X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fdatamodel%2FAlignedCodonFrame.js;h=043b032895a36b87fca9cc25a9a575dbf45d37d1;hp=8d854b47cdb6e4323538e047e11e6c8938aa67df;hb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/datamodel/AlignedCodonFrame.js b/bin/jalview/datamodel/AlignedCodonFrame.js
index 8d854b4..043b032 100644
--- a/bin/jalview/datamodel/AlignedCodonFrame.js
+++ b/bin/jalview/datamodel/AlignedCodonFrame.js
@@ -1,198 +1,198 @@
-Clazz.declarePackage ("jalview.datamodel");
-Clazz.load (null, "jalview.datamodel.AlignedCodonFrame", ["jalview.datamodel.Mapping", "jalview.util.MappingUtils", "java.util.ArrayList"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.dnaSeqs = null;
-this.dnaToProt = null;
-Clazz.instantialize (this, arguments);
-}, jalview.datamodel, "AlignedCodonFrame");
-Clazz.makeConstructor (c$, 
-function () {
-});
-Clazz.defineMethod (c$, "addMap", 
-function (dnaseq, aaseq, map) {
-var nlen = 1;
-if (this.dnaSeqs != null) {
-nlen = this.dnaSeqs.length + 1;
-}var ndna =  new Array (nlen);
-var ndtp =  new Array (nlen);
-if (this.dnaSeqs != null) {
-System.arraycopy (this.dnaSeqs, 0, ndna, 0, this.dnaSeqs.length);
-System.arraycopy (this.dnaToProt, 0, ndtp, 0, this.dnaSeqs.length);
-}this.dnaSeqs = ndna;
-this.dnaToProt = ndtp;
-nlen--;
-this.dnaSeqs[nlen] = (dnaseq.getDatasetSequence () == null) ? dnaseq : dnaseq.getDatasetSequence ();
-var mp =  new jalview.datamodel.Mapping (map);
-mp.to = (aaseq.getDatasetSequence () == null) ? aaseq : aaseq.getDatasetSequence ();
-this.dnaToProt[nlen] = mp;
-}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,jalview.util.MapList");
-Clazz.defineMethod (c$, "getdnaSeqs", 
-function () {
-return this.dnaSeqs;
-});
-Clazz.defineMethod (c$, "getAaSeqs", 
-function () {
-if (this.dnaToProt == null) {
-return null;
-}var sqs =  new Array (this.dnaToProt.length);
-for (var sz = 0; sz < this.dnaToProt.length; sz++) {
-sqs[sz] = this.dnaToProt[sz].to;
-}
-return sqs;
-});
-Clazz.defineMethod (c$, "getdnaToProt", 
-function () {
-if (this.dnaToProt == null) {
-return null;
-}var sqs =  new Array (this.dnaToProt.length);
-for (var sz = 0; sz < this.dnaToProt.length; sz++) {
-sqs[sz] = this.dnaToProt[sz].map;
-}
-return sqs;
-});
-Clazz.defineMethod (c$, "getProtMappings", 
-function () {
-return this.dnaToProt;
-});
-Clazz.defineMethod (c$, "getMappingForSequence", 
-function (seq) {
-if (this.dnaSeqs == null) {
-return null;
-}var seqDs = seq.getDatasetSequence ();
-seqDs = seqDs != null ? seqDs : seq;
-for (var ds = 0; ds < this.dnaSeqs.length; ds++) {
-if (this.dnaSeqs[ds] === seqDs || this.dnaToProt[ds].to === seqDs) {
-return this.dnaToProt[ds];
-}}
-return null;
-}, "jalview.datamodel.SequenceI");
-Clazz.defineMethod (c$, "getAaForDnaSeq", 
-function (dnaSeqRef) {
-if (this.dnaSeqs == null) {
-return null;
-}var dnads = dnaSeqRef.getDatasetSequence ();
-for (var ds = 0; ds < this.dnaSeqs.length; ds++) {
-if (this.dnaSeqs[ds] === dnaSeqRef || this.dnaSeqs[ds] === dnads) {
-return this.dnaToProt[ds].to;
-}}
-return null;
-}, "jalview.datamodel.SequenceI");
-Clazz.defineMethod (c$, "getDnaForAaSeq", 
-function (aaSeqRef) {
-if (this.dnaToProt == null) {
-return null;
-}var aads = aaSeqRef.getDatasetSequence ();
-for (var as = 0; as < this.dnaToProt.length; as++) {
-if (this.dnaToProt[as].to === aaSeqRef || this.dnaToProt[as].to === aads) {
-return this.dnaSeqs[as];
-}}
-return null;
-}, "jalview.datamodel.SequenceI");
-Clazz.defineMethod (c$, "involvesSequence", 
-function (seq) {
-return this.getAaForDnaSeq (seq) != null || this.getDnaForAaSeq (seq) != null;
-}, "jalview.datamodel.SequenceI");
-Clazz.defineMethod (c$, "markMappedRegion", 
-function (seq, index, results) {
-if (this.dnaToProt == null) {
-return;
-}var codon;
-var ds = seq.getDatasetSequence ();
-for (var mi = 0; mi < this.dnaToProt.length; mi++) {
-if (this.dnaSeqs[mi] === seq || this.dnaSeqs[mi] === ds) {
-codon = this.dnaToProt[mi].map.locateInTo (index, index);
-if (codon != null) {
-for (var i = 0; i < codon.length; i += 2) {
-results.addResult (this.dnaToProt[mi].to, codon[i], codon[i + 1]);
-}
-}} else if (this.dnaToProt[mi].to === seq || this.dnaToProt[mi].to === ds) {
-{
-codon = this.dnaToProt[mi].map.locateInFrom (index, index);
-if (codon != null) {
-for (var i = 0; i < codon.length; i += 2) {
-results.addResult (this.dnaSeqs[mi], codon[i], codon[i + 1]);
-}
-}}}}
-}, "jalview.datamodel.SequenceI,~N,jalview.datamodel.SearchResults");
-Clazz.defineMethod (c$, "getDnaPosition", 
-function (seq, aaPos) {
-var ml = null;
-for (var i = 0; i < this.dnaToProt.length; i++) {
-if (this.dnaSeqs[i] === seq) {
-ml = this.getdnaToProt ()[i];
-break;
-}}
-return ml == null ? null : ml.locateInFrom (aaPos, aaPos);
-}, "jalview.datamodel.SequenceI,~N");
-Clazz.defineMethod (c$, "findAlignedSequence", 
-function (seq, al) {
-if (this.dnaToProt != null) {
-for (var i = 0; i < this.dnaToProt.length; i++) {
-if (this.dnaSeqs[i] === seq) {
-for (var sourceAligned, $sourceAligned = al.getSequences ().iterator (); $sourceAligned.hasNext () && ((sourceAligned = $sourceAligned.next ()) || true);) {
-if (this.dnaToProt[i].to === sourceAligned.getDatasetSequence ()) {
-return sourceAligned;
-}}
-}}
-}if (this.dnaToProt != null) {
-for (var i = 0; i < this.dnaToProt.length; i++) {
-if (this.dnaToProt[i].to === seq) {
-for (var sourceAligned, $sourceAligned = al.getSequences ().iterator (); $sourceAligned.hasNext () && ((sourceAligned = $sourceAligned.next ()) || true);) {
-if (this.dnaSeqs[i] === sourceAligned.getDatasetSequence ()) {
-return sourceAligned;
-}}
-}}
-}return null;
-}, "jalview.datamodel.SequenceI,jalview.datamodel.AlignmentI");
-Clazz.defineMethod (c$, "getMappedRegion", 
-function (mappedFrom, mappedTo, pos) {
-var targetDs = mappedFrom.getDatasetSequence () == null ? mappedFrom : mappedFrom.getDatasetSequence ();
-var sourceDs = mappedTo.getDatasetSequence () == null ? mappedTo : mappedTo.getDatasetSequence ();
-if (targetDs == null || sourceDs == null || this.dnaToProt == null) {
-return null;
-}for (var mi = 0; mi < this.dnaToProt.length; mi++) {
-if (this.dnaSeqs[mi] === targetDs && this.dnaToProt[mi].to === sourceDs) {
-var codon = this.dnaToProt[mi].map.locateInFrom (pos, pos);
-if (codon != null) {
-return codon;
-}}}
-return null;
-}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~N");
-Clazz.defineMethod (c$, "getMappedCodon", 
-function (protein, aaPos) {
-if (this.dnaToProt == null) {
-return null;
-}var ml = null;
-var dnaSeq = null;
-for (var i = 0; i < this.dnaToProt.length; i++) {
-if (this.dnaToProt[i].to === protein) {
-ml = this.getdnaToProt ()[i];
-dnaSeq = this.dnaSeqs[i].getSequence ();
-break;
-}}
-if (ml == null) {
-return null;
-}var codonPos = ml.locateInFrom (aaPos, aaPos);
-if (codonPos == null) {
-return null;
-}codonPos = jalview.util.MappingUtils.flattenRanges (codonPos);
-return  Clazz.newCharArray (-1, [dnaSeq[codonPos[0] - 1], dnaSeq[codonPos[1] - 1], dnaSeq[codonPos[2] - 1]]);
-}, "jalview.datamodel.SequenceI,~N");
-Clazz.defineMethod (c$, "getMappingsForSequence", 
-function (seq) {
-var result =  new java.util.ArrayList ();
-if (this.dnaSeqs == null) {
-return result;
-}var related =  new java.util.ArrayList ();
-var seqDs = seq.getDatasetSequence ();
-seqDs = seqDs != null ? seqDs : seq;
-for (var ds = 0; ds < this.dnaSeqs.length; ds++) {
-var mapping = this.dnaToProt[ds];
-if (this.dnaSeqs[ds] === seqDs || mapping.to === seqDs) {
-if (!related.contains (mapping.to)) {
-result.add (mapping);
-related.add (mapping.to);
-}}}
-return result;
-}, "jalview.datamodel.SequenceI");
-});
+Clazz.declarePackage ("jalview.datamodel");
+Clazz.load (null, "jalview.datamodel.AlignedCodonFrame", ["jalview.datamodel.Mapping", "jalview.util.MappingUtils", "java.util.ArrayList"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.dnaSeqs = null;
+this.dnaToProt = null;
+Clazz.instantialize (this, arguments);
+}, jalview.datamodel, "AlignedCodonFrame");
+Clazz.makeConstructor (c$, 
+function () {
+});
+Clazz.defineMethod (c$, "addMap", 
+function (dnaseq, aaseq, map) {
+var nlen = 1;
+if (this.dnaSeqs != null) {
+nlen = this.dnaSeqs.length + 1;
+}var ndna =  new Array (nlen);
+var ndtp =  new Array (nlen);
+if (this.dnaSeqs != null) {
+System.arraycopy (this.dnaSeqs, 0, ndna, 0, this.dnaSeqs.length);
+System.arraycopy (this.dnaToProt, 0, ndtp, 0, this.dnaSeqs.length);
+}this.dnaSeqs = ndna;
+this.dnaToProt = ndtp;
+nlen--;
+this.dnaSeqs[nlen] = (dnaseq.getDatasetSequence () == null) ? dnaseq : dnaseq.getDatasetSequence ();
+var mp =  new jalview.datamodel.Mapping (map);
+mp.to = (aaseq.getDatasetSequence () == null) ? aaseq : aaseq.getDatasetSequence ();
+this.dnaToProt[nlen] = mp;
+}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,jalview.util.MapList");
+Clazz.defineMethod (c$, "getdnaSeqs", 
+function () {
+return this.dnaSeqs;
+});
+Clazz.defineMethod (c$, "getAaSeqs", 
+function () {
+if (this.dnaToProt == null) {
+return null;
+}var sqs =  new Array (this.dnaToProt.length);
+for (var sz = 0; sz < this.dnaToProt.length; sz++) {
+sqs[sz] = this.dnaToProt[sz].to;
+}
+return sqs;
+});
+Clazz.defineMethod (c$, "getdnaToProt", 
+function () {
+if (this.dnaToProt == null) {
+return null;
+}var sqs =  new Array (this.dnaToProt.length);
+for (var sz = 0; sz < this.dnaToProt.length; sz++) {
+sqs[sz] = this.dnaToProt[sz].map;
+}
+return sqs;
+});
+Clazz.defineMethod (c$, "getProtMappings", 
+function () {
+return this.dnaToProt;
+});
+Clazz.defineMethod (c$, "getMappingForSequence", 
+function (seq) {
+if (this.dnaSeqs == null) {
+return null;
+}var seqDs = seq.getDatasetSequence ();
+seqDs = seqDs != null ? seqDs : seq;
+for (var ds = 0; ds < this.dnaSeqs.length; ds++) {
+if (this.dnaSeqs[ds] === seqDs || this.dnaToProt[ds].to === seqDs) {
+return this.dnaToProt[ds];
+}}
+return null;
+}, "jalview.datamodel.SequenceI");
+Clazz.defineMethod (c$, "getAaForDnaSeq", 
+function (dnaSeqRef) {
+if (this.dnaSeqs == null) {
+return null;
+}var dnads = dnaSeqRef.getDatasetSequence ();
+for (var ds = 0; ds < this.dnaSeqs.length; ds++) {
+if (this.dnaSeqs[ds] === dnaSeqRef || this.dnaSeqs[ds] === dnads) {
+return this.dnaToProt[ds].to;
+}}
+return null;
+}, "jalview.datamodel.SequenceI");
+Clazz.defineMethod (c$, "getDnaForAaSeq", 
+function (aaSeqRef) {
+if (this.dnaToProt == null) {
+return null;
+}var aads = aaSeqRef.getDatasetSequence ();
+for (var as = 0; as < this.dnaToProt.length; as++) {
+if (this.dnaToProt[as].to === aaSeqRef || this.dnaToProt[as].to === aads) {
+return this.dnaSeqs[as];
+}}
+return null;
+}, "jalview.datamodel.SequenceI");
+Clazz.defineMethod (c$, "involvesSequence", 
+function (seq) {
+return this.getAaForDnaSeq (seq) != null || this.getDnaForAaSeq (seq) != null;
+}, "jalview.datamodel.SequenceI");
+Clazz.defineMethod (c$, "markMappedRegion", 
+function (seq, index, results) {
+if (this.dnaToProt == null) {
+return;
+}var codon;
+var ds = seq.getDatasetSequence ();
+for (var mi = 0; mi < this.dnaToProt.length; mi++) {
+if (this.dnaSeqs[mi] === seq || this.dnaSeqs[mi] === ds) {
+codon = this.dnaToProt[mi].map.locateInTo (index, index);
+if (codon != null) {
+for (var i = 0; i < codon.length; i += 2) {
+results.addResult (this.dnaToProt[mi].to, codon[i], codon[i + 1]);
+}
+}} else if (this.dnaToProt[mi].to === seq || this.dnaToProt[mi].to === ds) {
+{
+codon = this.dnaToProt[mi].map.locateInFrom (index, index);
+if (codon != null) {
+for (var i = 0; i < codon.length; i += 2) {
+results.addResult (this.dnaSeqs[mi], codon[i], codon[i + 1]);
+}
+}}}}
+}, "jalview.datamodel.SequenceI,~N,jalview.datamodel.SearchResults");
+Clazz.defineMethod (c$, "getDnaPosition", 
+function (seq, aaPos) {
+var ml = null;
+for (var i = 0; i < this.dnaToProt.length; i++) {
+if (this.dnaSeqs[i] === seq) {
+ml = this.getdnaToProt ()[i];
+break;
+}}
+return ml == null ? null : ml.locateInFrom (aaPos, aaPos);
+}, "jalview.datamodel.SequenceI,~N");
+Clazz.defineMethod (c$, "findAlignedSequence", 
+function (seq, al) {
+if (this.dnaToProt != null) {
+for (var i = 0; i < this.dnaToProt.length; i++) {
+if (this.dnaSeqs[i] === seq) {
+for (var sourceAligned, $sourceAligned = al.getSequences ().iterator (); $sourceAligned.hasNext () && ((sourceAligned = $sourceAligned.next ()) || true);) {
+if (this.dnaToProt[i].to === sourceAligned.getDatasetSequence ()) {
+return sourceAligned;
+}}
+}}
+}if (this.dnaToProt != null) {
+for (var i = 0; i < this.dnaToProt.length; i++) {
+if (this.dnaToProt[i].to === seq) {
+for (var sourceAligned, $sourceAligned = al.getSequences ().iterator (); $sourceAligned.hasNext () && ((sourceAligned = $sourceAligned.next ()) || true);) {
+if (this.dnaSeqs[i] === sourceAligned.getDatasetSequence ()) {
+return sourceAligned;
+}}
+}}
+}return null;
+}, "jalview.datamodel.SequenceI,jalview.datamodel.AlignmentI");
+Clazz.defineMethod (c$, "getMappedRegion", 
+function (mappedFrom, mappedTo, pos) {
+var targetDs = mappedFrom.getDatasetSequence () == null ? mappedFrom : mappedFrom.getDatasetSequence ();
+var sourceDs = mappedTo.getDatasetSequence () == null ? mappedTo : mappedTo.getDatasetSequence ();
+if (targetDs == null || sourceDs == null || this.dnaToProt == null) {
+return null;
+}for (var mi = 0; mi < this.dnaToProt.length; mi++) {
+if (this.dnaSeqs[mi] === targetDs && this.dnaToProt[mi].to === sourceDs) {
+var codon = this.dnaToProt[mi].map.locateInFrom (pos, pos);
+if (codon != null) {
+return codon;
+}}}
+return null;
+}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~N");
+Clazz.defineMethod (c$, "getMappedCodon", 
+function (protein, aaPos) {
+if (this.dnaToProt == null) {
+return null;
+}var ml = null;
+var dnaSeq = null;
+for (var i = 0; i < this.dnaToProt.length; i++) {
+if (this.dnaToProt[i].to === protein) {
+ml = this.getdnaToProt ()[i];
+dnaSeq = this.dnaSeqs[i].getSequence ();
+break;
+}}
+if (ml == null) {
+return null;
+}var codonPos = ml.locateInFrom (aaPos, aaPos);
+if (codonPos == null) {
+return null;
+}codonPos = jalview.util.MappingUtils.flattenRanges (codonPos);
+return  Clazz.newCharArray (-1, [dnaSeq[codonPos[0] - 1], dnaSeq[codonPos[1] - 1], dnaSeq[codonPos[2] - 1]]);
+}, "jalview.datamodel.SequenceI,~N");
+Clazz.defineMethod (c$, "getMappingsForSequence", 
+function (seq) {
+var result =  new java.util.ArrayList ();
+if (this.dnaSeqs == null) {
+return result;
+}var related =  new java.util.ArrayList ();
+var seqDs = seq.getDatasetSequence ();
+seqDs = seqDs != null ? seqDs : seq;
+for (var ds = 0; ds < this.dnaSeqs.length; ds++) {
+var mapping = this.dnaToProt[ds];
+if (this.dnaSeqs[ds] === seqDs || mapping.to === seqDs) {
+if (!related.contains (mapping.to)) {
+result.add (mapping);
+related.add (mapping.to);
+}}}
+return result;
+}, "jalview.datamodel.SequenceI");
+});