (DBRefEntry dbr : curDs.getDBRefs()) Alignment.java:1136: for (AlignedCodonFrame cf : codonFrameList) Alignment.java:1407,1885,1904: for (AlignedCodonFrame acf : getCodonFrames()) Alignment.java:1519: for (SequenceGroup _sg : sg) Alignment.java:1850,1861: for (SequenceI seq : getSequences()) Alignment.java:1883: for (SequenceI seq : seqs) Alignment.java:1924: for (int[] hiddenCol : hiddenCols) AlignmentAnnotation.java:1267: for (Entry ie : sequenceMapping.entrySet()) ColumnSelection.java:973,1681,1721: for (int[] region : hiddenColumns) HiddenSequences.java:58,81: for (SequenceI seq : hiddenSequences) SearchResults.java:189,216,335,352: for (Match m : matches) Sequence.java:288,424: for (PDBEntry pdb : ids) Sequence.java:985,1255: for (DBRefEntryI dbr : dbrefs Sequence.java:1170,1378: for (AlignmentAnnotation aa : annotation) SequenceGroup.java:310: for (SequenceI seq : sequences) SequenceGroup.java:316: for (SequenceI seq2 : hsg.getSequences()) gui/AlignFrame.java:1584,2203: for (AlignmentPanel ap : alignPanels) gui/AlignFrame.java:1759,4092,5805: for (SequenceI seq : viewport.getAlignment().getSequences()) gui/AlignFrame.java:1893: for (int[] region : viewport.getColumnSelection().getHiddenColumns()) gui/AlignFrame.java:2068,5750: for (AlignmentAnnotation alan : alignment.getAlignmentAnnotation() gui/AlignFrame.java:3947: for (SequenceI _s : sg.getSequences()) gui/AlignmentPanel.java:1858: for (SequenceI seq : seqs) gui/AlignViewport.java:659: for (SequenceI sq : alignment.getSequences()) gui/AlignViewport.java:1074: for (AlignmentViewPanel ap : af.getAlignPanels()) gui/AnnotationColourChooser.java:81,382: for (SequenceGroup sg : ap.av.getAlignment().getGroups()) gui/AnnotationLabels.java:865: for (SequenceI sgs : aa[selectedRow].groupRef.getSequences()) gui/AnnotationLabels.java:992: for (int[] region : av.getColumnSelection().getHiddenColumns()) gui/AnnotationRowFilter.java:362: for (SequenceGroup sg : ap.av.getAlignment().getGroups()) Desktop.java:1745,1785: for (AlignmentPanel ap : af.alignPanels) gui/IdPanel.java:382: for (SequenceFeature sf : sfs) PopupMenu.java:335,362: for (final AlignmentAnnotation aa : aas) gui/ScalePanel.java:443: for (int[] region : av.getColumnSelection().getHiddenColumns()) StructureChooser.java:161,227,406,964: for (SequenceI seq : selectedSequences) StructureChooser.java:278: for (DBRefEntry dbRef : seq.getDBRefs()) TextColourChooser.java:218: for (SequenceGroup sg : ap.av.getAlignment().getGroups()) gui/TreeCanvas.java:1038: for (SequenceI seq : mappedGroup.getSequences()) VamsasApplication.java:1045: for (SequenceI sel : seqsel.getSequences(null)) AnnotationFile.java:1114,1601: for (SequenceGroup theGroup : al.getGroups()) FeaturesFile.java:587,780: for (SequenceFeature sequenceFeature : features) JSONFile.java:304: for (SequenceI hiddenSeq : hiddenSeqs) JSONFile.java:325: for (SequenceI seq : seqs) JSONFile.java:338: for (SequenceFeature sf : seqFeatures) JSONFile.java:753: for (AlignmentAnnotation annot : annots) PhylipFile.java:265,316: for (SequenceI s : seqs) SequenceAnnotationReport.java:372: for (DBRefEntry ref : dbrefs) VamsasAppDatastore.java:575: for (SequenceI jvalsq : av.getAlignment().getSequences()) ClustalxColourScheme.java:102: for (SequenceI sq : seqs) RNAHelicesColourChooser.java:61: for (SequenceGroup sg : ap.getAlignment().getGroups()) RNAHelicesColourChooser.java:125: for (SequenceGroup sg : ap.getAlignment().getGroups()) MappingUtils.java:110,451,478: for (SequenceI seq : mapTo.getSequences()) MappingUtils.java:329: for (SequenceI selected : sg.getSequences()) MappingUtils.java:368: for (SequenceI seq : mapTo.getAlignment().getSequences()) MappingUtils.java:539: for (int[] hidden : colsel.getHiddenColumns()) AlignmentViewport.java:638,1876,1838,2113,2186: for (SequenceGroup sg : getAlignment().getGroups()) AlignmentViewport.java:1507,1777,2022: for (AlignmentAnnotation ann : anns) AlignmentViewport.java:2190: for (SequenceI s : sg.getSequences(getHiddenRepSequences())) DBRefFetcher.java:712: for (SequenceFeature sf : sfs) AADisorderClient.java:182: for (AlignmentAnnotation ala : al.getAlignmentAnnotation() SiftsClient.java:444: for (DBRefEntry dbref : seq.getDBRefs()) PDBfile.java:238: for (SequenceI sq : seqs) PDBfile.java:242: for (AlignmentAnnotation aa : sq.getAnnotation())