./ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java:129: for (ChimeraResidue residue : getResidues()) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java:152: for (ChimeraResidue residue : getResidues()) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java:70: for (ChimeraModel model : currentModelsMap.values()) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java:84: for (ChimeraModel model : currentModelsMap.values()) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java:130: for (ChimeraModel model : currentModelsMap.values()) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java:208: for (ChimeraModel newModel : getModelList()) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java:221: for (ChimeraModel chimeraModel : modelList) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java:367: for (String modelLine : chimeraReply) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java:392: for (String inputLine : chimeraReply) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java:411: for (String inputLine : chimeraReply) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java:440: for (String modelLine : list) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java:462: for (String preset : output) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java:512: for (String chimeraPath : chimeraPaths) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java:650: for (String inputLine : reply) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java:667: for (String inputLine : reply) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java:687: for (String inputLine : reply) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java:255: for (String residue : residues) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java:257: for (ChimeraChain chain : getChains()) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java:366: for (ChimeraChain chain : getChains()) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java:381: for (ChimeraChain chain : getChains()) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java:432: for (ChimeraChain chain : getChains()) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java:451: for (ChimeraChain chain : getChains()) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java:518: for (String cName : networkNames) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java:534: for (String cName : nodeNames) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraModel.java:550: for (String cName : edgeNames) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.java:137: for (ChimeraModel chimeraModel : chimeraManager.getChimeraModels()) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.java:176: for (ChimeraChain chimeraChain : chainList) ./ext/edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.java:207: for (ChimeraResidue res : sortedResidues) ./ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java:681: for (ChimeraModel model : models) ./ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java:798: for (String struct : structureNameMap.keySet()) ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:89: for (String chimObjName : names) ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:109: for (ChimeraModel currentModel : currentModels) ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:154: * for (CyIdentifiable cyObj : chimObjNames.keySet()) { // get possible res ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:163: * opened for (String chimObjName : chimObjNames.get(cyObj)) { // get or open ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:171: * // for each model for (ChimeraModel currentModel : currentModels) { // ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:176: * specsFound != null && specsFound.size() > 0) { for (String resSpec : ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:185: * rinNet.getNodeList().get(0), attrsFound); for (String resSpec : specsFound) ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:199: * specsFound.size() > 0) { for (String resSpec : specsFound) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:213: * be of length 1 for (CyNetwork net : potentialRINs) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:220: for (String modelName : chimObjNames) ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:224: for (ChimeraModel model : models) ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:260: // for (CyIdentifiable cyObj : model.getCyObjects().keySet()) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:266: // for (ChimeraResidue residue : model.getResidues()) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:268: // for (CyIdentifiable cyObjRes : currentChimMap.get(residue)) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:291: // for (CyNode node : rin.getNodeList()) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:299: // for (String residueSpec : specsFound) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:379: // for (CyIdentifiable currentCyObj : currentCyMap.keySet()) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:388: // for (CyNetwork network : currentCyNetworks) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:401: // for (ChimeraStructuralObject chimObj : chimSelectionList) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:412: // for (CyIdentifiable cyObj : currentCyObjs) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:421: // for (CyNetwork network : currentCyNetworks) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:433: // for (CyNetwork network : networks) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:436: // for (CyNetworkView view : views) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:451: // for (CyIdentifiable cyObj : currentCyMap.keySet()) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:456: // for (ChimeraStructuralObject chimObj : currentCyMap.get(cyObj)) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:471: // for (ChimeraResidue residue : ((ChimeraModel) chimObj) ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:526: for (ChimeraModel selectedModel : selectedModelsMap.values()) ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:545: for (ChimeraChain selectedChain : selectedModel.getChains()) ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:557: for (ChimeraResidue res : selectedChain.getResidues()) ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:586: for (ChimeraModel model : models) ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:588: for (ChimeraResidue residue : model.getFuncResidues()) ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:602: // for (ChimeraStructuralObject obj : chimObjects) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:605: // for (ChimeraResidue residue : model.getFuncResidues()) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:665: for (ChimeraStructuralObject cso : chimSelectionList) ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:693: for (ChimeraModel newModel : newModelList) ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:717: // for (CyIdentifiable cyObj : oldModelCyObjs.keySet()) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:741: // for (CyIdentifiable cyObj : newModel.getCyObjects().keySet()) { ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:818: for (ChimeraModel model : chimeraManager.getChimeraModels()) ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:822: for (ChimeraChain chain : model.getChains()) ./ext/edu/ucsf/rbvi/strucviz2/StructureManager.java:942: // for (CyTable table : manager.getGlobalTables()) { ./jalview/analysis/AAFrequency.java:484: for (SequenceI seq : alignment.getSequences()) ./jalview/analysis/AAFrequency.java:492: for (char[] codon : codons) ./jalview/analysis/AlignmentAnnotationUtils.java:84: for (AlignmentAnnotation aa : annotations) ./jalview/analysis/AlignmentAnnotationUtils.java:165: for (String calcId : groupLabels.keySet()) ./jalview/analysis/AlignmentAnnotationUtils.java:167: for (int group : groupLabels.get(calcId).keySet()) ./jalview/analysis/AlignmentAnnotationUtils.java:216: for (AlignmentAnnotation ann : annotations) ./jalview/analysis/AlignmentSorter.java:312: for (SequenceGroup sg : align.getGroups()) ./jalview/analysis/AlignmentSorter.java:741: for (String label : labs) ./jalview/analysis/AlignmentSorter.java:770: for (String label : featureLabels) ./jalview/analysis/AlignmentSorter.java:777: for (String label : groupLabels) ./jalview/analysis/AlignmentUtils.java:121: for (SequenceI s : core.getSequences()) ./jalview/analysis/AlignmentUtils.java:140: for (SequenceI s : sq) ./jalview/analysis/AlignmentUtils.java:198: for (SequenceI s : sq) ./jalview/analysis/AlignmentUtils.java:202: for (AlignmentAnnotation aa : s.getAnnotation()) ./jalview/analysis/AlignmentUtils.java:225: for (SequenceI alSeq : al.getSequences()) ./jalview/analysis/AlignmentUtils.java:248: for (SequenceI seq : al.getSequences()) ./jalview/analysis/AlignmentUtils.java:324: for (SequenceI aaSeq : thisSeqs) ./jalview/analysis/AlignmentUtils.java:329: for (SequenceI cdnaSeq : cdnaAlignment.getSequences()) ./jalview/analysis/AlignmentUtils.java:390: for (AlignedCodonFrame acf : mappings) ./jalview/analysis/AlignmentUtils.java:453: for (String stop : ResidueProperties.STOP) ./jalview/analysis/AlignmentUtils.java:600: for (AlignedCodonFrame mp : mappings) ./jalview/analysis/AlignmentUtils.java:659: for (char sourceChar : thatAligned) ./jalview/analysis/AlignmentUtils.java:896: for (SequenceI dnaSeq : dna.getSequences()) ./jalview/analysis/AlignmentUtils.java:907: for (SequenceI dnaSeq : dna.getSequences()) ./jalview/analysis/AlignmentUtils.java:943: for (AlignedCodonFrame mapping : dnaMappings) ./jalview/analysis/AlignmentUtils.java:991: for (char residue : alignedPeptide) ./jalview/analysis/AlignmentUtils.java:1080: for (SequenceI dnaSeq : dna.getSequences()) ./jalview/analysis/AlignmentUtils.java:1082: for (AlignedCodonFrame mapping : mappings) ./jalview/analysis/AlignmentUtils.java:1127: for (Entry> entry : alignedCodons ./jalview/analysis/AlignmentUtils.java:1130: for (Entry sequenceCodon : entry.getValue() ./jalview/analysis/AlignmentUtils.java:1181: for (Entry startCodon : toAdd.entrySet()) ./jalview/analysis/AlignmentUtils.java:1211: for (SequenceI seq : protein.getSequences()) ./jalview/analysis/AlignmentUtils.java:1220: for (AlignedCodon codon : alignedCodons.keySet()) ./jalview/analysis/AlignmentUtils.java:1224: for (Entry entry : columnResidues.entrySet()) ./jalview/analysis/AlignmentUtils.java:1330: for (SequenceI dnaSeq : dna.getSequences()) ./jalview/analysis/AlignmentUtils.java:1332: for (SequenceI proteinSeq : protein.getSequences()) ./jalview/analysis/AlignmentUtils.java:1365: for (AlignedCodonFrame mapping : mappings) ./jalview/analysis/AlignmentUtils.java:1415: for (SequenceI seq : sequenceScope) ./jalview/analysis/AlignmentUtils.java:1428: for (AlignmentAnnotation dsann : datasetAnnotations) ./jalview/analysis/AlignmentUtils.java:1471: for (SequenceI seq : annotations.keySet()) ./jalview/analysis/AlignmentUtils.java:1473: for (AlignmentAnnotation ann : annotations.get(seq)) ./jalview/analysis/AlignmentUtils.java:1525: for (AlignmentAnnotation aa : anns) ./jalview/analysis/AlignmentUtils.java:1572: for (DBRefEntry xref : xrefs) ./jalview/analysis/AlignmentUtils.java:1617: for (SequenceI seq : products) ./jalview/analysis/AlignmentUtils.java:1635: for (SequenceI dnaSeq : dna) ./jalview/analysis/AlignmentUtils.java:1642: for (AlignedCodonFrame mapping : seqMappings) ./jalview/analysis/AlignmentUtils.java:1647: for (Mapping aMapping : mappingsFromSequence) ./jalview/analysis/AlignmentUtils.java:1762: for (DBRefEntry primRef : dnaDss.getPrimaryDBRefs()) ./jalview/analysis/AlignmentUtils.java:1850: for (AlignedCodonFrame acf : mappingsToPeptide) ./jalview/analysis/AlignmentUtils.java:1852: for (SequenceToSequenceMapping map : acf.getMappings()) ./jalview/analysis/AlignmentUtils.java:1905: for (int[] range : fromRanges) ./jalview/analysis/AlignmentUtils.java:1938: for (SequenceI mtch : matches) ./jalview/analysis/AlignmentUtils.java:1989: for (DBRefEntry dbr : contig.getDBRefs()) ./jalview/analysis/AlignmentUtils.java:2009: for (DBRefEntry cdsref : direct) ./jalview/analysis/AlignmentUtils.java:2032: for (DBRefEntry srcref : sourceRefs) ./jalview/analysis/AlignmentUtils.java:2077: for (SequenceFeature sf : sfs) ./jalview/analysis/AlignmentUtils.java:2085: for (String toOmit : omitting) ./jalview/analysis/AlignmentUtils.java:2214: for (SequenceFeature sf : sfs) ./jalview/analysis/AlignmentUtils.java:2320: for (Entry[]> variant : variants.entrySet()) ./jalview/analysis/AlignmentUtils.java:2374: for (DnaVariant var : codonVariants[0]) ./jalview/analysis/AlignmentUtils.java:2381: for (String base : alleles.split(",")) ./jalview/analysis/AlignmentUtils.java:2396: for (DnaVariant var : codonVariants[1]) ./jalview/analysis/AlignmentUtils.java:2403: for (String base : alleles.split(",")) ./jalview/analysis/AlignmentUtils.java:2418: for (DnaVariant var : codonVariants[2]) ./jalview/analysis/AlignmentUtils.java:2425: for (String base : alleles.split(",")) ./jalview/analysis/AlignmentUtils.java:2550: for (SequenceFeature sf : dnaFeatures) ./jalview/analysis/AlignmentUtils.java:2587: for (String allele : alleles) ./jalview/analysis/AlignmentUtils.java:2661: for (SequenceI xref : xrefs) ./jalview/analysis/AlignmentUtils.java:2666: for (DBRefEntry dbref : dbrefs) ./jalview/analysis/AlignmentUtils.java:2722: for (SequenceI seq : unaligned.getSequences()) ./jalview/analysis/AlignmentUtils.java:2736: for (Integer column : columnMap.keySet()) ./jalview/analysis/AlignmentUtils.java:2790: for (SequenceI seq : aligned.getSequences()) ./jalview/analysis/AlignmentUtils.java:2804: for (SequenceI seq : unaligned.getSequences()) ./jalview/analysis/AlignmentUtils.java:2817: for (SequenceI seq : unaligned.getSequences()) ./jalview/analysis/AlignmentUtils.java:2860: for (SequenceI seq : unaligned.getSequences()) ./jalview/analysis/AlignmentUtils.java:2862: for (AlignedCodonFrame mapping : mappings) ./jalview/analysis/AlignmentUtils.java:2919: for (int[] fromRange : seqMap.getMap().getFromRanges()) ./jalview/analysis/AlignmentUtils.java:2974: for (SequenceI seq : alignment.getSequences()) ./jalview/analysis/AlignSeq.java:1064: for (Integer ip : as1) ./jalview/analysis/AlignSeq.java:1070: for (Integer ip : as2) ./jalview/analysis/AlignSeq.java:1112: for (SequenceI sq : ochains) ./jalview/analysis/AlignSeq.java:1117: for (SequenceI msq : al.getSequences()) ./jalview/analysis/AnnotationSorter.java:71: for (SequenceAnnotationOrder order : values()) ./jalview/analysis/AnnotationSorter.java:303: for (AlignmentAnnotation ann : alignmentAnnotations) ./jalview/analysis/Conservation.java:283: for (Entry> property : ResidueProperties.propHash ./jalview/analysis/Conservation.java:464: for (String type : resultHash.keySet()) ./jalview/analysis/CrossRef.java:103: for (SequenceI seq : fromSeqs) ./jalview/analysis/CrossRef.java:165: for (SequenceI rs : foundSeqs) ./jalview/analysis/CrossRef.java:185: for (DBRefEntry ref : xrefs) ./jalview/analysis/CrossRef.java:225: for (SequenceI seq : fromSeqs) ./jalview/analysis/CrossRef.java:437: for (SequenceI retrievedSequence : retrieved) ./jalview/analysis/CrossRef.java:451: for (SequenceI retrievedSequence : retrieved) ./jalview/analysis/CrossRef.java:461: for (SequenceI newToSeq : newDsSeqs) ./jalview/analysis/CrossRef.java:486: for (SequenceI sq : dataset.getSequences()) ./jalview/analysis/CrossRef.java:493: for (DBRefEntry dbr : sq.getPrimaryDBRefs()) ./jalview/analysis/CrossRef.java:495: for (DBRefEntry found : DBRefUtils.searchRefs(dbrSourceSet, dbr)) ./jalview/analysis/CrossRef.java:531: for (DBRefEntry dbref : dbr) ./jalview/analysis/CrossRef.java:598: for (DBRefEntry ref : toRefs) ./jalview/analysis/CrossRef.java:625: for (SequenceFeature feat : sfs) ./jalview/analysis/CrossRef.java:693: for (DBRefEntry toRef : dbrefs) ./jalview/analysis/CrossRef.java:741: for (SequenceI seq : dataset.getSequences()) ./jalview/analysis/CrossRef.java:823: for (DBRefEntry xref : xrefs) ./jalview/analysis/CrossRef.java:834: for (SequenceI seq : matches) ./jalview/analysis/CrossRef.java:876: for (DBRefEntry dbref : dsmapTo.getDBRefs()) ./jalview/analysis/CrossRef.java:1016: for (SequenceI nxt : ds) ./jalview/analysis/CrossRef.java:1074: for (DBRefEntry candidate : cands) ./jalview/analysis/Dna.java:264: for (AlignmentAnnotation annotation : annotations) ./jalview/analysis/Dna.java:719: for (SequenceI seq : proteinSeqs) ./jalview/analysis/Dna.java:791: for (SequenceFeature sf : sfs) ./jalview/analysis/Grouping.java:61: for (SequenceGroup sg : list) ./jalview/analysis/Grouping.java:63: for (SequenceI sq : sg.getSequences(null)) ./jalview/analysis/Grouping.java:92: for (String key : gps.keySet()) ./jalview/analysis/Grouping.java:122: for (SequenceGroup sg : list) ./jalview/analysis/Grouping.java:124: for (SequenceI sq : sg.getSequences(null)) ./jalview/analysis/Grouping.java:138: for (Integer pos : cs.getSelected()) ./jalview/analysis/Grouping.java:157: for (int p : spos) ./jalview/analysis/Grouping.java:179: for (String key : gps.keySet()) ./jalview/analysis/Rna.java:180: for (char opening : stacks.keySet()) ./jalview/analysis/scoremodels/FeatureScoreModel.java:57: for (float[] d : distance) ./jalview/analysis/scoremodels/FeatureScoreModel.java:85: for (SequenceFeature sf : sfs) ./jalview/analysis/scoremodels/FeatureScoreModel.java:113: for (String k : fi.keySet()) ./jalview/analysis/SecStrConsensus.java:84: for (ArrayList strs : bps) ./jalview/analysis/SecStrConsensus.java:86: for (SimpleBP bp : strs) ./jalview/analysis/SecStrConsensus.java:100: for (ArrayList strs : bps) ./jalview/analysis/SecStrConsensus.java:102: for (SimpleBP bp : strs) ./jalview/analysis/SecStrConsensus.java:131: for (SimpleBP bp : res) ./jalview/analysis/SecStrConsensus.java:210: for (int k : indices) ./jalview/analysis/SequenceIdMatcher.java:55: for (SequenceI seq : seqs) ./jalview/analysis/StructureFrequency.java:477: for (String i : test) ./jalview/analysis/StructureFrequency.java:479: for (String j : test) ./jalview/appletgui/AlignFrame.java:927: for (AlignmentAnnotation aa : alignPanel.getAlignment() ./jalview/appletgui/AlignFrame.java:1896: for (int[] region : viewport.getColumnSelection().getHiddenColumns()) ./jalview/appletgui/AlignFrame.java:2326: for (SequenceGroup sg : viewport.getAlignment().getGroups()) ./jalview/appletgui/AlignmentPanel.java:921: for (SequenceI seq : seqs) ./jalview/appletgui/AnnotationColourChooser.java:82: for (SequenceGroup sg : ap.av.getAlignment().getGroups()) ./jalview/appletgui/AnnotationColourChooser.java:513: for (SequenceGroup sg : ap.av.getAlignment().getGroups()) ./jalview/appletgui/AnnotationColourChooser.java:546: for (SequenceGroup sg : ap.av.getAlignment().getGroups()) ./jalview/appletgui/AnnotationLabels.java:739: for (SequenceI sgs : aa[selectedRow].groupRef.getSequences()) ./jalview/appletgui/AnnotationLabels.java:841: for (int[] region : av.getColumnSelection().getHiddenColumns()) ./jalview/appletgui/AnnotationPanel.java:166: for (int index : av.getColumnSelection().getSelected()) ./jalview/appletgui/AnnotationPanel.java:188: for (int index : av.getColumnSelection().getSelected()) ./jalview/appletgui/AnnotationPanel.java:212: for (int index : av.getColumnSelection().getSelected()) ./jalview/appletgui/AnnotationPanel.java:272: for (int index : av.getColumnSelection().getSelected()) ./jalview/appletgui/APopupMenu.java:314: for (String link : links) ./jalview/appletgui/APopupMenu.java:361: for (List linkstrset : linkset) ./jalview/appletgui/APopupMenu.java:806: for (SequenceI seq : sequences) ./jalview/appletgui/APopupMenu.java:1298: for (String calcId : hiddenTypes.keySet()) ./jalview/appletgui/APopupMenu.java:1300: for (List type : hiddenTypes.get(calcId)) ./jalview/appletgui/APopupMenu.java:1309: for (String calcId : shownTypes.keySet()) ./jalview/appletgui/APopupMenu.java:1311: for (List type : shownTypes.get(calcId)) ./jalview/appletgui/AppletJmol.java:382: for (String ch : chains) ./jalview/appletgui/EmbmenuFrame.java:250: for (Label lb : embeddedPopup.keySet()) ./jalview/appletgui/FeatureSettings.java:352: for (String group : fr.getFeatureGroups()) ./jalview/appletgui/ScalePanel.java:374: for (int[] region : av.getColumnSelection().getHiddenColumns()) ./jalview/appletgui/ScalePanel.java:417: for (int sel : cs.getSelected()) ./jalview/appletgui/ScalePanel.java:452: for (ScaleMark mark : marks) ./jalview/appletgui/SeqCanvas.java:97: for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx, ./jalview/appletgui/SeqCanvas.java:553: for (int[] region : av.getColumnSelection().getHiddenColumns()) ./jalview/appletgui/SeqPanel.java:470: for (Match m : results.getResults()) ./jalview/appletgui/SeqPanel.java:1179: for (SequenceI gs : groupSeqs) ./jalview/appletgui/SeqPanel.java:1237: for (SequenceI gs : groupSeqs) ./jalview/appletgui/TreeCanvas.java:702: for (SequenceI seq : mappedGroup.getSequences()) ./jalview/bin/JalviewLite.java:471: for (Integer selectedCol : cs) ./jalview/commands/ChangeCaseCommand.java:79: for (int[] r : regions) ./jalview/commands/EditCommand.java:1218: for (Edit e : getEdits()) ./jalview/commands/EditCommand.java:1220: for (SequenceI seq : e.getSequences()) ./jalview/commands/EditCommand.java:1252: for (SequenceI seq : oldEdit.getSequences()) ./jalview/controller/AlignViewController.java:116: for (SequenceI sq : gps[g].getSequences(null)) ./jalview/controller/AlignViewController.java:238: for (SequenceI sq : seqs) ./jalview/controller/AlignViewController.java:257: for (SequenceFeature sf : sfs) ./jalview/datamodel/AlignedCodonFrame.java:160: for (SequenceToSequenceMapping ssm : mappings) ./jalview/datamodel/AlignedCodonFrame.java:182: for (SequenceToSequenceMapping ssm : mappings) ./jalview/datamodel/AlignedCodonFrame.java:193: for (SequenceToSequenceMapping ssm : mappings) ./jalview/datamodel/AlignedCodonFrame.java:203: for (SequenceToSequenceMapping ssm : mappings) ./jalview/datamodel/AlignedCodonFrame.java:213: for (SequenceToSequenceMapping ssm : mappings) ./jalview/datamodel/AlignedCodonFrame.java:232: for (SequenceToSequenceMapping ssm : mappings) ./jalview/datamodel/AlignedCodonFrame.java:252: for (SequenceToSequenceMapping ssm : mappings) ./jalview/datamodel/AlignedCodonFrame.java:270: for (SequenceToSequenceMapping ssm : mappings) ./jalview/datamodel/AlignedCodonFrame.java:308: for (SequenceToSequenceMapping ssm : mappings) ./jalview/datamodel/AlignedCodonFrame.java:359: for (SequenceToSequenceMapping ssm : mappings) ./jalview/datamodel/AlignedCodonFrame.java:386: for (SequenceToSequenceMapping ssm : mappings) ./jalview/datamodel/AlignedCodonFrame.java:390: for (SequenceI sourceAligned : al.getSequences()) ./jalview/datamodel/AlignedCodonFrame.java:404: for (SequenceToSequenceMapping ssm : mappings) ./jalview/datamodel/AlignedCodonFrame.java:409: for (SequenceI sourceAligned : al.getSequences()) ./jalview/datamodel/AlignedCodonFrame.java:443: for (SequenceToSequenceMapping ssm : mappings) ./jalview/datamodel/AlignedCodonFrame.java:489: for (SequenceToSequenceMapping ssm : mappings) ./jalview/datamodel/AlignedCodonFrame.java:530: for (SequenceToSequenceMapping ssm : mappings) ./jalview/datamodel/AlignedCodonFrame.java:589: for (SequenceToSequenceMapping ssm : mappings) ./jalview/datamodel/AlignedCodonFrame.java:682: for (SequenceToSequenceMapping ssm : mappings) ./jalview/datamodel/AlignedCodonFrame.java:738: for (SequenceToSequenceMapping mapping : mappings) ./jalview/datamodel/Alignment.java:521: for (SequenceGroup sg : groups) ./jalview/datamodel/Alignment.java:723: for (SequenceI seq : sequences) ./jalview/datamodel/Alignment.java:791: for (AlignmentAnnotation alan : getAlignmentAnnotation()) ./jalview/datamodel/Alignment.java:1089: for (DBRefEntry dbr : curDs.getDBRefs()) ./jalview/datamodel/Alignment.java:1136: for (AlignedCodonFrame cf : codonFrameList) ./jalview/datamodel/Alignment.java:1138: for (SequenceToSequenceMapping ssm : cf.getMappings()) ./jalview/datamodel/Alignment.java:1339: for (SequenceI seq : sequences) ./jalview/datamodel/Alignment.java:1407: for (AlignedCodonFrame acf : getCodonFrames()) ./jalview/datamodel/Alignment.java:1486: for (SequenceI addedsq : sqs) ./jalview/datamodel/Alignment.java:1502: for (SequenceI addedsq : toappendsq) ./jalview/datamodel/Alignment.java:1519: for (SequenceGroup _sg : sg) ./jalview/datamodel/Alignment.java:1596: for (AlignmentAnnotation annot : getAlignmentAnnotation()) ./jalview/datamodel/Alignment.java:1626: for (AlignmentAnnotation a : getAlignmentAnnotation()) ./jalview/datamodel/Alignment.java:1647: for (AlignmentAnnotation ann : getAlignmentAnnotation()) ./jalview/datamodel/Alignment.java:1850: for (SequenceI seq : getSequences()) ./jalview/datamodel/Alignment.java:1861: for (SequenceI seq : getSequences()) ./jalview/datamodel/Alignment.java:1883: for (SequenceI seq : seqs) ./jalview/datamodel/Alignment.java:1885: for (AlignedCodonFrame mapping : getCodonFrames()) ./jalview/datamodel/Alignment.java:1904: for (AlignedCodonFrame acf : getCodonFrames()) ./jalview/datamodel/Alignment.java:1924: for (int[] hiddenCol : hiddenCols) ./jalview/datamodel/AlignmentAnnotation.java:701: for (Map.Entry val : annotation.properties.entrySet()) ./jalview/datamodel/AlignmentAnnotation.java:1267: for (Entry ie : sequenceMapping.entrySet()) ./jalview/datamodel/AlignmentAnnotation.java:1317: for (int mp[] : mapping.values()) ./jalview/datamodel/AlignmentOrder.java:85: for (SequenceI seq : orderFrom.getSequences()) ./jalview/datamodel/AlignmentView.java:189: for (SequenceGroup sg : grps) ./jalview/datamodel/AlignmentView.java:1127: for (SequenceGroup sg : visal.getGroups()) ./jalview/datamodel/ColumnSelection.java:812: for (int[] selregions : selection.getRanges()) ./jalview/datamodel/ColumnSelection.java:973: for (int[] region : hiddenColumns) ./jalview/datamodel/ColumnSelection.java:1314: for (Annotation[] chnk : annels) ./jalview/datamodel/ColumnSelection.java:1363: for (Integer col : colsel.getSelected()) ./jalview/datamodel/ColumnSelection.java:1392: for (Integer col : colsel.getSelected()) ./jalview/datamodel/ColumnSelection.java:1579: for (int[] r : inserts) ./jalview/datamodel/ColumnSelection.java:1681: for (int[] hidden : hiddenColumns) ./jalview/datamodel/ColumnSelection.java:1731: for (int[] thisRange : hiddenColumns) ./jalview/datamodel/DBRefEntry.java:322: for (String primsrc : Arrays.asList(DBRefSource.allSources())) ./jalview/datamodel/DBRefSource.java:109: for (Field f : DBRefSource.class.getFields()) ./jalview/datamodel/HiddenSequences.java:58: for (SequenceI seq : hiddenSequences) ./jalview/datamodel/HiddenSequences.java:81: for (SequenceI seq : hiddenSequences) ./jalview/datamodel/HiddenSequences.java:179: for (SequenceI seq : tmp) ./jalview/datamodel/PDBEntry.java:58: for (Type t : Type.values()) ./jalview/datamodel/SearchResults.java:189: for (Match m : matches) ./jalview/datamodel/SearchResults.java:216: for (Match m : matches) ./jalview/datamodel/SearchResults.java:335: for (Match m : matches) ./jalview/datamodel/SearchResults.java:352: for (Match m : matches) ./jalview/datamodel/Sequence.java:288: for (PDBEntry pdb : ids) ./jalview/datamodel/Sequence.java:424: for (PDBEntry pdbe : pdbIds) ./jalview/datamodel/Sequence.java:985: for (DBRefEntryI dbr : dbrefs) ./jalview/datamodel/Sequence.java:1170: for (AlignmentAnnotation aa : annotation) ./jalview/datamodel/Sequence.java:1255: for (DBRefEntry dbr : dbrefs) ./jalview/datamodel/Sequence.java:1378: for (AlignmentAnnotation ann : annotation) ./jalview/datamodel/Sequence.java:1408: for (PDBEntry entry : entries) ./jalview/datamodel/Sequence.java:1433: for (DBRefEntry ref : dbrefs) ./jalview/datamodel/SequenceGroup.java:310: for (SequenceI seq : sequences) ./jalview/datamodel/SequenceGroup.java:316: for (SequenceI seq2 : hsg.getSequences()) ./jalview/datamodel/SequenceGroup.java:801: for (SequenceI seq : sequences) ./jalview/datamodel/SequenceGroup.java:1243: for (SequenceI seq : sequences) ./jalview/datamodel/SequenceGroup.java:1248: for (AlignmentAnnotation al : aa) ./jalview/datamodel/SequenceGroup.java:1273: for (AlignmentAnnotation a : getAlignmentAnnotation()) ./jalview/datamodel/SequenceGroup.java:1294: for (AlignmentAnnotation ann : getAlignmentAnnotation()) ./jalview/datamodel/SequenceGroup.java:1316: for (AlignmentAnnotation a : getAlignmentAnnotation()) ./jalview/datamodel/xdb/embl/EmblEntry.java:207: for (DBRefEntry dbref : dbRefs) ./jalview/datamodel/xdb/embl/EmblEntry.java:217: for (EmblFeature feature : features) ./jalview/datamodel/xdb/embl/EmblEntry.java:293: for (Qualifier q : feature.getQualifiers()) ./jalview/datamodel/xdb/embl/EmblEntry.java:464: for (DBRefEntry ref : feature.dbRefs) ./jalview/datamodel/xdb/embl/EmblEntry.java:597: for (Entry val : vals.entrySet()) ./jalview/datamodel/xdb/embl/EmblEntry.java:650: for (int[] range : ranges) ./jalview/datamodel/xdb/embl/EmblFile.java:161: for (EmblEntry entry : record.getEntries()) ./jalview/datamodel/xdb/embl/EmblFile.java:165: for (DBRefEntry dbref : entry.getDbRefs()) ./jalview/datamodel/xdb/embl/EmblFile.java:176: for (EmblFeature feature : entry.getFeatures()) ./jalview/datamodel/xdb/embl/EmblFile.java:180: for (DBRefEntry dbref : feature.getDbRefs()) ./jalview/ext/ensembl/EnsemblFeatures.java:112: for (EnsemblFeatureType feature : featuresWanted) ./jalview/ext/ensembl/EnsemblGene.java:135: for (String geneId : geneIds) ./jalview/ext/ensembl/EnsemblGene.java:172: for (String acc : accessions.split(getAccessionSeparator())) ./jalview/ext/ensembl/EnsemblGene.java:202: for (String geneId : ids) ./jalview/ext/ensembl/EnsemblGene.java:227: for (String id : ids) ./jalview/ext/ensembl/EnsemblGene.java:254: for (SequenceFeature transcriptFeature : transcriptFeatures) ./jalview/ext/ensembl/EnsemblGene.java:275: for (SequenceFeature sf : sfs) ./jalview/ext/ensembl/EnsemblGene.java:341: for (SequenceFeature sf : splices) ./jalview/ext/ensembl/EnsemblGene.java:429: for (SequenceFeature sf : sfs) ./jalview/ext/ensembl/EnsemblRestClient.java:447: for (String id : ids) ./jalview/ext/ensembl/EnsemblSeqProxy.java:197: for (String accId : allIds) ./jalview/ext/ensembl/EnsemblSeqProxy.java:202: for (SequenceI seq : alignment.getSequences()) ./jalview/ext/ensembl/EnsemblSeqProxy.java:314: for (DBRefEntry up : uprots) ./jalview/ext/ensembl/EnsemblSeqProxy.java:378: for (DBRefEntry xref : xrefs) ./jalview/ext/ensembl/EnsemblSeqProxy.java:440: for (SequenceI sq : seqal.getSequences()) ./jalview/ext/ensembl/EnsemblSeqProxy.java:573: for (SequenceFeature sf : sfs) ./jalview/ext/ensembl/EnsemblSeqProxy.java:716: for (String allele : alleles.split(",")) ./jalview/ext/ensembl/EnsemblSeqProxy.java:827: for (SequenceFeature sf : features) ./jalview/ext/ensembl/EnsemblSeqProxy.java:924: for (SequenceFeature sf : sfs) ./jalview/ext/ensembl/EnsemblSymbol.java:121: for (String query : queries) ./jalview/ext/ensembl/EnsemblSymbol.java:123: for (Species taxon : Species.values()) ./jalview/ext/jmol/JalviewJmolBinding.java:147: for (String lbl : chainList) ./jalview/ext/jmol/JalviewJmolBinding.java:340: for (boolean b : matched) ./jalview/ext/jmol/JalviewJmolBinding.java:519: for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands( ./jalview/ext/jmol/JalviewJmolBinding.java:522: for (String cbyseq : cpdbbyseq.commands) ./jalview/ext/jmol/JalviewJmolBinding.java:755: for (AtomSpec atom : atoms) ./jalview/ext/jmol/JalviewJmolBinding.java:1305: for (String res : residueSet) ./jalview/ext/jmol/JmolParser.java:165: for (Atom tmpatom : significantAtoms) ./jalview/ext/jmol/JmolParser.java:189: for (PDBChain chain : getChains()) ./jalview/ext/jmol/JmolParser.java:221: for (org.jmol.modelset.Atom atom : ms.at) ./jalview/ext/jmol/JmolParser.java:324: for (Residue residue : chain.residues) ./jalview/ext/rbvi/chimera/ChimeraCommands.java:99: for (Color colour : colourMap.keySet()) ./jalview/ext/rbvi/chimera/ChimeraCommands.java:111: for (Integer model : colourData.keySet()) ./jalview/ext/rbvi/chimera/ChimeraCommands.java:122: for (String chain : modelData.keySet()) ./jalview/ext/rbvi/chimera/ChimeraCommands.java:125: for (int[] range : modelData.get(chain)) ./jalview/ext/rbvi/chimera/JalviewChimeraBinding.java:138: for (ChimeraModel open : oldList) ./jalview/ext/rbvi/chimera/JalviewChimeraBinding.java:156: for (ChimeraModel cm : newList) ./jalview/ext/rbvi/chimera/JalviewChimeraBinding.java:248: for (String chain : toshow) ./jalview/ext/rbvi/chimera/JalviewChimeraBinding.java:387: for (boolean b : matched) ./jalview/ext/rbvi/chimera/JalviewChimeraBinding.java:665: for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands( ./jalview/ext/rbvi/chimera/JalviewChimeraBinding.java:668: for (String command : cpdbbyseq.commands) ./jalview/ext/rbvi/chimera/JalviewChimeraBinding.java:800: for (AtomSpec atom : atoms) ./jalview/ext/rbvi/chimera/JalviewChimeraBinding.java:865: for (String atomSpec : selection) ./jalview/ext/rbvi/chimera/JalviewChimeraBinding.java:898: findfileloop: for (String pdbfile : this.chimeraMaps.keySet()) ./jalview/ext/rbvi/chimera/JalviewChimeraBinding.java:900: for (ChimeraModel cm : chimeraMaps.get(pdbfile)) ./jalview/ext/rbvi/chimera/JalviewChimeraBinding.java:951: for (String res : residueSet) ./jalview/ext/rbvi/chimera/JalviewChimeraBinding.java:1086: for (SequenceI seq : alignment.getSequences()) ./jalview/ext/rbvi/chimera/JalviewChimeraBinding.java:1093: for (Integer col : cols) ./jalview/ext/so/SequenceOntology.java:172: for (Term term : ontology.getTerms()) ./jalview/ext/so/SequenceOntology.java:380: for (Term parent : parents) ./jalview/ext/so/SequenceOntology.java:408: for (Triple triple : ontology.getTriples(childTerm, null, isA)) ./jalview/fts/core/FTSDataColumnPreferences.java:102: for (FTSDataColumnI field : allFTSDataColumns) ./jalview/fts/core/FTSRestClient.java:337: for (FTSDataColumnI field : wantedFields) ./jalview/fts/core/FTSRestClient.java:356: for (FTSDataColumnI field : dataColumnFields) ./jalview/fts/core/FTSRestClient.java:416: for (FTSDataColumnI column : dataColumns) ./jalview/fts/core/FTSRestClient.java:436: for (FTSDataColumnGroupI columnGroup : dataColumnGroups) ./jalview/fts/core/FTSRestResponse.java:121: for (FTSDataColumnI field : request.getWantedFields()) ./jalview/fts/core/FTSRestResponse.java:127: for (FTSData res : summariesList) ./jalview/fts/core/FTSRestResponse.java:140: for (FTSDataColumnI wantedField : wantedFields) ./jalview/fts/core/GFTSPanel.java:810: for (FTSDataColumnI searchTarget : searchableTargets) ./jalview/fts/core/GFTSPanel.java:926: for (int summaryRow : selectedRows) ./jalview/fts/service/pdb/PDBFTSPanel.java:158: for (String searchTerm : searchTerms) ./jalview/fts/service/pdb/PDBFTSPanel.java:204: for (int summaryRow : selectedRows) ./jalview/fts/service/pdb/PDBFTSPanel.java:211: for (String idStr : paginatorCart) ./jalview/fts/service/pdb/PDBFTSPanel.java:216: for (String selectedId : selectedIdsSet) ./jalview/fts/service/pdb/PDBFTSPanel.java:236: for (String foundTerm : foundTerms) ./jalview/fts/service/pdb/PDBFTSRestClient.java:310: for (FTSDataColumnI field : diplayFields) ./jalview/fts/service/pdb/PDBFTSRestClient.java:364: for (Object summaryField : summaryRowData1) ./jalview/fts/service/uniprot/UniprotFTSPanel.java:162: for (String searchTerm : searchTerms) ./jalview/fts/service/uniprot/UniprotFTSPanel.java:200: for (int summaryRow : selectedRows) ./jalview/fts/service/uniprot/UniprotFTSPanel.java:207: for (String selectedId : selectedIdsSet) ./jalview/fts/service/uniprot/UniProtFTSRestClient.java:163: for (String dataRow : foundDataRow) ./jalview/fts/service/uniprot/UniProtFTSRestClient.java:195: for (FTSDataColumnI field : dataColumnFields) ./jalview/fts/service/uniprot/UniProtFTSRestClient.java:223: for (FTSDataColumnI field : diplayFields) ./jalview/fts/service/uniprot/UniProtFTSRestClient.java:282: for (Object summaryField : summaryRowData1) ./jalview/gui/AlignFrame.java:1584: for (AlignmentPanel ap : alignPanels) ./jalview/gui/AlignFrame.java:1689: for (Component comp : comps) ./jalview/gui/AlignFrame.java:1759: for (SequenceI seq : viewport.getAlignment().getSequences()) ./jalview/gui/AlignFrame.java:1893: for (int[] region : viewport.getColumnSelection().getHiddenColumns()) ./jalview/gui/AlignFrame.java:2068: for (AlignmentAnnotation alan : alignment ./jalview/gui/AlignFrame.java:2203: for (AlignmentPanel ap : alignPanels) ./jalview/gui/AlignFrame.java:2224: for (int[] region : hc) ./jalview/gui/AlignFrame.java:2284: for (int region[] : hc) ./jalview/gui/AlignFrame.java:2580: for (SequenceGroup sg : viewport.getAlignment().getGroups()) ./jalview/gui/AlignFrame.java:2822: for (Component comp : comps) ./jalview/gui/AlignFrame.java:3947: for (SequenceI _s : sg.getSequences()) ./jalview/gui/AlignFrame.java:4092: for (SequenceI sqa : viewport.getAlignment().getSequences()) ./jalview/gui/AlignFrame.java:4135: for (final String type : new String[] { "NJ", "AV" }) ./jalview/gui/AlignFrame.java:4139: for (final String pwtype : ResidueProperties.scoreMatrices.keySet()) ./jalview/gui/AlignFrame.java:4170: for (Component comp : comps) ./jalview/gui/AlignFrame.java:4186: for (final TreePanel tp : treePanels) ./jalview/gui/AlignFrame.java:4543: for (Jws2Instance sv : jws2servs.getServices()) ./jalview/gui/AlignFrame.java:4547: for (JMenuItem jmi : legacyItems) ./jalview/gui/AlignFrame.java:4566: for (JMenu item : wsmenu) ./jalview/gui/AlignFrame.java:4619: for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient ./jalview/gui/AlignFrame.java:4656: for (final String source : ptypes) ./jalview/gui/AlignFrame.java:4921: for (Object[] fm : filesmatched) ./jalview/gui/AlignFrame.java:4926: for (SequenceI toassoc : (SequenceI[]) fm[2]) ./jalview/gui/AlignFrame.java:4967: for (String fn : filesnotmatched) ./jalview/gui/AlignFrame.java:5334: for (String dbclass : dbclasses) ./jalview/gui/AlignFrame.java:5460: for (DbSourceProxy sproxy : otherdb) ./jalview/gui/AlignFrame.java:5750: for (AlignmentAnnotation aa : anns) ./jalview/gui/AlignFrame.java:5805: for (SequenceI aaSeq : alignment.getSequences()) ./jalview/gui/AlignFrame.java:5807: for (AlignedCodonFrame acf : mappings) ./jalview/gui/AlignmentPanel.java:1858: for (SequenceI seq : seqs) ./jalview/gui/AlignViewport.java:454: for (AlignedCodonFrame acf : mappings) ./jalview/gui/AlignViewport.java:656: for (PDBEntry pdb : pdbEntries) ./jalview/gui/AlignViewport.java:659: for (SequenceI sq : alignment.getSequences()) ./jalview/gui/AlignViewport.java:667: for (PDBEntry pdbRefEntry : pdbRefEntries) ./jalview/gui/AlignViewport.java:1070: for (AlignFrame af : frames) ./jalview/gui/AlignViewport.java:1074: for (AlignmentViewPanel ap : af.getAlignPanels()) ./jalview/gui/AlignViewport.java:1115: for (String type : renderOrder) ./jalview/gui/AlignViewport.java:1132: for (String group : fr.getFeatureGroups()) ./jalview/gui/AnnotationChooser.java:158: for (final String type : annotationTypes) ./jalview/gui/AnnotationChooser.java:221: for (AlignmentAnnotation aa : this.ap.getAlignment() ./jalview/gui/AnnotationChooser.java:263: for (AlignmentAnnotation aa : this.ap.getAlignment() ./jalview/gui/AnnotationChooser.java:359: for (AlignmentAnnotation aa : alignment.getAlignmentAnnotation()) ./jalview/gui/AnnotationChooser.java:592: for (AlignmentAnnotation aa : this.ap.getAlignment() ./jalview/gui/AnnotationColourChooser.java:81: for (SequenceGroup sg : ap.av.getAlignment().getGroups()) ./jalview/gui/AnnotationColourChooser.java:382: for (SequenceGroup sg : ap.av.getAlignment().getGroups()) ./jalview/gui/AnnotationLabels.java:413: // for (AlignmentAnnotation ann : ap.av.getAlignment() ./jalview/gui/AnnotationLabels.java:793: // for (String prop : aa.getProperties()) ./jalview/gui/AnnotationLabels.java:865: for (SequenceI sgs : aa[selectedRow].groupRef.getSequences()) ./jalview/gui/AnnotationLabels.java:992: for (int[] region : av.getColumnSelection().getHiddenColumns()) ./jalview/gui/AnnotationPanel.java:186: for (MouseWheelListener mwl : _mwl) ./jalview/gui/AnnotationPanel.java:292: for (int index : av.getColumnSelection().getSelected()) ./jalview/gui/AnnotationPanel.java:316: for (int index : av.getColumnSelection().getSelected()) ./jalview/gui/AnnotationPanel.java:339: for (int index : av.getColumnSelection().getSelected()) ./jalview/gui/AnnotationPanel.java:399: for (int index : av.getColumnSelection().getSelected()) ./jalview/gui/AnnotationPanel.java:451: for (int index : selected) ./jalview/gui/AnnotationRowFilter.java:281: for (String anitem : getAnnotationItems(seqAssociated.isSelected())) ./jalview/gui/AnnotationRowFilter.java:362: for (SequenceGroup sg : ap.av.getAlignment().getGroups()) ./jalview/gui/AppJmol.java:351: for (JInternalFrame frame : frames) ./jalview/gui/AppJmol.java:463: for (String s : files) ./jalview/gui/AppJmol.java:537: for (AlignmentPanel ap : _colourwith) ./jalview/gui/AppJmol.java:832: for (AlignmentPanel ap : _colourwith) ./jalview/gui/AppJmol.java:1076: for (AlignmentPanel ap : _alignwith) ./jalview/gui/AppJmol.java:1086: for (AlignmentPanel ap : _alignwith) ./jalview/gui/AppJmol.java:1112: for (AlignmentPanel ap : getAllAlignmentPanels()) ./jalview/gui/AppVarna.java:501: for (RnaModel model : models.values()) ./jalview/gui/AppVarna.java:544: for (RnaModel model : models.values()) ./jalview/gui/AppVarnaBinding.java:278: for (RNA r : mdls) ./jalview/gui/BlogReader.java:372: for (Item i : (List) chan.getItems()) ./jalview/gui/BlogReader.java:497: for (HyperlinkListener hll : textDescription.getHyperlinkListeners()) ./jalview/gui/ChimeraViewFrame.java:354: for (JInternalFrame frame : frames) ./jalview/gui/ChimeraViewFrame.java:564: for (PDBEntry pe : filePDB) ./jalview/gui/ChimeraViewFrame.java:615: for (AlignmentPanel ap : _colourwith) ./jalview/gui/ChimeraViewFrame.java:851: for (AlignmentPanel ap : _colourwith) ./jalview/gui/ChimeraViewFrame.java:1010: for (AlignmentPanel ap : _alignwith) ./jalview/gui/ChimeraViewFrame.java:1020: for (AlignmentPanel ap : _alignwith) ./jalview/gui/ChimeraViewFrame.java:1044: for (AlignmentPanel ap : getAllAlignmentPanels()) ./jalview/gui/DasSourceBrowser.java:187: for (jalviewSourceI ds : sourceRegistry.getSources()) ./jalview/gui/DasSourceBrowser.java:231: for (PROP labl : latest.getPROP()) ./jalview/gui/DasSourceBrowser.java:262: for (COORDINATES dcs : latest.getCOORDINATES()) ./jalview/gui/DasSourceBrowser.java:355: for (String source : selectedSources) ./jalview/gui/DasSourceBrowser.java:385: for (jalviewSourceI ds : sourceRegistry2.getSources()) ./jalview/gui/DasSourceBrowser.java:389: for (COORDINATES cs : latest.getCOORDINATES()) ./jalview/gui/DasSourceBrowser.java:402: for (PROP slabel : latest.getPROP()) ./jalview/gui/DasSourceBrowser.java:616: for (jalviewSourceI ds : srcs) ./jalview/gui/Desktop.java:1743: for (AlignFrame af : frames) ./jalview/gui/Desktop.java:1745: for (AlignmentPanel ap : af.alignPanels) ./jalview/gui/Desktop.java:1777: for (AlignFrame afr : frames) ./jalview/gui/Desktop.java:1785: for (AlignmentPanel ap : afr.alignPanels) ./jalview/gui/Desktop.java:2316: for (JLabel url : urls) ./jalview/gui/Desktop.java:2635: for (AlignFrame af : alignFrames) ./jalview/gui/Desktop.java:3215: for (JInternalFrame frame : frames) ./jalview/gui/Desktop.java:3273: for (Object file : (List) t ./jalview/gui/Desktop.java:3339: for (DataFlavor fl : t.getTransferDataFlavors()) ./jalview/gui/IdPanel.java:382: for (SequenceFeature sf : sfs) ./jalview/gui/Jalview2XML.java:441: for (SequenceI s : incompleteSeqs.values()) ./jalview/gui/Jalview2XML.java:695: for (String dssids : dsses.keySet()) ./jalview/gui/Jalview2XML.java:810: for (final SequenceI jds : rjal.getSequences()) ./jalview/gui/Jalview2XML.java:1028: for (AlignedCodonFrame acf : jac) ./jalview/gui/Jalview2XML.java:1137: for (SequenceI sq : jal.getSequences()) ./jalview/gui/Jalview2XML.java:1163: for (jalview.datamodel.SequenceGroup sg : jal.getGroups()) ./jalview/gui/Jalview2XML.java:1222: for (SequenceI seq : sg.getSequences()) ./jalview/gui/Jalview2XML.java:1349: for (String featureType : renderOrder) ./jalview/gui/Jalview2XML.java:1431: for (String calcId : calcIdSet) ./jalview/gui/Jalview2XML.java:1542: for (RnaModel model : varna.getModels()) ./jalview/gui/Jalview2XML.java:1826: for (String pr : annotation.getProperties()) ./jalview/gui/Jalview2XML.java:1908: for (String urls : settings.getServiceURLs()) ./jalview/gui/Jalview2XML.java:2113: for (int[] range : r) ./jalview/gui/Jalview2XML.java:2121: for (int[] range : r) ./jalview/gui/Jalview2XML.java:2478: for (AlignFrame fr : gatherToThisFrame.values()) ./jalview/gui/Jalview2XML.java:2484: for (AlignmentI ds : importedDatasets.keySet()) ./jalview/gui/Jalview2XML.java:2519: for (Entry candidate : splitFrameCandidates ./jalview/gui/Jalview2XML.java:2532: for (Entry candidate : splitFrameCandidates ./jalview/gui/Jalview2XML.java:2560: for (Entry candidate : splitFrameCandidates ./jalview/gui/Jalview2XML.java:2578: for (SplitFrame sf : gatherTo) ./jalview/gui/Jalview2XML.java:3035: for (PdbentryItem item : ids[p].getPdbentryItem()) ./jalview/gui/Jalview2XML.java:3037: for (Property pr : item.getProperty()) ./jalview/gui/Jalview2XML.java:3303: for (jalview.schemabinding.version2.Property prop : an[i] ./jalview/gui/Jalview2XML.java:3418: for (AlignmentAnnotation jaa : jaal) ./jalview/gui/Jalview2XML.java:3571: for (JSeq jseq : jseqs) ./jalview/gui/Jalview2XML.java:3620: for (JInternalFrame frame : getAllFrames()) ./jalview/gui/Jalview2XML.java:3863: for (Entry entry : structureViewers ./jalview/gui/Jalview2XML.java:3948: for (Entry pdb : fileData) ./jalview/gui/Jalview2XML.java:4047: for (File id : oldFiles.keySet()) ./jalview/gui/Jalview2XML.java:4171: for (JInternalFrame frame : frames) ./jalview/gui/Jalview2XML.java:4226: for (File id : oldFiles.keySet()) ./jalview/gui/Jalview2XML.java:4331: for (JalviewStructureDisplayI sview : newStructureViewers) ./jalview/gui/Jalview2XML.java:4653: for (CalcIdParam calcIdParam : view.getCalcIdParam()) ./jalview/gui/Jalview2XML.java:4706: for (jalview.datamodel.SequenceGroup sg : al.getGroups()) ./jalview/gui/Jalview2XML.java:4832: for (String nm : magicNames) ./jalview/gui/Jalview2XML.java:4836: for (JvAnnotRow auan : autoAlan) ./jalview/gui/Jalview2XML.java:4889: for (String other : remains) ./jalview/gui/Jalview2XML.java:4901: for (JvAnnotRow jvar : reorder) ./jalview/gui/Jalview2XML.java:4909: for (JvAnnotRow jvar : rws) ./jalview/gui/JDatabaseTree.java:115: for (DbSourceProxy dbp : srcs) ./jalview/gui/JDatabaseTree.java:316: for (ActionListener al : lstners) ./jalview/gui/JDatabaseTree.java:377: for (TreePath tp : tsel) ./jalview/gui/JDatabaseTree.java:431: for (DbSourceProxy dbs : srcs) ./jalview/gui/JDatabaseTree.java:490: for (DbSourceProxy dbs : getSelectedSources()) ./jalview/gui/JDatabaseTree.java:554: for (DbSourceProxy pr : jdt.getSelectedSources()) ./jalview/gui/JvSwingUtils.java:70: for (String line : htmllines) ./jalview/gui/OptsAndParamsPage.java:131: for (Object str : opt.getPossibleValues()) ./jalview/gui/OptsAndParamsPage.java:646: for (Object val : vals) ./jalview/gui/OptsAndParamsPage.java:915: for (OptionBox opts : getOptSet().values()) ./jalview/gui/OptsAndParamsPage.java:923: for (ParamBox parambox : getParamSet().values()) ./jalview/gui/PaintRefresher.java:78: for (Entry> registered : components.entrySet()) ./jalview/gui/PaintRefresher.java:93: for (String id : emptied) ./jalview/gui/PaintRefresher.java:114: for (Component comp : comps) ./jalview/gui/PaintRefresher.java:249: for (Component comp : comps) ./jalview/gui/PCAPanel.java:137: for (final String sm : ResidueProperties.scoreMatrices.keySet()) ./jalview/gui/PopupMenu.java:335: for (final AlignmentAnnotation aa : aas) ./jalview/gui/PopupMenu.java:362: for (final AlignmentAnnotation aa : seqAnns) ./jalview/gui/PopupMenu.java:554: for (SequenceI sq : ap.av.getSequenceSelection()) ./jalview/gui/PopupMenu.java:560: for (PDBEntry pe : pes) ./jalview/gui/PopupMenu.java:621: for (String link : links) ./jalview/gui/PopupMenu.java:710: for (String calcId : hiddenTypes.keySet()) ./jalview/gui/PopupMenu.java:712: for (List type : hiddenTypes.get(calcId)) ./jalview/gui/PopupMenu.java:721: for (String calcId : shownTypes.keySet()) ./jalview/gui/PopupMenu.java:723: for (List type : shownTypes.get(calcId)) ./jalview/gui/PopupMenu.java:857: for (String link : groupLinks) ./jalview/gui/PopupMenu.java:943: for (List linkstrset : linkset) ./jalview/gui/PopupMenu.java:1593: for (String calcId : tipEntries.keySet()) ./jalview/gui/PopupMenu.java:1681: for (SequenceI seq : sequences) ./jalview/gui/Preferences.java:973: for (String path : paths) ./jalview/gui/RestInputParamEditDialog.java:134: for (OptionI ops : current.getOptions()) ./jalview/gui/RestInputParamEditDialog.java:182: for (Class type : RestServiceDescription.getInputTypes()) ./jalview/gui/RestInputParamEditDialog.java:195: for (OptionI opt : jtype.getOptions()) ./jalview/gui/RestInputParamEditDialog.java:208: for (JPanel pnl : prms) ./jalview/gui/RestInputParamEditDialog.java:232: for (JPanel opt : typeopts.get(typen)) ./jalview/gui/RestServiceEditorPane.java:186: for (Map.Entry inparam : currentservice ./jalview/gui/RestServiceEditorPane.java:194: for (JvDataType oparam : currentservice.getResultDataTypes()) ./jalview/gui/RestServiceEditorPane.java:275: for (final JvDataType type : JvDataType.values()) ./jalview/gui/RestServiceEditorPane.java:355: for (String its : _iparam) ./jalview/gui/RestServiceEditorPane.java:381: for (String its : _rparam) ./jalview/gui/ScalePanel.java:443: for (int[] region : av.getColumnSelection().getHiddenColumns()) ./jalview/gui/ScalePanel.java:496: for (int sel : cs.getSelected()) ./jalview/gui/ScalePanel.java:560: for (ScaleMark mark : marks) ./jalview/gui/SeqCanvas.java:127: for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx, ./jalview/gui/SeqCanvas.java:661: for (int[] region : regions) ./jalview/gui/SeqPanel.java:922: for (Match m : results.getResults()) ./jalview/gui/SeqPanel.java:1707: for (SequenceFeature sf : allFeatures) ./jalview/gui/SeqPanel.java:1711: for (String link : sf.links) ./jalview/gui/SequenceFetcher.java:309: for (DbSourceProxy sourcep : sp) ./jalview/gui/SequenceFetcher.java:544: for (DbSourceProxy dbs : database.getSelectedSources()) ./jalview/gui/SequenceFetcher.java:800: for (String s : nextFetch) ./jalview/gui/SequenceFetcher.java:942: for (String q : queries) ./jalview/gui/SequenceFetcher.java:1007: for (SequenceI sq : alsqs) ./jalview/gui/SplitFrame.java:275: for (KeyListener kl : af.getKeyListeners()) ./jalview/gui/SplitFrame.java:289: for (KeyListener kl : c.getKeyListeners()) ./jalview/gui/SplitFrame.java:426: for (Entry acc : ((AlignFrame) getTopFrame()) ./jalview/gui/SplitFrame.java:454: for (ActionListener a : ((AlignFrame) c).getAccelerators() ./jalview/gui/SplitFrame.java:629: for (ActionListener al : mi.getActionListeners()) ./jalview/gui/StructureChooser.java:161: for (SequenceI seq : selectedSequences) ./jalview/gui/StructureChooser.java:213: for (String error : errors) ./jalview/gui/StructureChooser.java:227: for (SequenceI seq : selectedSequences) ./jalview/gui/StructureChooser.java:232: for (PDBEntry pdbEntry : seq.getDatasetSequence() ./jalview/gui/StructureChooser.java:264: for (PDBEntry entry : seq.getAllPDBEntries()) ./jalview/gui/StructureChooser.java:278: for (DBRefEntry dbRef : seq.getDBRefs()) ./jalview/gui/StructureChooser.java:310: for (String name : names) ./jalview/gui/StructureChooser.java:320: for (String seqRef : seqRefs) ./jalview/gui/StructureChooser.java:369: for (String ignoredEntry : ignoreList.split(",")) ./jalview/gui/StructureChooser.java:406: for (SequenceI seq : selectedSequences) ./jalview/gui/StructureChooser.java:480: for (String error : errors) ./jalview/gui/StructureChooser.java:756: for (int row : selectedRows) ./jalview/gui/StructureChooser.java:792: for (int row : selectedRows) ./jalview/gui/StructureChooser.java:862: for (PDBEntry entry : pdbEntries) ./jalview/gui/StructureChooser.java:887: for (SequenceI seq : sequences) ./jalview/gui/StructureChooser.java:895: for (StructureMapping sm : smm) ./jalview/gui/StructureChooser.java:919: for (SequenceI fSeq : seqsWithoutSourceDBRef) ./jalview/gui/StructureChooser.java:930: for (SequenceI seq : sequences) ./jalview/gui/StructureChooser.java:964: for (SequenceI seq : selectedSequences) ./jalview/gui/StructureViewer.java:110: for (PDBEntry pdb : pdbs) ./jalview/gui/StructureViewer.java:120: for (SequenceI sq : pdbseqs) ./jalview/gui/StructureViewer.java:172: for (PDBEntry entry : pdbs) ./jalview/gui/StructureViewerBase.java:143: for (Component c : viewerActionMenu.getMenuComponents()) ./jalview/gui/StructureViewerBase.java:166: for (String setid : _aps) ./jalview/gui/StructureViewerBase.java:213: for (AlignmentPanel aps : getAllAlignmentPanels()) ./jalview/gui/StructureViewerBase.java:372: for (StructureViewerBase view : getViewersFor(apanel)) ./jalview/gui/StructureViewerBase.java:439: for (StructureViewerBase viewer : getViewersFor(null)) ./jalview/gui/StructureViewerBase.java:534: for (String chain : chainNames) ./jalview/gui/TextColourChooser.java:218: for (SequenceGroup sg : ap.av.getAlignment().getGroups()) ./jalview/gui/TreeCanvas.java:1038: for (SequenceI seq : mappedGroup.getSequences()) ./jalview/gui/TreePanel.java:578: for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av ./jalview/gui/TreePanel.java:589: for (CommandI tsort : commands) ./jalview/gui/TreePanel.java:611: for (CommandI tsort : commands) ./jalview/gui/TreePanel.java:617: for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av ./jalview/gui/UserDefinedColours.java:538: for (JButton btn : upperCaseButtons) ./jalview/gui/UserDefinedColours.java:562: for (JButton btn : lowerCaseButtons) ./jalview/gui/VamsasApplication.java:1045: for (SequenceI sel : seqsel.getSequences(null)) ./jalview/gui/VamsasApplication.java:1073: for (Integer ival : colsel.getSelected()) ./jalview/gui/ViewSelectionMenu.java:182: for (Component c : getMenuComponents()) ./jalview/gui/ViewSelectionMenu.java:207: for (Component c : getMenuComponents()) ./jalview/gui/ViewSelectionMenu.java:220: for (final AlignmentPanel ap : allviews) ./jalview/gui/ViewSelectionMenu.java:257: for (Component c : getMenuComponents()) ./jalview/gui/WsJobParameters.java:549: for (WsParamSetI pr : paramStore.getPresets()) ./jalview/gui/WsJobParameters.java:613: for (ArgumentI myarg : args) ./jalview/gui/WsJobParameters.java:670: for (ArgumentI arg : args) ./jalview/gui/WsJobParameters.java:860: for (OptionBox pbox : opanp.getOptSet().values()) ./jalview/gui/WsJobParameters.java:899: for (ParamBox pbox : opanp.getParamSet().values()) ./jalview/gui/WsJobParameters.java:921: * s = 2 * sep; for (ParamBox pbox : opanp.getParamSet().values()) { ./jalview/gui/WsJobParameters.java:973: for (Jws2Instance service : disc.getServices()) ./jalview/gui/WsJobParameters.java:1019: for (Option o : rg) ./jalview/gui/WsJobParameters.java:1039: for (Parameter o : rg) ./jalview/gui/WsJobParameters.java:1247: for (WsParamSetI upn : paramStore.getPresets()) ./jalview/gui/WsJobParameters.java:1311: for (AlignFrame alignFrame : Desktop.getAlignFrames()) ./jalview/gui/WsParamSetManager.java:71: for (WsParamSetI p : pset) ./jalview/gui/WsParamSetManager.java:76: for (String url : p.getApplicableUrls()) ./jalview/gui/WsParamSetManager.java:132: for (String url : wspset.getServiceURL()) ./jalview/gui/WsParamSetManager.java:172: for (String urls : parameterSet.getApplicableUrls()) ./jalview/gui/WsPreferences.java:123: for (String url : wsUrls) ./jalview/httpserver/AbstractRequestHandler.java:110: for (String hdr : Collections.list(request.getHeaderNames())) ./jalview/httpserver/AbstractRequestHandler.java:112: for (String val : Collections.list(request.getHeaders(hdr))) ./jalview/httpserver/AbstractRequestHandler.java:117: for (String param : Collections.list(request.getParameterNames())) ./jalview/httpserver/AbstractRequestHandler.java:119: for (String val : request.getParameterValues(param)) ./jalview/httpserver/HttpServer.java:194: for (String hdr : Collections.list(request.getHeaderNames())) ./jalview/httpserver/HttpServer.java:196: for (String val : Collections.list(request.getHeaders(hdr))) ./jalview/httpserver/HttpServer.java:201: for (String param : Collections.list(request.getParameterNames())) ./jalview/httpserver/HttpServer.java:203: for (String val : request.getParameterValues(param)) ./jalview/io/AlignFile.java:406: for (SequenceGroup sg : getSeqGroups()) ./jalview/io/AnnotationFile.java:174: for (int[] r : hc) ./jalview/io/AnnotationFile.java:429: for (Map.Entry combine_statement : graphGroup ./jalview/io/AnnotationFile.java:541: for (SequenceGroup sg : list) ./jalview/io/AnnotationFile.java:1114: for (SequenceGroup theGroup : al.getGroups()) ./jalview/io/AnnotationFile.java:1146: for (Object[] _deferred_args : deferredAnnotation_calls) ./jalview/io/AnnotationFile.java:1167: for (Object[] _combine_args : combineAnnotation_calls) ./jalview/io/AnnotationFile.java:1601: for (SequenceGroup _sg : al.getGroups()) ./jalview/io/AppletFormatAdapter.java:217: for (String element : format_list) ./jalview/io/AppletFormatAdapter.java:571: for (AlignmentAnnotation aa : ala) ./jalview/io/BioJsHTMLOutput.java:118: for (File file : directory.listFiles()) ./jalview/io/BioJsHTMLOutput.java:172: for (BioJSReleasePojo bjsRelease : repo.getReleases()) ./jalview/io/FeaturesFile.java:157: for (AlignedCodonFrame codons : dataset.getCodonFrames()) ./jalview/io/FeaturesFile.java:280: for (SequenceI newseq : newseqs) ./jalview/io/FeaturesFile.java:440: for (SequenceI m : newseqs) ./jalview/io/FeaturesFile.java:474: for (String link : parsed.getLinks()) ./jalview/io/FeaturesFile.java:587: for (SequenceFeature sequenceFeature : features) ./jalview/io/FeaturesFile.java:775: for (SequenceI seq : sequences) ./jalview/io/FeaturesFile.java:780: for (SequenceFeature sf : features) ./jalview/io/FeaturesFile.java:871: for (String range : alignedRegions) ./jalview/io/FeaturesFile.java:1006: for (Entry> attr : nameValues.entrySet()) ./jalview/io/FeaturesFile.java:1068: for (AlignedCodonFrame mapping : align.getCodonFrames()) ./jalview/io/FeaturesFile.java:1088: for (SequenceI seq : includedseqs) ./jalview/io/FileLoader.java:348: for (SequenceI sq : al.getSequences()) ./jalview/io/FileLoader.java:356: for (PDBEntry pdbe : sq.getAllPDBEntries()) ./jalview/io/gff/ExonerateHelper.java:205: for (String region : alignedRegions) ./jalview/io/gff/Gff3Helper.java:171: for (String target : targets) ./jalview/io/gff/Gff3Helper.java:298: for (String target : targets) ./jalview/io/gff/GffHelperBase.java:238: for (SequenceI m : newseqs) ./jalview/io/gff/GffHelperBase.java:294: for (String pair : text.trim().split(namesDelimiter)) ./jalview/io/gff/GffHelperBase.java:319: for (String val : values.split(valuesDelimiter)) ./jalview/io/gff/GffHelperBase.java:376: for (Entry> attr : attributes.entrySet()) ./jalview/io/gff/SequenceOntologyLite.java:135: for (String[] pair : TERMS) ./jalview/io/JSONFile.java:174: for (SequenceI seq : seqs) ./jalview/io/JSONFile.java:237: for (SequenceGroup seqGrp : seqGroups) ./jalview/io/JSONFile.java:250: for (SequenceI seq : seqGrp.getSequences()) ./jalview/io/JSONFile.java:284: for (int[] range : hiddenCols) ./jalview/io/JSONFile.java:304: for (SequenceI hiddenSeq : hiddenSeqs) ./jalview/io/JSONFile.java:325: for (SequenceI seq : seqs) ./jalview/io/JSONFile.java:338: for (SequenceFeature sf : seqFeatures) ./jalview/io/JSONFile.java:373: for (AlignmentAnnotation annot : annotations) ./jalview/io/JSONFile.java:398: for (Annotation annotation : annot.annotations) ./jalview/io/JSONFile.java:648: for (String seqRef : seqRefs) ./jalview/io/JSONFile.java:662: for (String rangeString : rangeStrings) ./jalview/io/JSONFile.java:753: for (AlignmentAnnotation annot : annots) ./jalview/io/packed/JalviewDataset.java:150: for (NewickFile nf : trees) ./jalview/io/packed/ParsePackedSet.java:60: for (DataProvider dta : files) ./jalview/io/packed/ParsePackedSet.java:291: for (Object o : newdm) ./jalview/io/PhylipFile.java:223: for (char c : invalidCharacters) ./jalview/io/PhylipFile.java:265: for (SequenceI s : seqs) ./jalview/io/PhylipFile.java:316: for (SequenceI s : seqs) ./jalview/io/SequenceAnnotationReport.java:94: for (String[] primary : PRIMARY_SOURCES) ./jalview/io/SequenceAnnotationReport.java:96: for (String s : primary) ./jalview/io/SequenceAnnotationReport.java:126: for (SequenceFeature feature : features) ./jalview/io/SequenceAnnotationReport.java:265: for (String urlstring : feature.links) ./jalview/io/SequenceAnnotationReport.java:269: for (List urllink : createLinksFrom(null, urlstring)) ./jalview/io/SequenceAnnotationReport.java:372: for (DBRefEntry ref : dbrefs) ./jalview/io/StockholmFile.java:271: for (Map.Entry skey : seqs.entrySet()) ./jalview/io/StockholmFile.java:654: for (AlignmentAnnotation alan : newStruc) ./jalview/io/StockholmFile.java:786: for (DBRefEntry d : dbrs) ./jalview/io/StructureFile.java:204: for (SequenceI sq : al.getSequences()) ./jalview/io/StructureFile.java:236: for (PDBChain ch : getChains()) ./jalview/io/StructureFile.java:239: for (SequenceI sq : (List) replaced.get(0)) ./jalview/io/StructureFile.java:328: for (SequenceI sq : al.getSequences()) ./jalview/io/StructureFile.java:349: for (PDBChain chain : getChains()) ./jalview/io/StructureFile.java:361: for (PDBChain chain : getChains()) ./jalview/io/StructureFile.java:369: for (PDBChain chain : getChains()) ./jalview/io/StructureFile.java:377: for (PDBChain chain : getChains()) ./jalview/io/StructureFile.java:385: for (PDBChain chain : getChains()) ./jalview/io/StructureFile.java:394: for (PDBChain chain : getChains()) ./jalview/io/StructureFile.java:402: for (char c : seq.getSequence()) ./jalview/io/StructureFile.java:499: for (StructureFileType sfType : StructureFileType.values()) ./jalview/io/TCoffeeScoreFile.java:178: for (Map.Entry it : scores.entrySet()) ./jalview/io/TCoffeeScoreFile.java:198: for (Map.Entry it : scores.entrySet()) ./jalview/io/TCoffeeScoreFile.java:233: for (Map.Entry entry : header.scores.entrySet()) ./jalview/io/TCoffeeScoreFile.java:248: for (Map.Entry entry : block.items.entrySet()) ./jalview/io/TCoffeeScoreFile.java:267: for (StringBuilder str : scores.values()) ./jalview/io/TCoffeeScoreFile.java:569: for (Map.Entry id : scores.entrySet()) ./jalview/io/vamsas/Rangetype.java:150: for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1) ./jalview/io/vamsas/Rangetype.java:235: for (int[] range : ranges) ./jalview/io/vamsas/Tree.java:277: for (SequenceI asq : jalsqs) ./jalview/io/VamsasAppDatastore.java:575: for (SequenceI jvalsq : av.getAlignment().getSequences()) ./jalview/io/VamsasAppDatastore.java:2520: for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1) ./jalview/io/VamsasAppDatastore.java:2582: for (int[] range : ranges) ./jalview/io/VamsasAppDatastore.java:2737: for (AlignedCodonFrame acf : cframes) ./jalview/javascript/JSFunctionExec.java:71: for (JSFunctionExec jx : q) ./jalview/javascript/MouseOverStructureListener.java:146: for (AtomSpec atom : atoms) ./jalview/javascript/MouseOverStructureListener.java:231: for (jalview.structure.StructureMappingcommandSet ccset : colcommands) ./jalview/javascript/MouseOverStructureListener.java:241: for (String[] ccset : ccomands) ./jalview/jbgui/GAlignExportSettings.java:78: for (String format : complexFormats) ./jalview/schemes/AnnotationColourGradient.java:181: for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation ./jalview/schemes/ClustalxColourScheme.java:102: for (SequenceI sq : seqs) ./jalview/schemes/ResidueProperties.java:770: for (Map.Entry acode : ambiguityCodes.entrySet()) ./jalview/schemes/ResidueProperties.java:772: for (String r : acode.getValue()) ./jalview/schemes/ResidueProperties.java:795: for (String codon : unambcodons) ./jalview/schemes/ResidueProperties.java:838: for (String ab : altbase) ./jalview/schemes/ResidueProperties.java:1222: for (String ph : propHash.keySet()) ./jalview/schemes/ResidueProperties.java:2753: for (String pname : propHash.keySet()) ./jalview/schemes/ResidueProperties.java:2756: for (String rname : phash.keySet()) ./jalview/schemes/ResidueProperties.java:2806: for (String nuc : nucleotideName.keySet()) ./jalview/schemes/ResidueProperties.java:2825: for (String res : aa3Hash.keySet()) ./jalview/schemes/RNAHelicesColourChooser.java:61: for (SequenceGroup sg : ap.getAlignment().getGroups()) ./jalview/schemes/RNAHelicesColourChooser.java:125: for (SequenceGroup sg : ap.getAlignment().getGroups()) ./jalview/schemes/TCoffeeColourScheme.java:94: for (AlignmentAnnotation al : alcontext ./jalview/schemes/TCoffeeColourScheme.java:106: for (Annotation an : al.annotations) ./jalview/structure/StructureMapping.java:120: for (Integer seqPos : mapping.keySet()) ./jalview/structure/StructureSelectionManager.java:164: for (StructureMapping sm : mappings) ./jalview/structure/StructureSelectionManager.java:299: for (StructureMapping sm : mappings) ./jalview/structure/StructureSelectionManager.java:359: for (SequenceI sq : sequenceArray) ./jalview/structure/StructureSelectionManager.java:369: for (AlignmentAnnotation ala : ds.getAnnotation()) ./jalview/structure/StructureSelectionManager.java:461: for (PDBChain chain : pdb.getChains()) ./jalview/structure/StructureSelectionManager.java:537: for (PDBChain chain : pdb.getChains()) ./jalview/structure/StructureSelectionManager.java:743: for (String pdbfile : sl.getPdbFile()) ./jalview/structure/StructureSelectionManager.java:757: for (StructureMapping sm : mappings) ./jalview/structure/StructureSelectionManager.java:809: for (AtomSpec atom : atoms) ./jalview/structure/StructureSelectionManager.java:813: for (StructureMapping sm : mappings) ./jalview/structure/StructureSelectionManager.java:825: for (AlignedCodonFrame acf : seqmappings) ./jalview/structure/StructureSelectionManager.java:833: for (Object li : listeners) ./jalview/structure/StructureSelectionManager.java:934: for (StructureMapping sm : mappings) ./jalview/structure/StructureSelectionManager.java:941: for (int index : positions) ./jalview/structure/StructureSelectionManager.java:1043: for (StructureMapping sm : mappings) ./jalview/structure/StructureSelectionManager.java:1069: for (StructureMapping sm : mappings) ./jalview/structure/StructureSelectionManager.java:1111: for (AlignedCodonFrame acf : mappings) ./jalview/structure/StructureSelectionManager.java:1192: for (SelectionListener slis : sel_listeners) ./jalview/structure/StructureSelectionManager.java:1291: for (CommandListener listener : commandListeners) ./jalview/structures/models/AAStructureBindingModel.java:174: for (PDBEntry pdb : pdbEntry) ./jalview/structures/models/AAStructureBindingModel.java:541: for (StructureMapping mapping : mappings) ./jalview/structures/models/AAStructureBindingModel.java:607: for (String file : files) ./jalview/structures/models/AAStructureBindingModel.java:643: for (SequenceI[] seqs : sequence) ./jalview/structures/models/AAStructureBindingModel.java:647: for (SequenceI s : seqs) ./jalview/util/Comparison.java:305: for (char[] seq : letters) ./jalview/util/Comparison.java:313: for (char c : seq) ./jalview/util/Comparison.java:407: for (SequenceI[] ss : seqs) ./jalview/util/Comparison.java:409: for (SequenceI s : ss) ./jalview/util/DBRefUtils.java:70: for (String k : keys) ./jalview/util/DBRefUtils.java:101: for (String src : sources) ./jalview/util/DBRefUtils.java:107: for (DBRefEntry dbr : dbrefs) ./jalview/util/DBRefUtils.java:602: for (DBRefEntry dbref : dbRefs) ./jalview/util/DBRefUtils.java:662: for (DBRefEntry p : pr) ./jalview/util/DBRefUtils.java:671: for (DBRefEntry p : pr) ./jalview/util/DBRefUtils.java:701: for (DBRefEntry cand : candidates) ./jalview/util/DnaUtils.java:115: for (int[] range : ranges) ./jalview/util/DnaUtils.java:145: for (String loc : locations) ./jalview/util/MapList.java:156: for (int[] r : shifts) ./jalview/util/MapList.java:284: for (int[] r : map.fromShifts) ./jalview/util/MapList.java:291: for (int[] r : map.toShifts) ./jalview/util/MapList.java:320: for (int[] range : fromRange) ./jalview/util/MapList.java:328: for (int[] range : toRange) ./jalview/util/MapList.java:358: for (final int[] range : ranges) ./jalview/util/MapList.java:984: for (int[] shift : fromShifts) ./jalview/util/MapList.java:991: for (int[] shift : toShifts) ./jalview/util/MapList.java:1017: for (int[] range : map.getFromRanges()) ./jalview/util/MapList.java:1021: for (int[] range : map.getToRanges()) ./jalview/util/MapList.java:1093: for (int[] range : getFromRanges()) ./jalview/util/MappingUtils.java:110: for (SequenceI seq : mapTo.getSequences()) ./jalview/util/MappingUtils.java:180: for (SequenceI seq : edit.getSequences()) ./jalview/util/MappingUtils.java:201: for (SequenceI targetSeq : targetSeqs) ./jalview/util/MappingUtils.java:291: for (AlignedCodonFrame acf : seqmappings) ./jalview/util/MappingUtils.java:329: for (SequenceI selected : sg.getSequences()) ./jalview/util/MappingUtils.java:362: for (AlignedCodonFrame acf : codonFrames) ./jalview/util/MappingUtils.java:368: for (SequenceI seq : mapTo.getAlignment().getSequences()) ./jalview/util/MappingUtils.java:381: for (Match m : sr.getResults()) ./jalview/util/MappingUtils.java:387: for (Match m : sr.getResults()) ./jalview/util/MappingUtils.java:443: for (SequenceI seq : sortOrder) ./jalview/util/MappingUtils.java:445: for (AlignedCodonFrame acf : mappings) ./jalview/util/MappingUtils.java:451: for (SequenceI seq2 : mapTo.getSequences()) ./jalview/util/MappingUtils.java:478: for (SequenceI seq : mapTo.getSequences()) ./jalview/util/MappingUtils.java:533: for (Integer sel : colsel.getSelected()) ./jalview/util/MappingUtils.java:539: for (int[] hidden : colsel.getHiddenColumns()) ./jalview/util/MappingUtils.java:636: for (SequenceI fromSeq : fromSequences) ./jalview/util/MappingUtils.java:651: for (Match m : sr.getResults()) ./jalview/util/MappingUtils.java:661: for (SequenceI toSeq : toSequences) ./jalview/util/MappingUtils.java:697: for (AlignedCodonFrame mapping : mappings) ./jalview/util/MappingUtils.java:779: for (AlignedCodonFrame mapping : mappings) ./jalview/util/MappingUtils.java:785: for (SequenceI otherseq : filterList) ./jalview/util/MappingUtils.java:827: for (int[] range : ranges) ./jalview/util/MappingUtils.java:856: for (int[] range : ranges) ./jalview/util/ShiftList.java:113: for (int[] sh : shifts) ./jalview/util/StringUtils.java:268: for (String term : terms) ./jalview/viewmodel/AlignmentViewport.java:638: for (SequenceGroup sg : getAlignment().getGroups()) ./jalview/viewmodel/AlignmentViewport.java:854: for (AlignedCodonFrame mapping : al.getCodonFrames()) ./jalview/viewmodel/AlignmentViewport.java:1399: for (SequenceI seq : tmp) ./jalview/viewmodel/AlignmentViewport.java:1426: for (SequenceI seq : tmp) ./jalview/viewmodel/AlignmentViewport.java:1507: for (AlignmentAnnotation ann : anns) ./jalview/viewmodel/AlignmentViewport.java:1777: for (AlignmentAnnotation annot : aa) ./jalview/viewmodel/AlignmentViewport.java:1838: for (SequenceGroup sg : groups) ./jalview/viewmodel/AlignmentViewport.java:1876: for (SequenceGroup sg : alignment.getGroups()) ./jalview/viewmodel/AlignmentViewport.java:1924: for (AlignedCodonFrame mapping : codonMappings) ./jalview/viewmodel/AlignmentViewport.java:2022: for (AlignmentAnnotation aa : anns) ./jalview/viewmodel/AlignmentViewport.java:2114: for (SequenceGroup sg : alignment.getGroups()) ./jalview/viewmodel/AlignmentViewport.java:2186: for (SequenceGroup sg : alignment.getGroups()) ./jalview/viewmodel/AlignmentViewport.java:2190: for (SequenceI s : sg.getSequences(getHiddenRepSequences())) ./jalview/viewmodel/seqfeatures/FeatureRendererModel.java:159: for (String featureType : featureTypes) ./jalview/viewmodel/seqfeatures/FeatureRendererModel.java:488: for (String newfeat : allfeatures) ./jalview/viewmodel/seqfeatures/FeatureRendererModel.java:719: for (String feature : visibleFeatures) ./jalview/viewmodel/seqfeatures/FeatureRendererModel.java:820: for (String grp : featureGroups.keySet()) ./jalview/viewmodel/seqfeatures/FeatureRendererModel.java:845: for (String gst : toset) ./jalview/viewmodel/seqfeatures/FeatureRendererModel.java:899: for (String type : typ) ./jalview/viewmodel/seqfeatures/FeatureRendererModel.java:916: for (String gp : getFeatureGroups()) ./jalview/workers/AlignCalcManager.java:230: for (AlignCalcWorkerI worker : restartable) ./jalview/workers/AlignCalcManager.java:242: for (AlignCalcWorkerI worker : inProgress) ./jalview/workers/AlignCalcManager.java:252: for (List workers : updating.values()) ./jalview/workers/AlignCalcManager.java:254: for (AlignCalcWorkerI worker : workers) ./jalview/workers/AlignCalcManager.java:276: for (AlignCalcWorkerI worker : workers) ./jalview/workers/AlignCalcManager.java:292: for (AlignCalcWorkerI worker : canUpdate) ./jalview/workers/AlignCalcManager.java:320: for (AlignCalcWorkerI worker : restartable) ./jalview/workers/AlignCalcManager.java:332: for (AlignCalcWorkerI worker : canUpdate) ./jalview/workers/AlignCalcManager.java:348: * if (workers == null) { return; } for (AlignCalcWorkerI worker : workers) ./jalview/workers/AlignCalcManager.java:368: for (AlignCalcWorkerI worker : restartable) ./jalview/workers/AlignCalcManager.java:383: for (AlignCalcWorkerI worker : toRemove) ./jalview/workers/AlignCalcWorker.java:90: for (AlignmentAnnotation aa : ourAnnots) ./jalview/workers/AlignCalcWorker.java:122: for (Annotation a : anns) ./jalview/workers/AnnotationWorker.java:90: for (AlignmentAnnotation ann : anns) ./jalview/ws/AWSThread.java:309: for (AlignedCodonFrame acf : codonframe) ./jalview/ws/DasSequenceFeatureFetcher.java:141: for (jalviewSourceI src : selectedSources2) ./jalview/ws/DasSequenceFeatureFetcher.java:169: for (jalviewSourceI source : selectedSources) ./jalview/ws/DasSequenceFeatureFetcher.java:171: for (COORDINATES coords : source.getVersion().getCOORDINATES()) ./jalview/ws/DasSequenceFeatureFetcher.java:329: for (jalviewSourceI _sr : selectedSources) ./jalview/ws/DasSequenceFeatureFetcher.java:336: for (SequenceI seq : sequences) ./jalview/ws/DasSequenceFeatureFetcher.java:349: for (String q : _qset) ./jalview/ws/DasSequenceFeatureFetcher.java:382: for (List idl : ids) ./jalview/ws/DasSequenceFeatureFetcher.java:388: for (String id : idl) ./jalview/ws/DasSequenceFeatureFetcher.java:433: for (jalviewSourceI source : srcobj) ./jalview/ws/DasSequenceFeatureFetcher.java:476: for (SEGMENT seg : segments) ./jalview/ws/DasSequenceFeatureFetcher.java:488: for (FEATURE feat : seg.getFEATURE()) ./jalview/ws/DasSequenceFeatureFetcher.java:626: for (SequenceI seq : seqs) ./jalview/ws/DasSequenceFeatureFetcher.java:665: for (COORDINATES csys : dasSource.getVersion().getCOORDINATES()) ./jalview/ws/DasSequenceFeatureFetcher.java:855: for (String note : feat.getNOTE()) ./jalview/ws/DasSequenceFeatureFetcher.java:894: for (LINK link : feat.getLINK()) ./jalview/ws/DBRefFetcher.java:172: for (jalviewSourceI src : dasselsrc) ./jalview/ws/DBRefFetcher.java:194: for (String ddb : defdb) ./jalview/ws/DBRefFetcher.java:199: for (DbSourceProxy src : srcesfordb) ./jalview/ws/DBRefFetcher.java:511: for (String msg : warningMessages) ./jalview/ws/DBRefFetcher.java:530: for (FetchFinishedListenerI listener : listeners) ./jalview/ws/DBRefFetcher.java:569: for (SequenceI retrievedSeq : retrieved) ./jalview/ws/DBRefFetcher.java:712: for (SequenceFeature sf : sfs) ./jalview/ws/dbsources/das/datamodel/DasSequenceSource.java:169: for (String sr : src) ./jalview/ws/dbsources/das/datamodel/DasSequenceSource.java:176: for (String q : toks) ./jalview/ws/dbsources/das/datamodel/DasSequenceSource.java:235: for (Map.Entry, DasSequenceAdapter>> resset : resultset ./jalview/ws/dbsources/das/datamodel/DasSequenceSource.java:238: for (Map.Entry, DasSequenceAdapter> result : resset ./jalview/ws/dbsources/das/datamodel/DasSequenceSource.java:243: for (SEQUENCE e : dasseqresp.getSequence()) ./jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java:128: for (SOURCE src : dassources) ./jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java:239: for (jalviewSourceI src : dasSources) ./jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java:353: for (String src : sources) ./jalview/ws/dbsources/das/datamodel/JalviewSource.java:113: for (String cp : getCapabilityList(getVersionFor(source))) ./jalview/ws/dbsources/das/datamodel/JalviewSource.java:128: for (String cp : getCapabilityList(getVersionFor(source))) ./jalview/ws/dbsources/das/datamodel/JalviewSource.java:142: for (VERSION v : ds.getVERSION()) ./jalview/ws/dbsources/das/datamodel/JalviewSource.java:205: for (PROP p : v.getPROP()) ./jalview/ws/dbsources/das/datamodel/JalviewSource.java:217: for (CAPABILITY p : getVersion().getCAPABILITY()) ./jalview/ws/dbsources/das/datamodel/JalviewSource.java:233: for (CAPABILITY p : v.getCAPABILITY()) ./jalview/ws/dbsources/das/datamodel/JalviewSource.java:258: for (COORDINATES cs : v.getCOORDINATES()) ./jalview/ws/dbsources/das/datamodel/JalviewSource.java:269: for (COORDINATES cs : latestc.values()) ./jalview/ws/dbsources/das/datamodel/JalviewSource.java:324: for (DbSourceProxy ssrc : tsort) ./jalview/ws/dbsources/das/datamodel/JalviewSource.java:343: for (CAPABILITY cap : getVersion().getCAPABILITY()) ./jalview/ws/dbsources/EmblXmlSource.java:113: for (EmblEntry entry : efile.getEntries()) ./jalview/ws/dbsources/Pdb.java:161: for (SequenceI pdbcs : pdbAlignment.getSequences()) ./jalview/ws/dbsources/Pdb.java:165: for (PDBEntry pid : pdbcs.getAllPDBEntries()) ./jalview/ws/dbsources/Pdb.java:211: for (SequenceI pdbcs : toremove) ./jalview/ws/dbsources/Pdb.java:216: for (AlignmentAnnotation aa : pdbcs.getAnnotation()) ./jalview/ws/dbsources/Uniprot.java:174: for (UniprotEntry entry : entries) ./jalview/ws/dbsources/Uniprot.java:205: for (String accessionId : entry.getAccession()) ./jalview/ws/dbsources/Uniprot.java:215: for (PDBEntry pdb : entry.getDbReference()) ./jalview/ws/dbsources/Uniprot.java:263: for (SequenceFeature sf : entry.getFeature()) ./jalview/ws/dbsources/Uniprot.java:269: for (DBRefEntry dbr : dbRefs) ./jalview/ws/dbsources/Uniprot.java:288: for (String nm : entry.getProtein().getName()) ./jalview/ws/dbsources/Uniprot.java:313: for (String accessionId : entry.getAccession()) ./jalview/ws/dbsources/Uniprot.java:318: for (String n : entry.getName()) ./jalview/ws/HttpClientUtils.java:112: for (NameValuePair nvp : vals) ./jalview/ws/HttpClientUtils.java:145: for (NameValuePair nvp : vals) ./jalview/ws/jws1/JPredThread.java:237: for (AlignmentAnnotation alant : al.getAlignmentAnnotation()) ./jalview/ws/jws1/JPredThread.java:271: for (AlignmentAnnotation dssan : dsan) ./jalview/ws/jws2/AAConClient.java:72: for (String score : scoremap.keySet()) ./jalview/ws/jws2/AAConClient.java:75: for (Score scr : scores) ./jalview/ws/jws2/AADisorderClient.java:182: for (AlignmentAnnotation ala : alignViewport.getAlignment() ./jalview/ws/jws2/AADisorderClient.java:192: for (String seqId : seqNames.keySet()) ./jalview/ws/jws2/AADisorderClient.java:220: for (Score scr : scores.scores) ./jalview/ws/jws2/AADisorderClient.java:227: for (Range rn : scr.getRanges()) ./jalview/ws/jws2/AADisorderClient.java:338: for (String ft : fc.keySet()) ./jalview/ws/jws2/AbstractJabaCalcWorker.java:123: for (Argument rg : arguments) ./jalview/ws/jws2/AbstractJabaCalcWorker.java:465: for (SequenceI sq : ((List) inputSeqs.getSequences())) ./jalview/ws/jws2/AbstractJabaCalcWorker.java:492: for (int apos : sq.gapMap()) ./jalview/ws/jws2/AbstractJabaCalcWorker.java:606: for (AlignmentAnnotation an : our) ./jalview/ws/jws2/dm/AAConSettings.java:65: for (String url : preset.getApplicableUrls()) ./jalview/ws/jws2/dm/AAConSettings.java:82: for (ArgumentI newparg : pr.getArguments()) ./jalview/ws/jws2/dm/AAConSettings.java:134: for (String ps : ParameterUtils.writeParameterSet(opts, " ")) ./jalview/ws/jws2/dm/JabaWsParamSet.java:82: for (Object jp : jobParams) ./jalview/ws/jws2/dm/JabaWsParamSet.java:187: for (ArgumentI rg : args) ./jalview/ws/jws2/JabaParamStore.java:79: for (WsParamSetI paramset : prams) ./jalview/ws/jws2/JabaParamStore.java:111: for (Object pr : pset) ./jalview/ws/jws2/JabaParamStore.java:119: for (JabaPreset pr : servicePresets.values()) ./jalview/ws/jws2/JabaParamStore.java:123: for (WsParamSetI wspset : editedParams.values()) ./jalview/ws/jws2/JabaParamStore.java:133: for (WsParamSetI pr : getPresets()) ./jalview/ws/jws2/JabaParamStore.java:153: for (Object rg : jabargs) ./jalview/ws/jws2/JabaParamStore.java:200: for (ArgumentI rg : jwsargs) ./jalview/ws/jws2/JabaParamStore.java:308: for (String url : urls) ./jalview/ws/jws2/JabaParamStore.java:367: for (String ln : ParameterUtils.writeParameterSet( ./jalview/ws/jws2/JabawsCalcWorker.java:178: for (AlignmentAnnotation dssan : dsan) ./jalview/ws/jws2/JabaWsServerQuery.java:147: for (Services srv : JABAWS1SERVERS) ./jalview/ws/jws2/JabaWsServerQuery.java:153: for (Category cat : categories) ./jalview/ws/jws2/JabaWsServerQuery.java:155: for (Services srv : cat.getServices()) ./jalview/ws/jws2/JPred301Client.java:53: for (ArgumentI argi : service.getParamStore().getServiceParameters()) ./jalview/ws/jws2/JPred301Client.java:125: for (FastaSequence fsq : jpres.getJpredSequences()) ./jalview/ws/jws2/JPred301Client.java:172: for (FastaSequence fsq : jpres.getSequences()) ./jalview/ws/jws2/Jws2Client.java:75: * JabaWsParamSet pset = ((JabaWsParamSet) preset); for (Option opt : ./jalview/ws/jws2/Jws2Client.java:78: * arguments. for (Argument opt : arguments) { newargs.add(opt); } } ./jalview/ws/jws2/Jws2Discoverer.java:176: for (String ignored : Cache.getDefault("IGNORED_JABAWS_SERVICETYPES", ./jalview/ws/jws2/Jws2Discoverer.java:216: for (final String jwsserver : getServiceUrls()) ./jalview/ws/jws2/Jws2Discoverer.java:223: for (Services sv : squery.JABAWS2SERVERS) ./jalview/ws/jws2/Jws2Discoverer.java:246: for (JabaWsServerQuery squery : qrys) ./jalview/ws/jws2/Jws2Discoverer.java:257: for (JabaWsServerQuery squery : qrys) ./jalview/ws/jws2/Jws2Discoverer.java:274: for (Jws2Instance svc : services) ./jalview/ws/jws2/Jws2Discoverer.java:282: for (Jws2Instance svc : svcs) ./jalview/ws/jws2/Jws2Discoverer.java:362: for (Jws2Instance service : services.toArray(new Jws2Instance[0])) ./jalview/ws/jws2/Jws2Discoverer.java:402: for (final Jws2Instance service : preferredHosts.values()) ./jalview/ws/jws2/Jws2Discoverer.java:432: for (final Jws2Instance sv : alternates.get(service.serviceType)) ./jalview/ws/jws2/Jws2Discoverer.java:489: for (Jws2Instance service : enumerableServices) ./jalview/ws/jws2/Jws2Discoverer.java:501: for (String host : hostlist) ./jalview/ws/jws2/Jws2Discoverer.java:511: for (final Jws2Instance service : orderedsvcs) ./jalview/ws/jws2/Jws2Discoverer.java:583: for (String url : args) ./jalview/ws/jws2/Jws2Discoverer.java:600: for (Jws2Instance instance : getDiscoverer().services) ./jalview/ws/jws2/Jws2Discoverer.java:659: for (String url : wsUrls) ./jalview/ws/jws2/Jws2Discoverer.java:858: for (String svcurl : getInvalidServiceUrls()) ./jalview/ws/jws2/Jws2Discoverer.java:874: for (String svcurl : getUrlsWithoutServices()) ./jalview/ws/jws2/Jws2Discoverer.java:926: for (Jws2Instance svc : services) ./jalview/ws/jws2/Jws2Discoverer.java:980: for (Jws2Instance svc : services) ./jalview/ws/jws2/MsaWSClient.java:318: for (final WsParamSetI preset : presets) ./jalview/ws/jws2/MsaWSThread.java:211: for (compbio.data.sequence.FastaSequence seq : alignment ./jalview/ws/jws2/MsaWSThread.java:408: for (Argument opt : ((JabaWsParamSet) preset).getjabaArguments()) ./jalview/ws/jws2/MsaWSThread.java:419: for (Argument opt : arguments) ./jalview/ws/jws2/ParameterUtils.java:41: for (Option o : optSet) ./jalview/ws/jws2/ParameterUtils.java:68: for (String param : params) ./jalview/ws/jws2/RNAalifoldClient.java:236: for (Score score : data) ./jalview/ws/jws2/RNAalifoldClient.java:266: for (Range contact : contacts.keySet()) ./jalview/ws/jws2/RNAalifoldClient.java:384: for (Range contact : basePairs.keySet()) ./jalview/ws/jws2/SequenceAnnotationWSClient.java:210: for (final WsParamSetI preset : presets) ./jalview/ws/rest/HttpResultSet.java:93: for (JvDataType type : restJob.rsd.getResultDataTypes()) ./jalview/ws/rest/InputType.java:64: for (molType type : values()) ./jalview/ws/rest/InputType.java:90: for (Class t : types) ./jalview/ws/rest/InputType.java:108: for (Class cl : inputData) ./jalview/ws/rest/InputType.java:213: for (String tok : tokenstring) ./jalview/ws/rest/InputType.java:300: for (ArgumentI arg : currentSettings) ./jalview/ws/rest/params/Alignment.java:150: for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS) ./jalview/ws/rest/params/Alignment.java:160: for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS) ./jalview/ws/rest/params/Alignment.java:176: for (molType v : molType.values()) ./jalview/ws/rest/params/AnnotationFile.java:114: for (String fmt : new String[] { CSVANNOT, JVANNOT }) ./jalview/ws/rest/params/AnnotationFile.java:124: for (String fmt : new String[] { CSVANNOT, JVANNOT }) ./jalview/ws/rest/params/SeqGroupIndexVector.java:98: for (SequenceGroup sg : sgs) ./jalview/ws/rest/params/SeqGroupIndexVector.java:112: for (SequenceI sq : sg.getSequencesInOrder(al)) ./jalview/ws/rest/params/SeqGroupIndexVector.java:177: for (int[] range : vals) ./jalview/ws/rest/params/SeqGroupIndexVector.java:266: for (molType v : molType.values()) ./jalview/ws/rest/params/SeqIdVector.java:65: for (SequenceI seq : rj.getSequencesForInput(token, type)) ./jalview/ws/rest/params/SeqIdVector.java:114: for (molType v : molType.values()) ./jalview/ws/rest/params/SeqVector.java:62: for (SequenceI seq : rj.getSequencesForInput(token, type)) ./jalview/ws/rest/params/SeqVector.java:112: for (molType v : molType.values()) ./jalview/ws/rest/RestClient.java:384: for (AlignmentPanel alp : aps) ./jalview/ws/rest/RestClient.java:411: for (RestServiceDescription descr : RestServiceDescription ./jalview/ws/rest/RestClient.java:428: for (String svc : services) ./jalview/ws/rest/RestClient.java:448: for (RestClient rsbs : getRestClients()) ./jalview/ws/rest/RestClient.java:462: for (String s : services) ./jalview/ws/rest/RestJob.java:104: for (Map.Entry prm : rsd.inputParams.entrySet()) ./jalview/ws/rest/RestJob.java:287: for (AlignmentAnnotation alan : contextAl ./jalview/ws/rest/RestJob.java:370: for (InputType itype : itypes) ./jalview/ws/rest/RestJobThread.java:228: for (Entry input : rj.getInputParams()) ./jalview/ws/rest/RestJobThread.java:466: for (RestJob rj : (RestJob[]) jobs) ./jalview/ws/rest/RestJobThread.java:841: for (SequenceGroup sg : sgrp[nrj]) ./jalview/ws/rest/RestJobThread.java:867: for (SequenceI oseq : sg.getSequences(null)) ./jalview/ws/rest/RestJobThread.java:969: for (AlignmentAnnotation v : visAlAn) ./jalview/ws/rest/RestJobThread.java:1005: for (NewickFile nf : trees.get(nrj)) ./jalview/ws/rest/RestJobThread.java:1018: for (AlignmentAnnotation v : visAlAn) ./jalview/ws/rest/RestJobThread.java:1025: for (SequenceGroup sg : visgrps) ./jalview/ws/rest/RestJobThread.java:1043: for (AddDataTo action : resultDest) ./jalview/ws/rest/RestJobThread.java:1264: for (RestJob rj : (RestJob[]) jobs) ./jalview/ws/rest/RestJobThread.java:1282: for (String st : _warnings) ./jalview/ws/rest/RestServiceDescription.java:386: for (String prop : props) ./jalview/ws/rest/RestServiceDescription.java:436: for (JvDataType type : resultData) ./jalview/ws/rest/RestServiceDescription.java:468: for (JvDataType vl : JvDataType.values()) ./jalview/ws/rest/RestServiceDescription.java:609: for (Map.Entry param : inputParams.entrySet()) ./jalview/ws/rest/RestServiceDescription.java:722: for (Class type : getInputTypes()) ./jalview/ws/rest/RestServiceDescription.java:730: for (String prprm : StringUtils.separatorListToArray(iprmparams, ./jalview/ws/rest/RestServiceDescription.java:810: for (InputType val : inputParams.values()) ./jalview/ws/seqfetcher/ASequenceFetcher.java:108: for (String db : fetchableDbs.keySet()) ./jalview/ws/seqfetcher/ASequenceFetcher.java:131: for (DBRefEntry ref : refs) ./jalview/ws/seqfetcher/ASequenceFetcher.java:161: for (DbSourceProxy fetcher : proxies) ./jalview/ws/seqfetcher/ASequenceFetcher.java:209: for (DBRefEntry dbr : frefs) ./jalview/ws/seqfetcher/ASequenceFetcher.java:265: for (SequenceI s : rseqs) ./jalview/ws/seqfetcher/ASequenceFetcher.java:281: for (String qv : queriesMade) ./jalview/ws/seqfetcher/ASequenceFetcher.java:400: for (DbSourceProxy dbp : fetchableDbs.get(dbn).values()) ./jalview/ws/seqfetcher/ASequenceFetcher.java:418: for (String fetchable : getSupportedDb()) ./jalview/ws/seqfetcher/ASequenceFetcher.java:420: for (DbSourceProxy pr : getSourceProxy(fetchable)) ./jalview/ws/seqfetcher/ASequenceFetcher.java:448: for (DbSourceProxy proxy : getSourceProxy(source)) ./jalview/ws/SequenceFetcher.java:86: for (DbSourceProxy dbs : getSourceProxy(srcs[i])) ./jalview/ws/SequenceFetcher.java:161: for (jalviewSourceI source : jalview.bin.Cache.getDasSourceRegistry() ./jalview/ws/SequenceFetcher.java:167: for (DbSourceProxy seqsrc : dassources) ./jalview/ws/sifts/SiftsClient.java:334: for (DBRefEntry dbRef : dbRefs) ./jalview/ws/sifts/SiftsClient.java:372: for (Entity entity : entities) ./jalview/ws/sifts/SiftsClient.java:375: for (Segment segment : segments) ./jalview/ws/sifts/SiftsClient.java:379: for (MapRegion mapRegion : mapRegions) ./jalview/ws/sifts/SiftsClient.java:444: for (DBRefEntry dbref : seq.getDBRefs()) ./jalview/ws/sifts/SiftsClient.java:506: for (String res : resNumMap.values()) ./jalview/ws/sifts/SiftsClient.java:538: for (Segment segment : segments) ./jalview/ws/sifts/SiftsClient.java:543: for (Residue residue : residues) ./jalview/ws/sifts/SiftsClient.java:548: for (CrossRefDb cRefDb : cRefDbs) ./jalview/ws/sifts/SiftsClient.java:638: for (int[] map : mapping.values()) ./jalview/ws/sifts/SiftsClient.java:669: for (Atom atom : atoms) ./jalview/ws/sifts/SiftsClient.java:693: for (String annotation : annotations) ./jalview/ws/sifts/SiftsClient.java:715: for (ResidueDetail resDetail : resDetails) ./jalview/ws/sifts/SiftsClient.java:794: for (Entity entity : entities) ./jalview/ws/sifts/SiftsClient.java:800: for (Segment segment : segments) ./jalview/ws/sifts/SiftsClient.java:803: for (Residue residue : residues) ./jalview/ws/sifts/SiftsClient.java:806: for (CrossRefDb cRefDb : cRefDbs) ./jalview/ws/sifts/SiftsClient.java:834: for (Entity entity : entities) ./MCview/AppletPDBCanvas.java:335: for (Bond tmp : bonds) ./MCview/AppletPDBCanvas.java:465: for (Bond b : bonds) ./MCview/AppletPDBCanvas.java:909: for (PDBChain chain : pdb.getChains()) ./MCview/AppletPDBCanvas.java:911: for (Bond tmpBond : chain.bonds) ./MCview/AppletPDBCanvas.java:947: for (PDBChain chain : pdb.getChains()) ./MCview/AppletPDBCanvas.java:951: for (Bond tmpBond : chain.bonds) ./MCview/AppletPDBCanvas.java:1160: for (AtomSpec atom : atoms) ./MCview/AppletPDBCanvas.java:1249: for (SequenceI s : sequence) ./MCview/PDBCanvas.java:280: for (PDBChain chain : pdb.getChains()) ./MCview/PDBCanvas.java:284: for (Bond bond : chain.bonds) ./MCview/PDBCanvas.java:310: for (PDBChain chain : pdb.getChains()) ./MCview/PDBCanvas.java:314: for (Bond tmp : chain.bonds) ./MCview/PDBCanvas.java:441: for (PDBChain chain : pdb.getChains()) ./MCview/PDBCanvas.java:447: for (Bond bond : chain.bonds) ./MCview/PDBCanvas.java:873: for (PDBChain chain : pdb.getChains()) ./MCview/PDBCanvas.java:875: for (Bond tmpBond : chain.bonds) ./MCview/PDBCanvas.java:911: for (PDBChain chain : pdb.getChains()) ./MCview/PDBCanvas.java:915: for (Bond tmpBond : chain.bonds) ./MCview/PDBCanvas.java:968: for (Bond bond : chain.bonds) ./MCview/PDBCanvas.java:1117: for (AtomSpec atom : atoms) ./MCview/PDBCanvas.java:1207: for (SequenceI s : sequence) ./MCview/PDBChain.java:111: for (Bond b : bonds) ./MCview/PDBChain.java:133: for (Atom atom : atoms) ./MCview/PDBChain.java:159: for (Atom atom : res.atoms) ./MCview/PDBChain.java:471: for (Bond b : bonds) ./MCview/PDBChain.java:514: for (Bond b : bonds) ./MCview/PDBChain.java:534: for (Bond b : bonds) ./MCview/PDBChain.java:566: for (AlignmentAnnotation ana : shadow.getAnnotation()) ./MCview/PDBChain.java:587: for (AlignmentAnnotation ana : sequence.getAnnotation()) ./MCview/PDBfile.java:172: for (PDBChain chain : getChains()) ./MCview/PDBfile.java:238: for (SequenceI sq : seqs) ./MCview/PDBfile.java:242: for (AlignmentAnnotation aa : sq.getAnnotation()) ./MCview/Residue.java:42: for (Atom atom : atoms)