-Clazz.declarePackage ("jalview.analysis");
-Clazz.load (["jalview.analysis.CodonComparator"], "jalview.analysis.Dna", ["jalview.datamodel.AlignedCodon", "$.AlignedCodonFrame", "$.Alignment", "$.AlignmentAnnotation", "$.Annotation", "$.DBRefSource", "$.FeatureProperties", "$.GraphLine", "$.Sequence", "jalview.schemes.ResidueProperties", "jalview.util.Comparison", "$.DBRefUtils", "$.MapList", "$.ShiftList", "java.lang.IllegalStateException", "$.StringBuilder", "java.util.ArrayList", "$.Arrays"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.selection = null;
-this.seqstring = null;
-this.contigs = null;
-this.gapChar = '\0';
-this.annotations = null;
-this.dnaWidth = 0;
-this.dataset = null;
-this.aaWidth = 0;
-this.alignedCodons = null;
-Clazz.instantialize (this, arguments);
-}, jalview.analysis, "Dna");
-Clazz.makeConstructor (c$,
-function (viewport, visibleContigs) {
-this.selection = java.util.Arrays.asList (viewport.getSequenceSelection ());
-this.seqstring = viewport.getViewAsString (true);
-this.contigs = visibleContigs;
-this.gapChar = viewport.getGapCharacter ();
-this.annotations = viewport.getAlignment ().getAlignmentAnnotation ();
-this.dnaWidth = viewport.getAlignment ().getWidth ();
-this.dataset = viewport.getAlignment ().getDataset ();
-}, "jalview.api.AlignViewportI,~A");
-c$.compareCodonPos = Clazz.defineMethod (c$, "compareCodonPos",
-function (ac1, ac2) {
-return jalview.analysis.Dna.comparator.compare (ac1, ac2);
-}, "jalview.datamodel.AlignedCodon,jalview.datamodel.AlignedCodon");
-Clazz.defineMethod (c$, "translateCdna",
-function () {
-var acf = new jalview.datamodel.AlignedCodonFrame ();
-this.alignedCodons = new Array (this.dnaWidth);
-var s;
-var sSize = this.selection.size ();
-var pepseqs = new java.util.ArrayList ();
-for (s = 0; s < sSize; s++) {
-var newseq = this.translateCodingRegion (this.selection.get (s), this.seqstring[s], acf, pepseqs);
-if (newseq != null) {
-pepseqs.add (newseq);
-var ds = newseq;
-if (this.dataset != null) {
-while (ds.getDatasetSequence () != null) {
-ds = ds.getDatasetSequence ();
-}
-this.dataset.addSequence (ds);
-}}}
-var newseqs = pepseqs.toArray ( new Array (pepseqs.size ()));
-var al = new jalview.datamodel.Alignment (newseqs);
-al.padGaps ();
-al.setDataset (this.dataset);
-this.translateAlignedAnnotations (al, acf);
-al.addCodonFrame (acf);
-return al;
-});
-c$.canTranslate = Clazz.defineMethod (c$, "canTranslate",
-function (selection, viscontigs) {
-for (var gd = 0; gd < selection.length; gd++) {
-var dna = selection[gd];
-var dnarefs = jalview.util.DBRefUtils.selectRefs (dna.getDBRef (), jalview.datamodel.DBRefSource.DNACODINGDBS);
-if (dnarefs != null) {
-var mappedrefs = new java.util.ArrayList ();
-var refs = dna.getDBRef ();
-for (var d = 0; d < refs.length; d++) {
-if (refs[d].getMap () != null && refs[d].getMap ().getMap () != null && refs[d].getMap ().getMap ().getFromRatio () == 3 && refs[d].getMap ().getMap ().getToRatio () == 1) {
-mappedrefs.add (refs[d]);
-}}
-dnarefs = mappedrefs.toArray ( new Array (mappedrefs.size ()));
-for (var d = 0; d < dnarefs.length; d++) {
-var mp = dnarefs[d].getMap ();
-if (mp != null) {
-for (var vc = 0; vc < viscontigs.length; vc += 2) {
-var mpr = mp.locateMappedRange (viscontigs[vc], viscontigs[vc + 1]);
-if (mpr != null) {
-return true;
-}}
-}}
-}}
-return false;
-}, "~A,~A");
-Clazz.defineMethod (c$, "translateAlignedAnnotations",
-function (al, acf) {
-if (this.annotations != null) {
-for (var annotation, $annotation = 0, $$annotation = this.annotations; $annotation < $$annotation.length && ((annotation = $$annotation[$annotation]) || true); $annotation++) {
-if (annotation.autoCalculated || !annotation.visible || annotation.isRNA ()) {
-continue;
-}var aSize = this.aaWidth;
-var anots = (annotation.annotations == null) ? null : new Array (aSize);
-if (anots != null) {
-for (var a = 0; a < aSize; a++) {
-if (a < this.alignedCodons.length && this.alignedCodons[a] != null && this.alignedCodons[a].pos1 == (this.alignedCodons[a].pos3 - 2)) {
-anots[a] = jalview.analysis.Dna.getCodonAnnotation (this.alignedCodons[a], annotation.annotations);
-}}
-}var aa = new jalview.datamodel.AlignmentAnnotation (annotation.label, annotation.description, anots);
-aa.graph = annotation.graph;
-aa.graphGroup = annotation.graphGroup;
-aa.graphHeight = annotation.graphHeight;
-if (annotation.getThreshold () != null) {
-aa.setThreshold ( new jalview.datamodel.GraphLine (annotation.getThreshold ()));
-}if (annotation.$hasScore) {
-aa.setScore (annotation.getScore ());
-}var seqRef = annotation.sequenceRef;
-if (seqRef != null) {
-var aaSeq = acf.getAaForDnaSeq (seqRef);
-if (aaSeq != null) {
-aa.setSequenceRef (aaSeq);
-aa.createSequenceMapping (aaSeq, aaSeq.getStart (), true);
-aa.adjustForAlignment ();
-aaSeq.addAlignmentAnnotation (aa);
-}}al.addAnnotation (aa);
-}
-}}, "jalview.datamodel.AlignmentI,jalview.datamodel.AlignedCodonFrame");
-c$.getCodonAnnotation = Clazz.defineMethod (c$, "getCodonAnnotation",
-($fz = function (is, annotations) {
-var contrib = 0;
-var annot = null;
-for (var p = 1; p <= 3; p++) {
-var dnaCol = is.getBaseColumn (p);
-if (annotations[dnaCol] != null) {
-if (annot == null) {
-annot = new jalview.datamodel.Annotation (annotations[dnaCol]);
-contrib = 1;
-} else {
-var cpy = new jalview.datamodel.Annotation (annotations[dnaCol]);
-if (annot.colour == null) {
-annot.colour = cpy.colour;
-}if (annot.description == null || annot.description.length == 0) {
-annot.description = cpy.description;
-}if (annot.displayCharacter == null) {
-annot.displayCharacter = cpy.displayCharacter;
-}if (annot.secondaryStructure.charCodeAt (0) == 0) {
-annot.secondaryStructure = cpy.secondaryStructure;
-}annot.value += cpy.value;
-contrib++;
-}}}
-if (contrib > 1) {
-annot.value /= contrib;
-}return annot;
-}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignedCodon,~A");
-Clazz.defineMethod (c$, "translateCodingRegion",
-function (selection, seqstring, acf, proteinSeqs) {
-var skip = new java.util.ArrayList ();
-var skipint = null;
-var vismapping = new jalview.util.ShiftList ();
-var vc;
-var scontigs = Clazz.newIntArray (this.contigs.length, 0);
-var npos = 0;
-for (vc = 0; vc < this.contigs.length; vc += 2) {
-if (vc == 0) {
-vismapping.addShift (npos, this.contigs[vc]);
-} else {
-vismapping.addShift (npos, this.contigs[vc] - this.contigs[vc - 1] + 1);
-}scontigs[vc] = this.contigs[vc];
-scontigs[vc + 1] = this.contigs[vc + 1];
-}
-var protein = new StringBuilder (Clazz.doubleToInt (seqstring.length / 2));
-var seq = seqstring.$replace ('U', 'T').$replace ('u', 'T');
-var codon = Clazz.newCharArray (3, '\0');
-var cdp = Clazz.newIntArray (3, 0);
-var rf = 0;
-var lastnpos = 0;
-var nend;
-var aspos = 0;
-var resSize = 0;
-for (npos = 0, nend = seq.length; npos < nend; npos++) {
-if (!jalview.util.Comparison.isGap (seq.charAt (npos))) {
-cdp[rf] = npos;
-codon[rf++] = seq.charAt (npos);
-}if (rf == 3) {
-var alignedCodon = new jalview.datamodel.AlignedCodon (cdp[0], cdp[1], cdp[2]);
-var aa = jalview.schemes.ResidueProperties.codonTranslate ( String.instantialize (codon));
-rf = 0;
-var gapString = String.valueOf (this.gapChar);
-if (aa == null) {
-aa = gapString;
-if (skipint == null) {
-skipint = Clazz.newIntArray (-1, [alignedCodon.pos1, alignedCodon.pos3]);
-}skipint[1] = alignedCodon.pos3;
-} else {
-if (skipint != null) {
-skipint[0] = vismapping.shift (skipint[0]);
-skipint[1] = vismapping.shift (skipint[1]);
-for (vc = 0; vc < scontigs.length; ) {
-if (scontigs[vc + 1] < skipint[0]) {
-vc += 2;
-continue;
-}if (scontigs[vc] > skipint[1]) {
-break;
-}var t;
-if (scontigs[vc] <= skipint[0]) {
-if (skipint[0] == scontigs[vc]) {
-if (scontigs[vc + 1] > skipint[1]) {
-scontigs[vc] = skipint[1];
-vc += 2;
-} else {
-if (scontigs[vc + 1] == skipint[1]) {
-t = Clazz.newIntArray (scontigs.length - 2, 0);
-if (vc > 0) {
-System.arraycopy (scontigs, 0, t, 0, vc - 1);
-}if (vc + 2 < t.length) {
-System.arraycopy (scontigs, vc + 2, t, vc, t.length - vc + 2);
-}scontigs = t;
-} else {
-scontigs[vc + 1] = skipint[0] - 1;
-vc += 2;
-}}} else {
-if (scontigs[vc + 1] < skipint[1]) {
-scontigs[vc + 1] = skipint[0] - 1;
-vc += 2;
-} else {
-t = Clazz.newIntArray (scontigs.length + 2, 0);
-System.arraycopy (scontigs, 0, t, 0, vc + 1);
-t[vc + 1] = skipint[0];
-t[vc + 2] = skipint[1];
-System.arraycopy (scontigs, vc + 1, t, vc + 3, scontigs.length - (vc + 1));
-scontigs = t;
-vc += 4;
-}}}}
-skip.add (skipint);
-skipint = null;
-}if (aa.equals ("STOP")) {
-aa = "X";
-}resSize++;
-}var findpos = true;
-while (findpos) {
-var compareCodonPos = jalview.analysis.Dna.compareCodonPos (alignedCodon, this.alignedCodons[aspos]);
-switch (compareCodonPos) {
-case -1:
-this.insertAAGap (aspos, proteinSeqs);
-findpos = false;
-break;
-case 1:
-aa = gapString + aa;
-aspos++;
-break;
-case 0:
-findpos = false;
-}
-}
-protein.append (aa);
-lastnpos = npos;
-if (this.alignedCodons[aspos] == null) {
-this.alignedCodons[aspos] = alignedCodon;
-} else if (!this.alignedCodons[aspos].equals (alignedCodon)) {
-throw new IllegalStateException ("Tried to coalign " + this.alignedCodons[aspos].toString () + " with " + alignedCodon.toString ());
-}if (aspos >= this.aaWidth) {
-this.aaWidth = aspos;
-}aspos++;
-}}
-if (resSize > 0) {
-var newseq = new jalview.datamodel.Sequence (selection.getName (), protein.toString ());
-if (rf != 0) {
-var errMsg = "trimming contigs for incomplete terminal codon.";
-System.err.println ("trimming contigs for incomplete terminal codon.");
-vc = scontigs.length - 1;
-lastnpos = vismapping.shift (lastnpos);
-while (vc >= 0 && scontigs[vc] > lastnpos) {
-if (vc > 0 && scontigs[vc - 1] > lastnpos) {
-vc -= 2;
-} else {
-scontigs[vc] = lastnpos;
-}}
-if (vc > 0 && (vc + 1) < scontigs.length) {
-var t = Clazz.newIntArray (vc + 1, 0);
-System.arraycopy (scontigs, 0, t, 0, vc + 1);
-scontigs = t;
-}if (vc <= 0) {
-scontigs = null;
-}}if (scontigs != null) {
-npos = 0;
-for (vc = 0; vc < scontigs.length; vc += 2) {
-scontigs[vc] = selection.findPosition (scontigs[vc]);
-scontigs[vc + 1] = selection.findPosition (scontigs[vc + 1]);
-if (scontigs[vc + 1] == selection.getEnd ()) {
-break;
-}}
-if ((vc + 2) < scontigs.length) {
-var t = Clazz.newIntArray (vc + 2, 0);
-System.arraycopy (scontigs, 0, t, 0, vc + 2);
-scontigs = t;
-}var map = new jalview.util.MapList (scontigs, Clazz.newIntArray (-1, [1, resSize]), 3, 1);
-jalview.analysis.Dna.transferCodedFeatures (selection, newseq, map, null, null);
-var rseq = newseq.deriveSequence ();
-acf.addMap (selection, rseq, map);
-return rseq;
-}}return null;
-}, "jalview.datamodel.SequenceI,~S,jalview.datamodel.AlignedCodonFrame,java.util.List");
-Clazz.defineMethod (c$, "insertAAGap",
-function (pos, proteinSeqs) {
-this.aaWidth++;
-for (var seq, $seq = proteinSeqs.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) {
-seq.insertCharAt (pos, this.gapChar);
-}
-this.checkCodonFrameWidth ();
-if (pos < this.aaWidth) {
-this.aaWidth++;
-System.arraycopy (this.alignedCodons, pos, this.alignedCodons, pos + 1, this.alignedCodons.length - pos - 1);
-this.alignedCodons[pos] = null;
-}}, "~N,java.util.List");
-Clazz.defineMethod (c$, "checkCodonFrameWidth",
-function () {
-if (this.alignedCodons[this.alignedCodons.length - 1] != null) {
-var c = new Array (this.alignedCodons.length + 10);
-System.arraycopy (this.alignedCodons, 0, c, 0, this.alignedCodons.length);
-this.alignedCodons = c;
-}});
-c$.transferCodedFeatures = Clazz.defineMethod (c$, "transferCodedFeatures",
-($fz = function (dna, pep, map, featureTypes, featureGroups) {
-var sfs = dna.getSequenceFeatures ();
-var fgstate;
-var dnarefs = jalview.util.DBRefUtils.selectRefs (dna.getDBRef (), jalview.datamodel.DBRefSource.DNACODINGDBS);
-if (dnarefs != null) {
-for (var d = 0; d < dnarefs.length; d++) {
-var mp = dnarefs[d].getMap ();
-if (mp != null) {
-}}
-}if (sfs != null) {
-for (var sf, $sf = 0, $$sf = sfs; $sf < $$sf.length && ((sf = $$sf[$sf]) || true); $sf++) {
-fgstate = (featureGroups == null) ? null : featureGroups.get (sf.featureGroup);
-if ((featureTypes == null || featureTypes.containsKey (sf.getType ())) && (fgstate == null || fgstate.booleanValue ())) {
-if (jalview.datamodel.FeatureProperties.isCodingFeature (null, sf.getType ())) {
-{
-}}}}
-}}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,jalview.util.MapList,java.util.Map,java.util.Map");
-Clazz.defineStatics (c$,
-"STOP_X", "X");
-c$.comparator = c$.prototype.comparator = new jalview.analysis.CodonComparator ();
-});
+Clazz.declarePackage ("jalview.analysis");\r
+Clazz.load (["jalview.analysis.CodonComparator"], "jalview.analysis.Dna", ["jalview.datamodel.AlignedCodon", "$.AlignedCodonFrame", "$.Alignment", "$.AlignmentAnnotation", "$.Annotation", "$.DBRefSource", "$.FeatureProperties", "$.GraphLine", "$.Sequence", "jalview.schemes.ResidueProperties", "jalview.util.Comparison", "$.DBRefUtils", "$.MapList", "$.ShiftList", "java.lang.IllegalStateException", "$.StringBuilder", "java.util.ArrayList", "$.Arrays"], function () {\r
+c$ = Clazz.decorateAsClass (function () {\r
+this.selection = null;\r
+this.seqstring = null;\r
+this.contigs = null;\r
+this.gapChar = '\0';\r
+this.annotations = null;\r
+this.dnaWidth = 0;\r
+this.dataset = null;\r
+this.aaWidth = 0;\r
+this.alignedCodons = null;\r
+Clazz.instantialize (this, arguments);\r
+}, jalview.analysis, "Dna");\r
+Clazz.makeConstructor (c$, \r
+function (viewport, visibleContigs) {\r
+this.selection = java.util.Arrays.asList (viewport.getSequenceSelection ());\r
+this.seqstring = viewport.getViewAsString (true);\r
+this.contigs = visibleContigs;\r
+this.gapChar = viewport.getGapCharacter ();\r
+this.annotations = viewport.getAlignment ().getAlignmentAnnotation ();\r
+this.dnaWidth = viewport.getAlignment ().getWidth ();\r
+this.dataset = viewport.getAlignment ().getDataset ();\r
+}, "jalview.api.AlignViewportI,~A");\r
+c$.compareCodonPos = Clazz.defineMethod (c$, "compareCodonPos", \r
+function (ac1, ac2) {\r
+return jalview.analysis.Dna.comparator.compare (ac1, ac2);\r
+}, "jalview.datamodel.AlignedCodon,jalview.datamodel.AlignedCodon");\r
+Clazz.defineMethod (c$, "translateCdna", \r
+function () {\r
+var acf = new jalview.datamodel.AlignedCodonFrame ();\r
+this.alignedCodons = new Array (this.dnaWidth);\r
+var s;\r
+var sSize = this.selection.size ();\r
+var pepseqs = new java.util.ArrayList ();\r
+for (s = 0; s < sSize; s++) {\r
+var newseq = this.translateCodingRegion (this.selection.get (s), this.seqstring[s], acf, pepseqs);\r
+if (newseq != null) {\r
+pepseqs.add (newseq);\r
+var ds = newseq;\r
+if (this.dataset != null) {\r
+while (ds.getDatasetSequence () != null) {\r
+ds = ds.getDatasetSequence ();\r
+}\r
+this.dataset.addSequence (ds);\r
+}}}\r
+var newseqs = pepseqs.toArray ( new Array (pepseqs.size ()));\r
+var al = new jalview.datamodel.Alignment (newseqs);\r
+al.padGaps ();\r
+al.setDataset (this.dataset);\r
+this.translateAlignedAnnotations (al, acf);\r
+al.addCodonFrame (acf);\r
+return al;\r
+});\r
+c$.canTranslate = Clazz.defineMethod (c$, "canTranslate", \r
+function (selection, viscontigs) {\r
+for (var gd = 0; gd < selection.length; gd++) {\r
+var dna = selection[gd];\r
+var dnarefs = jalview.util.DBRefUtils.selectRefs (dna.getDBRef (), jalview.datamodel.DBRefSource.DNACODINGDBS);\r
+if (dnarefs != null) {\r
+var mappedrefs = new java.util.ArrayList ();\r
+var refs = dna.getDBRef ();\r
+for (var d = 0; d < refs.length; d++) {\r
+if (refs[d].getMap () != null && refs[d].getMap ().getMap () != null && refs[d].getMap ().getMap ().getFromRatio () == 3 && refs[d].getMap ().getMap ().getToRatio () == 1) {\r
+mappedrefs.add (refs[d]);\r
+}}\r
+dnarefs = mappedrefs.toArray ( new Array (mappedrefs.size ()));\r
+for (var d = 0; d < dnarefs.length; d++) {\r
+var mp = dnarefs[d].getMap ();\r
+if (mp != null) {\r
+for (var vc = 0; vc < viscontigs.length; vc += 2) {\r
+var mpr = mp.locateMappedRange (viscontigs[vc], viscontigs[vc + 1]);\r
+if (mpr != null) {\r
+return true;\r
+}}\r
+}}\r
+}}\r
+return false;\r
+}, "~A,~A");\r
+Clazz.defineMethod (c$, "translateAlignedAnnotations", \r
+function (al, acf) {\r
+if (this.annotations != null) {\r
+for (var annotation, $annotation = 0, $$annotation = this.annotations; $annotation < $$annotation.length && ((annotation = $$annotation[$annotation]) || true); $annotation++) {\r
+if (annotation.autoCalculated || !annotation.visible || annotation.isRNA ()) {\r
+continue;\r
+}var aSize = this.aaWidth;\r
+var anots = (annotation.annotations == null) ? null : new Array (aSize);\r
+if (anots != null) {\r
+for (var a = 0; a < aSize; a++) {\r
+if (a < this.alignedCodons.length && this.alignedCodons[a] != null && this.alignedCodons[a].pos1 == (this.alignedCodons[a].pos3 - 2)) {\r
+anots[a] = jalview.analysis.Dna.getCodonAnnotation (this.alignedCodons[a], annotation.annotations);\r
+}}\r
+}var aa = new jalview.datamodel.AlignmentAnnotation (annotation.label, annotation.description, anots);\r
+aa.graph = annotation.graph;\r
+aa.graphGroup = annotation.graphGroup;\r
+aa.graphHeight = annotation.graphHeight;\r
+if (annotation.getThreshold () != null) {\r
+aa.setThreshold ( new jalview.datamodel.GraphLine (annotation.getThreshold ()));\r
+}if (annotation.$hasScore) {\r
+aa.setScore (annotation.getScore ());\r
+}var seqRef = annotation.sequenceRef;\r
+if (seqRef != null) {\r
+var aaSeq = acf.getAaForDnaSeq (seqRef);\r
+if (aaSeq != null) {\r
+aa.setSequenceRef (aaSeq);\r
+aa.createSequenceMapping (aaSeq, aaSeq.getStart (), true);\r
+aa.adjustForAlignment ();\r
+aaSeq.addAlignmentAnnotation (aa);\r
+}}al.addAnnotation (aa);\r
+}\r
+}}, "jalview.datamodel.AlignmentI,jalview.datamodel.AlignedCodonFrame");\r
+c$.getCodonAnnotation = Clazz.defineMethod (c$, "getCodonAnnotation", \r
+($fz = function (is, annotations) {\r
+var contrib = 0;\r
+var annot = null;\r
+for (var p = 1; p <= 3; p++) {\r
+var dnaCol = is.getBaseColumn (p);\r
+if (annotations[dnaCol] != null) {\r
+if (annot == null) {\r
+annot = new jalview.datamodel.Annotation (annotations[dnaCol]);\r
+contrib = 1;\r
+} else {\r
+var cpy = new jalview.datamodel.Annotation (annotations[dnaCol]);\r
+if (annot.colour == null) {\r
+annot.colour = cpy.colour;\r
+}if (annot.description == null || annot.description.length == 0) {\r
+annot.description = cpy.description;\r
+}if (annot.displayCharacter == null) {\r
+annot.displayCharacter = cpy.displayCharacter;\r
+}if (annot.secondaryStructure.charCodeAt (0) == 0) {\r
+annot.secondaryStructure = cpy.secondaryStructure;\r
+}annot.value += cpy.value;\r
+contrib++;\r
+}}}\r
+if (contrib > 1) {\r
+annot.value /= contrib;\r
+}return annot;\r
+}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignedCodon,~A");\r
+Clazz.defineMethod (c$, "translateCodingRegion", \r
+function (selection, seqstring, acf, proteinSeqs) {\r
+var skip = new java.util.ArrayList ();\r
+var skipint = null;\r
+var vismapping = new jalview.util.ShiftList ();\r
+var vc;\r
+var scontigs = Clazz.newIntArray (this.contigs.length, 0);\r
+var npos = 0;\r
+for (vc = 0; vc < this.contigs.length; vc += 2) {\r
+if (vc == 0) {\r
+vismapping.addShift (npos, this.contigs[vc]);\r
+} else {\r
+vismapping.addShift (npos, this.contigs[vc] - this.contigs[vc - 1] + 1);\r
+}scontigs[vc] = this.contigs[vc];\r
+scontigs[vc + 1] = this.contigs[vc + 1];\r
+}\r
+var protein = new StringBuilder (Clazz.doubleToInt (seqstring.length / 2));\r
+var seq = seqstring.$replace ('U', 'T').$replace ('u', 'T');\r
+var codon = Clazz.newCharArray (3, '\0');\r
+var cdp = Clazz.newIntArray (3, 0);\r
+var rf = 0;\r
+var lastnpos = 0;\r
+var nend;\r
+var aspos = 0;\r
+var resSize = 0;\r
+for (npos = 0, nend = seq.length; npos < nend; npos++) {\r
+if (!jalview.util.Comparison.isGap (seq.charAt (npos))) {\r
+cdp[rf] = npos;\r
+codon[rf++] = seq.charAt (npos);\r
+}if (rf == 3) {\r
+var alignedCodon = new jalview.datamodel.AlignedCodon (cdp[0], cdp[1], cdp[2]);\r
+var aa = jalview.schemes.ResidueProperties.codonTranslate ( String.instantialize (codon));\r
+rf = 0;\r
+var gapString = String.valueOf (this.gapChar);\r
+if (aa == null) {\r
+aa = gapString;\r
+if (skipint == null) {\r
+skipint = Clazz.newIntArray (-1, [alignedCodon.pos1, alignedCodon.pos3]);\r
+}skipint[1] = alignedCodon.pos3;\r
+} else {\r
+if (skipint != null) {\r
+skipint[0] = vismapping.shift (skipint[0]);\r
+skipint[1] = vismapping.shift (skipint[1]);\r
+for (vc = 0; vc < scontigs.length; ) {\r
+if (scontigs[vc + 1] < skipint[0]) {\r
+vc += 2;\r
+continue;\r
+}if (scontigs[vc] > skipint[1]) {\r
+break;\r
+}var t;\r
+if (scontigs[vc] <= skipint[0]) {\r
+if (skipint[0] == scontigs[vc]) {\r
+if (scontigs[vc + 1] > skipint[1]) {\r
+scontigs[vc] = skipint[1];\r
+vc += 2;\r
+} else {\r
+if (scontigs[vc + 1] == skipint[1]) {\r
+t = Clazz.newIntArray (scontigs.length - 2, 0);\r
+if (vc > 0) {\r
+System.arraycopy (scontigs, 0, t, 0, vc - 1);\r
+}if (vc + 2 < t.length) {\r
+System.arraycopy (scontigs, vc + 2, t, vc, t.length - vc + 2);\r
+}scontigs = t;\r
+} else {\r
+scontigs[vc + 1] = skipint[0] - 1;\r
+vc += 2;\r
+}}} else {\r
+if (scontigs[vc + 1] < skipint[1]) {\r
+scontigs[vc + 1] = skipint[0] - 1;\r
+vc += 2;\r
+} else {\r
+t = Clazz.newIntArray (scontigs.length + 2, 0);\r
+System.arraycopy (scontigs, 0, t, 0, vc + 1);\r
+t[vc + 1] = skipint[0];\r
+t[vc + 2] = skipint[1];\r
+System.arraycopy (scontigs, vc + 1, t, vc + 3, scontigs.length - (vc + 1));\r
+scontigs = t;\r
+vc += 4;\r
+}}}}\r
+skip.add (skipint);\r
+skipint = null;\r
+}if (aa.equals ("STOP")) {\r
+aa = "X";\r
+}resSize++;\r
+}var findpos = true;\r
+while (findpos) {\r
+var compareCodonPos = jalview.analysis.Dna.compareCodonPos (alignedCodon, this.alignedCodons[aspos]);\r
+switch (compareCodonPos) {\r
+case -1:\r
+this.insertAAGap (aspos, proteinSeqs);\r
+findpos = false;\r
+break;\r
+case 1:\r
+aa = gapString + aa;\r
+aspos++;\r
+break;\r
+case 0:\r
+findpos = false;\r
+}\r
+}\r
+protein.append (aa);\r
+lastnpos = npos;\r
+if (this.alignedCodons[aspos] == null) {\r
+this.alignedCodons[aspos] = alignedCodon;\r
+} else if (!this.alignedCodons[aspos].equals (alignedCodon)) {\r
+throw new IllegalStateException ("Tried to coalign " + this.alignedCodons[aspos].toString () + " with " + alignedCodon.toString ());\r
+}if (aspos >= this.aaWidth) {\r
+this.aaWidth = aspos;\r
+}aspos++;\r
+}}\r
+if (resSize > 0) {\r
+var newseq = new jalview.datamodel.Sequence (selection.getName (), protein.toString ());\r
+if (rf != 0) {\r
+var errMsg = "trimming contigs for incomplete terminal codon.";\r
+System.err.println ("trimming contigs for incomplete terminal codon.");\r
+vc = scontigs.length - 1;\r
+lastnpos = vismapping.shift (lastnpos);\r
+while (vc >= 0 && scontigs[vc] > lastnpos) {\r
+if (vc > 0 && scontigs[vc - 1] > lastnpos) {\r
+vc -= 2;\r
+} else {\r
+scontigs[vc] = lastnpos;\r
+}}\r
+if (vc > 0 && (vc + 1) < scontigs.length) {\r
+var t = Clazz.newIntArray (vc + 1, 0);\r
+System.arraycopy (scontigs, 0, t, 0, vc + 1);\r
+scontigs = t;\r
+}if (vc <= 0) {\r
+scontigs = null;\r
+}}if (scontigs != null) {\r
+npos = 0;\r
+for (vc = 0; vc < scontigs.length; vc += 2) {\r
+scontigs[vc] = selection.findPosition (scontigs[vc]);\r
+scontigs[vc + 1] = selection.findPosition (scontigs[vc + 1]);\r
+if (scontigs[vc + 1] == selection.getEnd ()) {\r
+break;\r
+}}\r
+if ((vc + 2) < scontigs.length) {\r
+var t = Clazz.newIntArray (vc + 2, 0);\r
+System.arraycopy (scontigs, 0, t, 0, vc + 2);\r
+scontigs = t;\r
+}var map = new jalview.util.MapList (scontigs, Clazz.newIntArray (-1, [1, resSize]), 3, 1);\r
+jalview.analysis.Dna.transferCodedFeatures (selection, newseq, map, null, null);\r
+var rseq = newseq.deriveSequence ();\r
+acf.addMap (selection, rseq, map);\r
+return rseq;\r
+}}return null;\r
+}, "jalview.datamodel.SequenceI,~S,jalview.datamodel.AlignedCodonFrame,java.util.List");\r
+Clazz.defineMethod (c$, "insertAAGap", \r
+function (pos, proteinSeqs) {\r
+this.aaWidth++;\r
+for (var seq, $seq = proteinSeqs.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) {\r
+seq.insertCharAt (pos, this.gapChar);\r
+}\r
+this.checkCodonFrameWidth ();\r
+if (pos < this.aaWidth) {\r
+this.aaWidth++;\r
+System.arraycopy (this.alignedCodons, pos, this.alignedCodons, pos + 1, this.alignedCodons.length - pos - 1);\r
+this.alignedCodons[pos] = null;\r
+}}, "~N,java.util.List");\r
+Clazz.defineMethod (c$, "checkCodonFrameWidth", \r
+function () {\r
+if (this.alignedCodons[this.alignedCodons.length - 1] != null) {\r
+var c = new Array (this.alignedCodons.length + 10);\r
+System.arraycopy (this.alignedCodons, 0, c, 0, this.alignedCodons.length);\r
+this.alignedCodons = c;\r
+}});\r
+c$.transferCodedFeatures = Clazz.defineMethod (c$, "transferCodedFeatures", \r
+($fz = function (dna, pep, map, featureTypes, featureGroups) {\r
+var sfs = dna.getSequenceFeatures ();\r
+var fgstate;\r
+var dnarefs = jalview.util.DBRefUtils.selectRefs (dna.getDBRef (), jalview.datamodel.DBRefSource.DNACODINGDBS);\r
+if (dnarefs != null) {\r
+for (var d = 0; d < dnarefs.length; d++) {\r
+var mp = dnarefs[d].getMap ();\r
+if (mp != null) {\r
+}}\r
+}if (sfs != null) {\r
+for (var sf, $sf = 0, $$sf = sfs; $sf < $$sf.length && ((sf = $$sf[$sf]) || true); $sf++) {\r
+fgstate = (featureGroups == null) ? null : featureGroups.get (sf.featureGroup);\r
+if ((featureTypes == null || featureTypes.containsKey (sf.getType ())) && (fgstate == null || fgstate.booleanValue ())) {\r
+if (jalview.datamodel.FeatureProperties.isCodingFeature (null, sf.getType ())) {\r
+{\r
+}}}}\r
+}}, $fz.isPrivate = true, $fz), "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,jalview.util.MapList,java.util.Map,java.util.Map");\r
+Clazz.defineStatics (c$,\r
+"STOP_X", "X");\r
+c$.comparator = c$.prototype.comparator = new jalview.analysis.CodonComparator ();\r
+});\r
git://source.jalview.org / jalviewjs.git / blobdiff