-Clazz.declarePackage ("jalview.datamodel");
-Clazz.load (["jalview.datamodel.AnnotatedCollectionI", "java.awt.Color", "java.util.ArrayList"], "jalview.datamodel.SequenceGroup", ["jalview.analysis.AAFrequency", "$.Conservation", "jalview.datamodel.AlignmentAnnotation", "$.Sequence", "jalview.schemes.ResidueProperties", "jalview.util.Comparison", "java.lang.StringBuffer"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.groupName = null;
-this.description = null;
-this.conserve = null;
-this.aaFrequency = null;
-this.displayBoxes = true;
-this.displayText = true;
-this.colourText = false;
-this.showNonconserved = false;
-this.sequences = null;
-this.seqrep = null;
-this.width = -1;
-this.cs = null;
-this.startRes = 0;
-this.endRes = 0;
-this.outlineColour = null;
-this.idColour = null;
-this.thresholdTextColour = 0;
-this.textColour = null;
-this.textColour2 = null;
-this.ignoreGapsInConsensus = true;
-this.showSequenceLogo = false;
-this.normaliseSequenceLogo = false;
-this.consPercGaps = 25;
-this.consensusData = null;
-this.hidereps = false;
-this.hidecols = false;
-this.consensus = null;
-this.conservation = null;
-this.showConsensusHistogram = false;
-this.context = null;
-Clazz.instantialize (this, arguments);
-}, jalview.datamodel, "SequenceGroup", null, jalview.datamodel.AnnotatedCollectionI);
-Clazz.prepareFields (c$, function () {
-this.sequences = new java.util.ArrayList ();
-this.outlineColour = java.awt.Color.black;
-this.textColour = java.awt.Color.black;
-this.textColour2 = java.awt.Color.white;
-});
-Clazz.defineMethod (c$, "isShowSequenceLogo",
-function () {
-return this.showSequenceLogo;
-});
-Clazz.makeConstructor (c$,
-function () {
-this.groupName = "JGroup:" + this.hashCode ();
-});
-Clazz.makeConstructor (c$,
-function (sequences, groupName, scheme, displayBoxes, displayText, colourText, start, end) {
-this.sequences = sequences;
-this.groupName = groupName;
-this.displayBoxes = displayBoxes;
-this.displayText = displayText;
-this.colourText = colourText;
-this.cs = scheme;
-this.startRes = start;
-this.endRes = end;
-this.recalcConservation ();
-}, "java.util.List,~S,jalview.schemes.ColourSchemeI,~B,~B,~B,~N,~N");
-Clazz.makeConstructor (c$,
-function (seqsel) {
-if (seqsel != null) {
-this.sequences = new java.util.ArrayList ();
-this.sequences.addAll (seqsel.sequences);
-if (seqsel.groupName != null) {
-this.groupName = String.instantialize (seqsel.groupName);
-}this.displayBoxes = seqsel.displayBoxes;
-this.displayText = seqsel.displayText;
-this.colourText = seqsel.colourText;
-this.startRes = seqsel.startRes;
-this.endRes = seqsel.endRes;
-this.cs = seqsel.cs;
-if (seqsel.description != null) {
-this.description = String.instantialize (seqsel.description);
-}this.hidecols = seqsel.hidecols;
-this.hidereps = seqsel.hidereps;
-this.idColour = seqsel.idColour;
-this.outlineColour = seqsel.outlineColour;
-this.seqrep = seqsel.seqrep;
-this.textColour = seqsel.textColour;
-this.textColour2 = seqsel.textColour2;
-this.thresholdTextColour = seqsel.thresholdTextColour;
-this.width = seqsel.width;
-this.ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
-if (seqsel.conserve != null) {
-this.recalcConservation ();
-}}}, "jalview.datamodel.SequenceGroup");
-Clazz.defineMethod (c$, "getSelectionAsNewSequences",
-function (align) {
-var iSize = this.sequences.size ();
-var seqs = new Array (iSize);
-var inorder = this.getSequencesInOrder (align);
-for (var i = 0, ipos = 0; i < inorder.length; i++) {
-var seq = inorder[i];
-seqs[ipos] = seq.getSubSequence (this.startRes, this.endRes + 1);
-if (seqs[ipos] != null) {
-seqs[ipos].setDescription (seq.getDescription ());
-seqs[ipos].setDBRef (seq.getDBRef ());
-seqs[ipos].setSequenceFeatures (seq.getSequenceFeatures ());
-if (seq.getDatasetSequence () != null) {
-seqs[ipos].setDatasetSequence (seq.getDatasetSequence ());
-}if (seq.getAnnotation () != null) {
-var alann = align.getAlignmentAnnotation ();
-for (var a = 0; a < seq.getAnnotation ().length; a++) {
-var tocopy = seq.getAnnotation ()[a];
-if (alann != null) {
-var found = false;
-for (var pos = 0; pos < alann.length; pos++) {
-if (alann[pos] === tocopy) {
-found = true;
-break;
-}}
-if (!found) {
-continue;
-}}var newannot = new jalview.datamodel.AlignmentAnnotation (seq.getAnnotation ()[a]);
-newannot.restrict (this.startRes, this.endRes);
-newannot.setSequenceRef (seqs[ipos]);
-newannot.adjustForAlignment ();
-seqs[ipos].addAlignmentAnnotation (newannot);
-}
-}ipos++;
-} else {
-iSize--;
-}}
-if (iSize != inorder.length) {
-var nseqs = new Array (iSize);
-System.arraycopy (seqs, 0, nseqs, 0, iSize);
-seqs = nseqs;
-}return seqs;
-}, "jalview.datamodel.AlignmentI");
-Clazz.defineMethod (c$, "findEndRes",
-function (seq) {
-var eres = 0;
-var ch;
-for (var j = 0; j < this.endRes + 1 && j < seq.getLength (); j++) {
-ch = seq.getCharAt (j);
-if (!jalview.util.Comparison.isGap ((ch))) {
-eres++;
-}}
-if (eres > 0) {
-eres += seq.getStart () - 1;
-}return eres;
-}, "jalview.datamodel.SequenceI");
-Clazz.defineMethod (c$, "getSequences",
-function () {
-return this.sequences;
-});
-Clazz.defineMethod (c$, "getSequences",
-function (hiddenReps) {
-if (hiddenReps == null) {
-return this.sequences;
-} else {
-var allSequences = new java.util.ArrayList ();
-for (var seq, $seq = this.sequences.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) {
-allSequences.add (seq);
-if (hiddenReps.containsKey (seq)) {
-var hsg = hiddenReps.get (seq);
-for (var seq2, $seq2 = hsg.getSequences ().iterator (); $seq2.hasNext () && ((seq2 = $seq2.next ()) || true);) {
-if (seq2 !== seq && !allSequences.contains (seq2)) {
-allSequences.add (seq2);
-}}
-}}
-return allSequences;
-}}, "java.util.Map");
-Clazz.defineMethod (c$, "getSequencesAsArray",
-function (map) {
-var tmp = this.getSequences (map);
-if (tmp == null) {
-return null;
-}return tmp.toArray ( new Array (tmp.size ()));
-}, "java.util.Map");
-Clazz.defineMethod (c$, "adjustForRemoveLeft",
-function (col) {
-if (this.startRes >= col) {
-this.startRes = this.startRes - col;
-}if (this.endRes >= col) {
-this.endRes = this.endRes - col;
-if (this.startRes > this.endRes) {
-this.startRes = 0;
-}} else {
-return false;
-}return true;
-}, "~N");
-Clazz.defineMethod (c$, "adjustForRemoveRight",
-function (col) {
-if (this.startRes > col) {
-return false;
-}if (this.endRes >= col) {
-this.endRes = col;
-}return true;
-}, "~N");
-Clazz.defineMethod (c$, "getName",
-function () {
-return this.groupName;
-});
-Clazz.defineMethod (c$, "getDescription",
-function () {
-return this.description;
-});
-Clazz.defineMethod (c$, "setName",
-function (name) {
-this.groupName = name;
-}, "~S");
-Clazz.defineMethod (c$, "setDescription",
-function (desc) {
-this.description = desc;
-}, "~S");
-Clazz.defineMethod (c$, "getConservation",
-function () {
-return this.conserve;
-});
-Clazz.defineMethod (c$, "setConservation",
-function (c) {
-this.conserve = c;
-}, "jalview.analysis.Conservation");
-Clazz.defineMethod (c$, "addSequence",
-function (s, recalc) {
-{
-if (s != null && !this.sequences.contains (s)) {
-this.sequences.add (s);
-}if (recalc) {
-this.recalcConservation ();
-}}}, "jalview.datamodel.SequenceI,~B");
-Clazz.defineMethod (c$, "getConsPercGaps",
-function () {
-return this.consPercGaps;
-});
-Clazz.defineMethod (c$, "setConsPercGaps",
-function (consPercGaps) {
-this.consPercGaps = consPercGaps;
-}, "~N");
-Clazz.defineMethod (c$, "recalcConservation",
-function () {
-if (this.cs == null && this.consensus == null && this.conservation == null) {
-return;
-}try {
-var cnsns = jalview.analysis.AAFrequency.calculate (this.sequences, this.startRes, this.endRes + 1, this.showSequenceLogo);
-if (this.consensus != null) {
-this._updateConsensusRow (cnsns, this.sequences.size ());
-}if (this.cs != null) {
-this.cs.setConsensus (cnsns);
-}if ((this.conservation != null) || (this.cs != null && this.cs.conservationApplied ())) {
-var c = new jalview.analysis.Conservation (this.groupName, jalview.schemes.ResidueProperties.propHash, 3, this.sequences, this.startRes, this.endRes + 1);
-c.calculate ();
-c.verdict (false, this.consPercGaps);
-if (this.conservation != null) {
-this._updateConservationRow (c);
-}if (this.cs != null) {
-if (this.cs.conservationApplied ()) {
-this.cs.setConservation (c);
-}}}if (this.cs != null) {
-this.cs.alignmentChanged (this.context != null ? this.context : this, null);
-}} catch (err) {
-if (Clazz.exceptionOf (err, OutOfMemoryError)) {
-System.out.println ("Out of memory loading groups: " + err);
-} else {
-throw err;
-}
-}
-});
-Clazz.defineMethod (c$, "_updateConservationRow",
-($fz = function (c) {
-if (this.conservation == null) {
-this.getConservation ();
-}this.conservation.label = "Conservation for " + this.getName ();
-this.conservation.description = "Conservation for group " + this.getName () + " less than " + this.consPercGaps + "% gaps";
-var aWidth = (this.conservation.annotations != null) ? (this.endRes < this.conservation.annotations.length ? this.conservation.annotations.length : this.endRes + 1) : this.endRes + 1;
-this.conservation.annotations = null;
-this.conservation.annotations = new Array (aWidth);
-c.completeAnnotations (this.conservation, null, this.startRes, this.endRes + 1);
-}, $fz.isPrivate = true, $fz), "jalview.analysis.Conservation");
-Clazz.defineMethod (c$, "_updateConsensusRow",
-($fz = function (cnsns, nseq) {
-if (this.consensus == null) {
-this.getConsensus ();
-}this.consensus.label = "Consensus for " + this.getName ();
-this.consensus.description = "Percent Identity";
-this.consensusData = cnsns;
-var aWidth = (this.consensus.annotations != null) ? (this.endRes < this.consensus.annotations.length ? this.consensus.annotations.length : this.endRes + 1) : this.endRes + 1;
-this.consensus.annotations = null;
-this.consensus.annotations = new Array (aWidth);
-jalview.analysis.AAFrequency.completeConsensus (this.consensus, cnsns, this.startRes, this.endRes + 1, this.ignoreGapsInConsensus, this.showSequenceLogo, nseq);
-}, $fz.isPrivate = true, $fz), "~A,~N");
-Clazz.defineMethod (c$, "addOrRemove",
-function (s, recalc) {
-{
-if (this.sequences.contains (s)) {
-this.deleteSequence (s, recalc);
-} else {
-this.addSequence (s, recalc);
-}}}, "jalview.datamodel.SequenceI,~B");
-Clazz.defineMethod (c$, "deleteSequence",
-function (s, recalc) {
-{
-this.sequences.remove (s);
-if (recalc) {
-this.recalcConservation ();
-}}}, "jalview.datamodel.SequenceI,~B");
-Clazz.overrideMethod (c$, "getStartRes",
-function () {
-return this.startRes;
-});
-Clazz.overrideMethod (c$, "getEndRes",
-function () {
-return this.endRes;
-});
-Clazz.defineMethod (c$, "setStartRes",
-function (i) {
-this.startRes = i;
-}, "~N");
-Clazz.defineMethod (c$, "setEndRes",
-function (i) {
-this.endRes = i;
-}, "~N");
-Clazz.defineMethod (c$, "getSize",
-function () {
-return this.sequences.size ();
-});
-Clazz.defineMethod (c$, "getSequenceAt",
-function (i) {
-return this.sequences.get (i);
-}, "~N");
-Clazz.defineMethod (c$, "setColourText",
-function (state) {
-this.colourText = state;
-}, "~B");
-Clazz.defineMethod (c$, "getColourText",
-function () {
-return this.colourText;
-});
-Clazz.defineMethod (c$, "setDisplayText",
-function (state) {
-this.displayText = state;
-}, "~B");
-Clazz.defineMethod (c$, "getDisplayText",
-function () {
-return this.displayText;
-});
-Clazz.defineMethod (c$, "setDisplayBoxes",
-function (state) {
-this.displayBoxes = state;
-}, "~B");
-Clazz.defineMethod (c$, "getDisplayBoxes",
-function () {
-return this.displayBoxes;
-});
-Clazz.overrideMethod (c$, "getWidth",
-function () {
-{
-var first = true;
-for (var seq, $seq = this.sequences.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) {
-if (first || seq.getLength () > this.width) {
-this.width = seq.getLength ();
-first = false;
-}}
-return this.width;
-}});
-Clazz.defineMethod (c$, "setOutlineColour",
-function (c) {
-this.outlineColour = c;
-}, "java.awt.Color");
-Clazz.defineMethod (c$, "getOutlineColour",
-function () {
-return this.outlineColour;
-});
-Clazz.defineMethod (c$, "getSequencesInOrder",
-function (al) {
-return this.getSequencesInOrder (al, true);
-}, "jalview.datamodel.AlignmentI");
-Clazz.defineMethod (c$, "getSequencesInOrder",
-function (al, trim) {
-{
-var sSize = this.sequences.size ();
-var alHeight = al.getHeight ();
-var seqs = new Array ((trim) ? sSize : alHeight);
-var index = 0;
-for (var i = 0; i < alHeight && index < sSize; i++) {
-if (this.sequences.contains (al.getSequenceAt (i))) {
-seqs[(trim) ? index : i] = al.getSequenceAt (i);
-index++;
-}}
-if (index == 0) {
-return null;
-}if (!trim) {
-return seqs;
-}if (index < seqs.length) {
-var dummy = seqs;
-seqs = new Array (index);
-while (--index >= 0) {
-seqs[index] = dummy[index];
-dummy[index] = null;
-}
-}return seqs;
-}}, "jalview.datamodel.AlignmentI,~B");
-Clazz.defineMethod (c$, "getIdColour",
-function () {
-return this.idColour;
-});
-Clazz.defineMethod (c$, "setIdColour",
-function (idColour) {
-this.idColour = idColour;
-}, "java.awt.Color");
-Clazz.overrideMethod (c$, "getSeqrep",
-function () {
-return this.seqrep;
-});
-Clazz.overrideMethod (c$, "setSeqrep",
-function (seqrep) {
-this.seqrep = seqrep;
-}, "jalview.datamodel.SequenceI");
-Clazz.overrideMethod (c$, "hasSeqrep",
-function () {
-return this.seqrep != null;
-});
-Clazz.defineMethod (c$, "setHidereps",
-function (visibility) {
-this.hidereps = visibility;
-}, "~B");
-Clazz.defineMethod (c$, "isHidereps",
-function () {
-return this.hidereps;
-});
-Clazz.defineMethod (c$, "setHideCols",
-function (visibility) {
-this.hidecols = visibility;
-}, "~B");
-Clazz.defineMethod (c$, "isHideCols",
-function () {
-return this.hidecols;
-});
-Clazz.defineMethod (c$, "intersect",
-function (alignment, map) {
-var sgroup = new jalview.datamodel.SequenceGroup (this);
-var insect = this.getSequencesInOrder (alignment);
-sgroup.sequences = new java.util.ArrayList ();
-for (var s = 0; insect != null && s < insect.length; s++) {
-if (map == null || map.containsKey (insect[s])) {
-sgroup.sequences.add (insect[s]);
-}}
-return sgroup;
-}, "jalview.datamodel.AlignmentI,java.util.Map");
-Clazz.defineMethod (c$, "getShowNonconserved",
-function () {
-return this.showNonconserved;
-});
-Clazz.defineMethod (c$, "setShowNonconserved",
-function (displayNonconserved) {
-this.showNonconserved = displayNonconserved;
-}, "~B");
-Clazz.defineMethod (c$, "setConsensus",
-function (aan) {
-if (this.consensus == null) {
-this.consensus = aan;
-}}, "jalview.datamodel.AlignmentAnnotation");
-Clazz.defineMethod (c$, "getConsensus",
-function () {
-var aWidth = this.getWidth ();
-if (aWidth < 0) {
-return null;
-}if (this.consensus == null) {
-this.consensus = new jalview.datamodel.AlignmentAnnotation ("", "", new Array (1), 0, 100, 1);
-this.consensus.hasText = true;
-this.consensus.autoCalculated = true;
-this.consensus.groupRef = this;
-this.consensus.label = "Consensus for " + this.getName ();
-this.consensus.description = "Percent Identity";
-}return this.consensus;
-});
-Clazz.defineMethod (c$, "setConservationRow",
-function (aan) {
-if (this.conservation == null) {
-this.conservation = aan;
-}}, "jalview.datamodel.AlignmentAnnotation");
-Clazz.defineMethod (c$, "getConservationRow",
-function () {
-if (this.conservation == null) {
-this.conservation = new jalview.datamodel.AlignmentAnnotation ("", "", new Array (1), 0, 11, 1);
-}this.conservation.hasText = true;
-this.conservation.autoCalculated = true;
-this.conservation.groupRef = this;
-this.conservation.label = "Conservation for " + this.getName ();
-this.conservation.description = "Conservation for group " + this.getName () + " less than " + this.consPercGaps + "% gaps";
-return this.conservation;
-});
-Clazz.defineMethod (c$, "hasAnnotationRows",
-function () {
-return this.consensus != null || this.conservation != null;
-});
-Clazz.defineMethod (c$, "getConsensusSeq",
-function () {
-this.getConsensus ();
-var seqs = new StringBuffer ();
-for (var i = 0; i < this.consensus.annotations.length; i++) {
-if (this.consensus.annotations[i] != null) {
-if (this.consensus.annotations[i].description.charAt (0) == '[') {
-seqs.append (this.consensus.annotations[i].description.charAt (1));
-} else {
-seqs.append (this.consensus.annotations[i].displayCharacter);
-}}}
-var sq = new jalview.datamodel.Sequence ("Group" + this.getName () + " Consensus", seqs.toString ());
-sq.setDescription ("Percentage Identity Consensus " + ((this.ignoreGapsInConsensus) ? " without gaps" : ""));
-return sq;
-});
-Clazz.defineMethod (c$, "setIgnoreGapsConsensus",
-function (state) {
-if (this.ignoreGapsInConsensus != state && this.consensus != null) {
-this.ignoreGapsInConsensus = state;
-this.recalcConservation ();
-}this.ignoreGapsInConsensus = state;
-}, "~B");
-Clazz.defineMethod (c$, "getIgnoreGapsConsensus",
-function () {
-return this.ignoreGapsInConsensus;
-});
-Clazz.defineMethod (c$, "setshowSequenceLogo",
-function (showSequenceLogo) {
-if (this.showSequenceLogo != showSequenceLogo && this.consensus != null) {
-this.showSequenceLogo = showSequenceLogo;
-this.recalcConservation ();
-}this.showSequenceLogo = showSequenceLogo;
-}, "~B");
-Clazz.defineMethod (c$, "setShowConsensusHistogram",
-function (showConsHist) {
-if (this.showConsensusHistogram != showConsHist && this.consensus != null) {
-this.showConsensusHistogram = showConsHist;
-this.recalcConservation ();
-}this.showConsensusHistogram = showConsHist;
-}, "~B");
-Clazz.defineMethod (c$, "isShowConsensusHistogram",
-function () {
-return this.showConsensusHistogram;
-});
-Clazz.defineMethod (c$, "setNormaliseSequenceLogo",
-function (norm) {
-this.normaliseSequenceLogo = norm;
-}, "~B");
-Clazz.defineMethod (c$, "isNormaliseSequenceLogo",
-function () {
-return this.normaliseSequenceLogo;
-});
-Clazz.overrideMethod (c$, "getAlignmentAnnotation",
-function () {
-var annot = new java.util.ArrayList ();
-{
-for (var seq, $seq = this.sequences.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) {
-var aa = seq.getAnnotation ();
-if (aa != null) {
-for (var al, $al = 0, $$al = aa; $al < $$al.length && ((al = $$al[$al]) || true); $al++) {
-if (al.groupRef === this) {
-annot.add (al);
-}}
-}}
-if (this.consensus != null) {
-annot.add (this.consensus);
-}if (this.conservation != null) {
-annot.add (this.conservation);
-}}return annot.toArray ( new Array (0));
-});
-Clazz.overrideMethod (c$, "findAnnotation",
-function (calcId) {
-var aa = new java.util.ArrayList ();
-for (var a, $a = 0, $$a = this.getAlignmentAnnotation (); $a < $$a.length && ((a = $$a[$a]) || true); $a++) {
-if (a.getCalcId () === calcId) {
-aa.add (a);
-}}
-return aa;
-}, "~S");
-Clazz.overrideMethod (c$, "findAnnotations",
-function (seq, calcId, label) {
-var aa = new java.util.ArrayList ();
-for (var ann, $ann = 0, $$ann = this.getAlignmentAnnotation (); $ann < $$ann.length && ((ann = $$ann[$ann]) || true); $ann++) {
-if (ann.getCalcId () != null && ann.getCalcId ().equals (calcId) && ann.sequenceRef != null && ann.sequenceRef === seq && ann.label != null && ann.label.equals (label)) {
-aa.add (ann);
-}}
-return aa;
-}, "jalview.datamodel.SequenceI,~S,~S");
-Clazz.defineMethod (c$, "hasAnnotation",
-function (calcId) {
-if (calcId != null && !"".equals (calcId)) {
-for (var a, $a = 0, $$a = this.getAlignmentAnnotation (); $a < $$a.length && ((a = $$a[$a]) || true); $a++) {
-if (a.getCalcId () === calcId) {
-return true;
-}}
-}return false;
-}, "~S");
-Clazz.defineMethod (c$, "clear",
-function () {
-{
-this.sequences.clear ();
-}});
-Clazz.defineMethod (c$, "setContext",
-function (context) {
-this.context = context;
-}, "jalview.datamodel.AnnotatedCollectionI");
-Clazz.overrideMethod (c$, "getContext",
-function () {
-return this.context;
-});
-});
+Clazz.declarePackage ("jalview.datamodel");\r
+Clazz.load (["jalview.datamodel.AnnotatedCollectionI", "java.awt.Color", "java.util.ArrayList"], "jalview.datamodel.SequenceGroup", ["jalview.analysis.AAFrequency", "$.Conservation", "jalview.datamodel.AlignmentAnnotation", "$.Sequence", "jalview.schemes.ResidueProperties", "jalview.util.Comparison", "java.lang.StringBuffer"], function () {\r
+c$ = Clazz.decorateAsClass (function () {\r
+this.groupName = null;\r
+this.description = null;\r
+this.conserve = null;\r
+this.aaFrequency = null;\r
+this.displayBoxes = true;\r
+this.displayText = true;\r
+this.colourText = false;\r
+this.showNonconserved = false;\r
+this.sequences = null;\r
+this.seqrep = null;\r
+this.width = -1;\r
+this.cs = null;\r
+this.startRes = 0;\r
+this.endRes = 0;\r
+this.outlineColour = null;\r
+this.idColour = null;\r
+this.thresholdTextColour = 0;\r
+this.textColour = null;\r
+this.textColour2 = null;\r
+this.ignoreGapsInConsensus = true;\r
+this.showSequenceLogo = false;\r
+this.normaliseSequenceLogo = false;\r
+this.consPercGaps = 25;\r
+this.consensusData = null;\r
+this.hidereps = false;\r
+this.hidecols = false;\r
+this.consensus = null;\r
+this.conservation = null;\r
+this.showConsensusHistogram = false;\r
+this.context = null;\r
+Clazz.instantialize (this, arguments);\r
+}, jalview.datamodel, "SequenceGroup", null, jalview.datamodel.AnnotatedCollectionI);\r
+Clazz.prepareFields (c$, function () {\r
+this.sequences = new java.util.ArrayList ();\r
+this.outlineColour = java.awt.Color.black;\r
+this.textColour = java.awt.Color.black;\r
+this.textColour2 = java.awt.Color.white;\r
+});\r
+Clazz.defineMethod (c$, "isShowSequenceLogo", \r
+function () {\r
+return this.showSequenceLogo;\r
+});\r
+Clazz.makeConstructor (c$, \r
+function () {\r
+this.groupName = "JGroup:" + this.hashCode ();\r
+});\r
+Clazz.makeConstructor (c$, \r
+function (sequences, groupName, scheme, displayBoxes, displayText, colourText, start, end) {\r
+this.sequences = sequences;\r
+this.groupName = groupName;\r
+this.displayBoxes = displayBoxes;\r
+this.displayText = displayText;\r
+this.colourText = colourText;\r
+this.cs = scheme;\r
+this.startRes = start;\r
+this.endRes = end;\r
+this.recalcConservation ();\r
+}, "java.util.List,~S,jalview.schemes.ColourSchemeI,~B,~B,~B,~N,~N");\r
+Clazz.makeConstructor (c$, \r
+function (seqsel) {\r
+if (seqsel != null) {\r
+this.sequences = new java.util.ArrayList ();\r
+this.sequences.addAll (seqsel.sequences);\r
+if (seqsel.groupName != null) {\r
+this.groupName = String.instantialize (seqsel.groupName);\r
+}this.displayBoxes = seqsel.displayBoxes;\r
+this.displayText = seqsel.displayText;\r
+this.colourText = seqsel.colourText;\r
+this.startRes = seqsel.startRes;\r
+this.endRes = seqsel.endRes;\r
+this.cs = seqsel.cs;\r
+if (seqsel.description != null) {\r
+this.description = String.instantialize (seqsel.description);\r
+}this.hidecols = seqsel.hidecols;\r
+this.hidereps = seqsel.hidereps;\r
+this.idColour = seqsel.idColour;\r
+this.outlineColour = seqsel.outlineColour;\r
+this.seqrep = seqsel.seqrep;\r
+this.textColour = seqsel.textColour;\r
+this.textColour2 = seqsel.textColour2;\r
+this.thresholdTextColour = seqsel.thresholdTextColour;\r
+this.width = seqsel.width;\r
+this.ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;\r
+if (seqsel.conserve != null) {\r
+this.recalcConservation ();\r
+}}}, "jalview.datamodel.SequenceGroup");\r
+Clazz.defineMethod (c$, "getSelectionAsNewSequences", \r
+function (align) {\r
+var iSize = this.sequences.size ();\r
+var seqs = new Array (iSize);\r
+var inorder = this.getSequencesInOrder (align);\r
+for (var i = 0, ipos = 0; i < inorder.length; i++) {\r
+var seq = inorder[i];\r
+seqs[ipos] = seq.getSubSequence (this.startRes, this.endRes + 1);\r
+if (seqs[ipos] != null) {\r
+seqs[ipos].setDescription (seq.getDescription ());\r
+seqs[ipos].setDBRef (seq.getDBRef ());\r
+seqs[ipos].setSequenceFeatures (seq.getSequenceFeatures ());\r
+if (seq.getDatasetSequence () != null) {\r
+seqs[ipos].setDatasetSequence (seq.getDatasetSequence ());\r
+}if (seq.getAnnotation () != null) {\r
+var alann = align.getAlignmentAnnotation ();\r
+for (var a = 0; a < seq.getAnnotation ().length; a++) {\r
+var tocopy = seq.getAnnotation ()[a];\r
+if (alann != null) {\r
+var found = false;\r
+for (var pos = 0; pos < alann.length; pos++) {\r
+if (alann[pos] === tocopy) {\r
+found = true;\r
+break;\r
+}}\r
+if (!found) {\r
+continue;\r
+}}var newannot = new jalview.datamodel.AlignmentAnnotation (seq.getAnnotation ()[a]);\r
+newannot.restrict (this.startRes, this.endRes);\r
+newannot.setSequenceRef (seqs[ipos]);\r
+newannot.adjustForAlignment ();\r
+seqs[ipos].addAlignmentAnnotation (newannot);\r
+}\r
+}ipos++;\r
+} else {\r
+iSize--;\r
+}}\r
+if (iSize != inorder.length) {\r
+var nseqs = new Array (iSize);\r
+System.arraycopy (seqs, 0, nseqs, 0, iSize);\r
+seqs = nseqs;\r
+}return seqs;\r
+}, "jalview.datamodel.AlignmentI");\r
+Clazz.defineMethod (c$, "findEndRes", \r
+function (seq) {\r
+var eres = 0;\r
+var ch;\r
+for (var j = 0; j < this.endRes + 1 && j < seq.getLength (); j++) {\r
+ch = seq.getCharAt (j);\r
+if (!jalview.util.Comparison.isGap ((ch))) {\r
+eres++;\r
+}}\r
+if (eres > 0) {\r
+eres += seq.getStart () - 1;\r
+}return eres;\r
+}, "jalview.datamodel.SequenceI");\r
+Clazz.defineMethod (c$, "getSequences", \r
+function () {\r
+return this.sequences;\r
+});\r
+Clazz.defineMethod (c$, "getSequences", \r
+function (hiddenReps) {\r
+if (hiddenReps == null) {\r
+return this.sequences;\r
+} else {\r
+var allSequences = new java.util.ArrayList ();\r
+for (var seq, $seq = this.sequences.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) {\r
+allSequences.add (seq);\r
+if (hiddenReps.containsKey (seq)) {\r
+var hsg = hiddenReps.get (seq);\r
+for (var seq2, $seq2 = hsg.getSequences ().iterator (); $seq2.hasNext () && ((seq2 = $seq2.next ()) || true);) {\r
+if (seq2 !== seq && !allSequences.contains (seq2)) {\r
+allSequences.add (seq2);\r
+}}\r
+}}\r
+return allSequences;\r
+}}, "java.util.Map");\r
+Clazz.defineMethod (c$, "getSequencesAsArray", \r
+function (map) {\r
+var tmp = this.getSequences (map);\r
+if (tmp == null) {\r
+return null;\r
+}return tmp.toArray ( new Array (tmp.size ()));\r
+}, "java.util.Map");\r
+Clazz.defineMethod (c$, "adjustForRemoveLeft", \r
+function (col) {\r
+if (this.startRes >= col) {\r
+this.startRes = this.startRes - col;\r
+}if (this.endRes >= col) {\r
+this.endRes = this.endRes - col;\r
+if (this.startRes > this.endRes) {\r
+this.startRes = 0;\r
+}} else {\r
+return false;\r
+}return true;\r
+}, "~N");\r
+Clazz.defineMethod (c$, "adjustForRemoveRight", \r
+function (col) {\r
+if (this.startRes > col) {\r
+return false;\r
+}if (this.endRes >= col) {\r
+this.endRes = col;\r
+}return true;\r
+}, "~N");\r
+Clazz.defineMethod (c$, "getName", \r
+function () {\r
+return this.groupName;\r
+});\r
+Clazz.defineMethod (c$, "getDescription", \r
+function () {\r
+return this.description;\r
+});\r
+Clazz.defineMethod (c$, "setName", \r
+function (name) {\r
+this.groupName = name;\r
+}, "~S");\r
+Clazz.defineMethod (c$, "setDescription", \r
+function (desc) {\r
+this.description = desc;\r
+}, "~S");\r
+Clazz.defineMethod (c$, "getConservation", \r
+function () {\r
+return this.conserve;\r
+});\r
+Clazz.defineMethod (c$, "setConservation", \r
+function (c) {\r
+this.conserve = c;\r
+}, "jalview.analysis.Conservation");\r
+Clazz.defineMethod (c$, "addSequence", \r
+function (s, recalc) {\r
+{\r
+if (s != null && !this.sequences.contains (s)) {\r
+this.sequences.add (s);\r
+}if (recalc) {\r
+this.recalcConservation ();\r
+}}}, "jalview.datamodel.SequenceI,~B");\r
+Clazz.defineMethod (c$, "getConsPercGaps", \r
+function () {\r
+return this.consPercGaps;\r
+});\r
+Clazz.defineMethod (c$, "setConsPercGaps", \r
+function (consPercGaps) {\r
+this.consPercGaps = consPercGaps;\r
+}, "~N");\r
+Clazz.defineMethod (c$, "recalcConservation", \r
+function () {\r
+if (this.cs == null && this.consensus == null && this.conservation == null) {\r
+return;\r
+}try {\r
+var cnsns = jalview.analysis.AAFrequency.calculate (this.sequences, this.startRes, this.endRes + 1, this.showSequenceLogo);\r
+if (this.consensus != null) {\r
+this._updateConsensusRow (cnsns, this.sequences.size ());\r
+}if (this.cs != null) {\r
+this.cs.setConsensus (cnsns);\r
+}if ((this.conservation != null) || (this.cs != null && this.cs.conservationApplied ())) {\r
+var c = new jalview.analysis.Conservation (this.groupName, jalview.schemes.ResidueProperties.propHash, 3, this.sequences, this.startRes, this.endRes + 1);\r
+c.calculate ();\r
+c.verdict (false, this.consPercGaps);\r
+if (this.conservation != null) {\r
+this._updateConservationRow (c);\r
+}if (this.cs != null) {\r
+if (this.cs.conservationApplied ()) {\r
+this.cs.setConservation (c);\r
+}}}if (this.cs != null) {\r
+this.cs.alignmentChanged (this.context != null ? this.context : this, null);\r
+}} catch (err) {\r
+if (Clazz.exceptionOf (err, OutOfMemoryError)) {\r
+System.out.println ("Out of memory loading groups: " + err);\r
+} else {\r
+throw err;\r
+}\r
+}\r
+});\r
+Clazz.defineMethod (c$, "_updateConservationRow", \r
+($fz = function (c) {\r
+if (this.conservation == null) {\r
+this.getConservation ();\r
+}this.conservation.label = "Conservation for " + this.getName ();\r
+this.conservation.description = "Conservation for group " + this.getName () + " less than " + this.consPercGaps + "% gaps";\r
+var aWidth = (this.conservation.annotations != null) ? (this.endRes < this.conservation.annotations.length ? this.conservation.annotations.length : this.endRes + 1) : this.endRes + 1;\r
+this.conservation.annotations = null;\r
+this.conservation.annotations = new Array (aWidth);\r
+c.completeAnnotations (this.conservation, null, this.startRes, this.endRes + 1);\r
+}, $fz.isPrivate = true, $fz), "jalview.analysis.Conservation");\r
+Clazz.defineMethod (c$, "_updateConsensusRow", \r
+($fz = function (cnsns, nseq) {\r
+if (this.consensus == null) {\r
+this.getConsensus ();\r
+}this.consensus.label = "Consensus for " + this.getName ();\r
+this.consensus.description = "Percent Identity";\r
+this.consensusData = cnsns;\r
+var aWidth = (this.consensus.annotations != null) ? (this.endRes < this.consensus.annotations.length ? this.consensus.annotations.length : this.endRes + 1) : this.endRes + 1;\r
+this.consensus.annotations = null;\r
+this.consensus.annotations = new Array (aWidth);\r
+jalview.analysis.AAFrequency.completeConsensus (this.consensus, cnsns, this.startRes, this.endRes + 1, this.ignoreGapsInConsensus, this.showSequenceLogo, nseq);\r
+}, $fz.isPrivate = true, $fz), "~A,~N");\r
+Clazz.defineMethod (c$, "addOrRemove", \r
+function (s, recalc) {\r
+{\r
+if (this.sequences.contains (s)) {\r
+this.deleteSequence (s, recalc);\r
+} else {\r
+this.addSequence (s, recalc);\r
+}}}, "jalview.datamodel.SequenceI,~B");\r
+Clazz.defineMethod (c$, "deleteSequence", \r
+function (s, recalc) {\r
+{\r
+this.sequences.remove (s);\r
+if (recalc) {\r
+this.recalcConservation ();\r
+}}}, "jalview.datamodel.SequenceI,~B");\r
+Clazz.overrideMethod (c$, "getStartRes", \r
+function () {\r
+return this.startRes;\r
+});\r
+Clazz.overrideMethod (c$, "getEndRes", \r
+function () {\r
+return this.endRes;\r
+});\r
+Clazz.defineMethod (c$, "setStartRes", \r
+function (i) {\r
+this.startRes = i;\r
+}, "~N");\r
+Clazz.defineMethod (c$, "setEndRes", \r
+function (i) {\r
+this.endRes = i;\r
+}, "~N");\r
+Clazz.defineMethod (c$, "getSize", \r
+function () {\r
+return this.sequences.size ();\r
+});\r
+Clazz.defineMethod (c$, "getSequenceAt", \r
+function (i) {\r
+return this.sequences.get (i);\r
+}, "~N");\r
+Clazz.defineMethod (c$, "setColourText", \r
+function (state) {\r
+this.colourText = state;\r
+}, "~B");\r
+Clazz.defineMethod (c$, "getColourText", \r
+function () {\r
+return this.colourText;\r
+});\r
+Clazz.defineMethod (c$, "setDisplayText", \r
+function (state) {\r
+this.displayText = state;\r
+}, "~B");\r
+Clazz.defineMethod (c$, "getDisplayText", \r
+function () {\r
+return this.displayText;\r
+});\r
+Clazz.defineMethod (c$, "setDisplayBoxes", \r
+function (state) {\r
+this.displayBoxes = state;\r
+}, "~B");\r
+Clazz.defineMethod (c$, "getDisplayBoxes", \r
+function () {\r
+return this.displayBoxes;\r
+});\r
+Clazz.overrideMethod (c$, "getWidth", \r
+function () {\r
+{\r
+var first = true;\r
+for (var seq, $seq = this.sequences.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) {\r
+if (first || seq.getLength () > this.width) {\r
+this.width = seq.getLength ();\r
+first = false;\r
+}}\r
+return this.width;\r
+}});\r
+Clazz.defineMethod (c$, "setOutlineColour", \r
+function (c) {\r
+this.outlineColour = c;\r
+}, "java.awt.Color");\r
+Clazz.defineMethod (c$, "getOutlineColour", \r
+function () {\r
+return this.outlineColour;\r
+});\r
+Clazz.defineMethod (c$, "getSequencesInOrder", \r
+function (al) {\r
+return this.getSequencesInOrder (al, true);\r
+}, "jalview.datamodel.AlignmentI");\r
+Clazz.defineMethod (c$, "getSequencesInOrder", \r
+function (al, trim) {\r
+{\r
+var sSize = this.sequences.size ();\r
+var alHeight = al.getHeight ();\r
+var seqs = new Array ((trim) ? sSize : alHeight);\r
+var index = 0;\r
+for (var i = 0; i < alHeight && index < sSize; i++) {\r
+if (this.sequences.contains (al.getSequenceAt (i))) {\r
+seqs[(trim) ? index : i] = al.getSequenceAt (i);\r
+index++;\r
+}}\r
+if (index == 0) {\r
+return null;\r
+}if (!trim) {\r
+return seqs;\r
+}if (index < seqs.length) {\r
+var dummy = seqs;\r
+seqs = new Array (index);\r
+while (--index >= 0) {\r
+seqs[index] = dummy[index];\r
+dummy[index] = null;\r
+}\r
+}return seqs;\r
+}}, "jalview.datamodel.AlignmentI,~B");\r
+Clazz.defineMethod (c$, "getIdColour", \r
+function () {\r
+return this.idColour;\r
+});\r
+Clazz.defineMethod (c$, "setIdColour", \r
+function (idColour) {\r
+this.idColour = idColour;\r
+}, "java.awt.Color");\r
+Clazz.overrideMethod (c$, "getSeqrep", \r
+function () {\r
+return this.seqrep;\r
+});\r
+Clazz.overrideMethod (c$, "setSeqrep", \r
+function (seqrep) {\r
+this.seqrep = seqrep;\r
+}, "jalview.datamodel.SequenceI");\r
+Clazz.overrideMethod (c$, "hasSeqrep", \r
+function () {\r
+return this.seqrep != null;\r
+});\r
+Clazz.defineMethod (c$, "setHidereps", \r
+function (visibility) {\r
+this.hidereps = visibility;\r
+}, "~B");\r
+Clazz.defineMethod (c$, "isHidereps", \r
+function () {\r
+return this.hidereps;\r
+});\r
+Clazz.defineMethod (c$, "setHideCols", \r
+function (visibility) {\r
+this.hidecols = visibility;\r
+}, "~B");\r
+Clazz.defineMethod (c$, "isHideCols", \r
+function () {\r
+return this.hidecols;\r
+});\r
+Clazz.defineMethod (c$, "intersect", \r
+function (alignment, map) {\r
+var sgroup = new jalview.datamodel.SequenceGroup (this);\r
+var insect = this.getSequencesInOrder (alignment);\r
+sgroup.sequences = new java.util.ArrayList ();\r
+for (var s = 0; insect != null && s < insect.length; s++) {\r
+if (map == null || map.containsKey (insect[s])) {\r
+sgroup.sequences.add (insect[s]);\r
+}}\r
+return sgroup;\r
+}, "jalview.datamodel.AlignmentI,java.util.Map");\r
+Clazz.defineMethod (c$, "getShowNonconserved", \r
+function () {\r
+return this.showNonconserved;\r
+});\r
+Clazz.defineMethod (c$, "setShowNonconserved", \r
+function (displayNonconserved) {\r
+this.showNonconserved = displayNonconserved;\r
+}, "~B");\r
+Clazz.defineMethod (c$, "setConsensus", \r
+function (aan) {\r
+if (this.consensus == null) {\r
+this.consensus = aan;\r
+}}, "jalview.datamodel.AlignmentAnnotation");\r
+Clazz.defineMethod (c$, "getConsensus", \r
+function () {\r
+var aWidth = this.getWidth ();\r
+if (aWidth < 0) {\r
+return null;\r
+}if (this.consensus == null) {\r
+this.consensus = new jalview.datamodel.AlignmentAnnotation ("", "", new Array (1), 0, 100, 1);\r
+this.consensus.hasText = true;\r
+this.consensus.autoCalculated = true;\r
+this.consensus.groupRef = this;\r
+this.consensus.label = "Consensus for " + this.getName ();\r
+this.consensus.description = "Percent Identity";\r
+}return this.consensus;\r
+});\r
+Clazz.defineMethod (c$, "setConservationRow", \r
+function (aan) {\r
+if (this.conservation == null) {\r
+this.conservation = aan;\r
+}}, "jalview.datamodel.AlignmentAnnotation");\r
+Clazz.defineMethod (c$, "getConservationRow", \r
+function () {\r
+if (this.conservation == null) {\r
+this.conservation = new jalview.datamodel.AlignmentAnnotation ("", "", new Array (1), 0, 11, 1);\r
+}this.conservation.hasText = true;\r
+this.conservation.autoCalculated = true;\r
+this.conservation.groupRef = this;\r
+this.conservation.label = "Conservation for " + this.getName ();\r
+this.conservation.description = "Conservation for group " + this.getName () + " less than " + this.consPercGaps + "% gaps";\r
+return this.conservation;\r
+});\r
+Clazz.defineMethod (c$, "hasAnnotationRows", \r
+function () {\r
+return this.consensus != null || this.conservation != null;\r
+});\r
+Clazz.defineMethod (c$, "getConsensusSeq", \r
+function () {\r
+this.getConsensus ();\r
+var seqs = new StringBuffer ();\r
+for (var i = 0; i < this.consensus.annotations.length; i++) {\r
+if (this.consensus.annotations[i] != null) {\r
+if (this.consensus.annotations[i].description.charAt (0) == '[') {\r
+seqs.append (this.consensus.annotations[i].description.charAt (1));\r
+} else {\r
+seqs.append (this.consensus.annotations[i].displayCharacter);\r
+}}}\r
+var sq = new jalview.datamodel.Sequence ("Group" + this.getName () + " Consensus", seqs.toString ());\r
+sq.setDescription ("Percentage Identity Consensus " + ((this.ignoreGapsInConsensus) ? " without gaps" : ""));\r
+return sq;\r
+});\r
+Clazz.defineMethod (c$, "setIgnoreGapsConsensus", \r
+function (state) {\r
+if (this.ignoreGapsInConsensus != state && this.consensus != null) {\r
+this.ignoreGapsInConsensus = state;\r
+this.recalcConservation ();\r
+}this.ignoreGapsInConsensus = state;\r
+}, "~B");\r
+Clazz.defineMethod (c$, "getIgnoreGapsConsensus", \r
+function () {\r
+return this.ignoreGapsInConsensus;\r
+});\r
+Clazz.defineMethod (c$, "setshowSequenceLogo", \r
+function (showSequenceLogo) {\r
+if (this.showSequenceLogo != showSequenceLogo && this.consensus != null) {\r
+this.showSequenceLogo = showSequenceLogo;\r
+this.recalcConservation ();\r
+}this.showSequenceLogo = showSequenceLogo;\r
+}, "~B");\r
+Clazz.defineMethod (c$, "setShowConsensusHistogram", \r
+function (showConsHist) {\r
+if (this.showConsensusHistogram != showConsHist && this.consensus != null) {\r
+this.showConsensusHistogram = showConsHist;\r
+this.recalcConservation ();\r
+}this.showConsensusHistogram = showConsHist;\r
+}, "~B");\r
+Clazz.defineMethod (c$, "isShowConsensusHistogram", \r
+function () {\r
+return this.showConsensusHistogram;\r
+});\r
+Clazz.defineMethod (c$, "setNormaliseSequenceLogo", \r
+function (norm) {\r
+this.normaliseSequenceLogo = norm;\r
+}, "~B");\r
+Clazz.defineMethod (c$, "isNormaliseSequenceLogo", \r
+function () {\r
+return this.normaliseSequenceLogo;\r
+});\r
+Clazz.overrideMethod (c$, "getAlignmentAnnotation", \r
+function () {\r
+var annot = new java.util.ArrayList ();\r
+{\r
+for (var seq, $seq = this.sequences.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) {\r
+var aa = seq.getAnnotation ();\r
+if (aa != null) {\r
+for (var al, $al = 0, $$al = aa; $al < $$al.length && ((al = $$al[$al]) || true); $al++) {\r
+if (al.groupRef === this) {\r
+annot.add (al);\r
+}}\r
+}}\r
+if (this.consensus != null) {\r
+annot.add (this.consensus);\r
+}if (this.conservation != null) {\r
+annot.add (this.conservation);\r
+}}return annot.toArray ( new Array (0));\r
+});\r
+Clazz.overrideMethod (c$, "findAnnotation", \r
+function (calcId) {\r
+var aa = new java.util.ArrayList ();\r
+for (var a, $a = 0, $$a = this.getAlignmentAnnotation (); $a < $$a.length && ((a = $$a[$a]) || true); $a++) {\r
+if (a.getCalcId () === calcId) {\r
+aa.add (a);\r
+}}\r
+return aa;\r
+}, "~S");\r
+Clazz.overrideMethod (c$, "findAnnotations", \r
+function (seq, calcId, label) {\r
+var aa = new java.util.ArrayList ();\r
+for (var ann, $ann = 0, $$ann = this.getAlignmentAnnotation (); $ann < $$ann.length && ((ann = $$ann[$ann]) || true); $ann++) {\r
+if (ann.getCalcId () != null && ann.getCalcId ().equals (calcId) && ann.sequenceRef != null && ann.sequenceRef === seq && ann.label != null && ann.label.equals (label)) {\r
+aa.add (ann);\r
+}}\r
+return aa;\r
+}, "jalview.datamodel.SequenceI,~S,~S");\r
+Clazz.defineMethod (c$, "hasAnnotation", \r
+function (calcId) {\r
+if (calcId != null && !"".equals (calcId)) {\r
+for (var a, $a = 0, $$a = this.getAlignmentAnnotation (); $a < $$a.length && ((a = $$a[$a]) || true); $a++) {\r
+if (a.getCalcId () === calcId) {\r
+return true;\r
+}}\r
+}return false;\r
+}, "~S");\r
+Clazz.defineMethod (c$, "clear", \r
+function () {\r
+{\r
+this.sequences.clear ();\r
+}});\r
+Clazz.defineMethod (c$, "setContext", \r
+function (context) {\r
+this.context = context;\r
+}, "jalview.datamodel.AnnotatedCollectionI");\r
+Clazz.overrideMethod (c$, "getContext", \r
+function () {\r
+return this.context;\r
+});\r
+});\r
git://source.jalview.org / jalviewjs.git / blobdiff