X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fdatamodel%2FHiddenSequences.js;h=65b1c2bc2f3f201c71e23b01e9b3d1217291799d;hp=9111dd8375aad2da25b1ecb6ffba4676a37debf2;hb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/datamodel/HiddenSequences.js b/bin/jalview/datamodel/HiddenSequences.js
index 9111dd8..65b1c2b 100644
--- a/bin/jalview/datamodel/HiddenSequences.js
+++ b/bin/jalview/datamodel/HiddenSequences.js
@@ -1,162 +1,162 @@
-Clazz.declarePackage ("jalview.datamodel");
-Clazz.load (null, "jalview.datamodel.HiddenSequences", ["jalview.datamodel.Alignment", "java.util.ArrayList"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.hiddenSequences = null;
-this.alignment = null;
-Clazz.instantialize (this, arguments);
-}, jalview.datamodel, "HiddenSequences");
-Clazz.makeConstructor (c$, 
-function (al) {
-this.alignment = al;
-}, "jalview.datamodel.AlignmentI");
-Clazz.defineMethod (c$, "getSize", 
-function () {
-if (this.hiddenSequences == null) {
-return 0;
-}var count = 0;
-for (var i = 0; i < this.hiddenSequences.length; i++) {
-if (this.hiddenSequences[i] != null) {
-count++;
-}}
-return count;
-});
-Clazz.defineMethod (c$, "getWidth", 
-function () {
-var width = 0;
-for (var i = 0; i < this.hiddenSequences.length; i++) {
-if (this.hiddenSequences[i] != null && this.hiddenSequences[i].getLength () > width) {
-width = this.hiddenSequences[i].getLength ();
-}}
-return width;
-});
-Clazz.defineMethod (c$, "adjustHeightSequenceDeleted", 
-function (seqIndex) {
-if (this.hiddenSequences == null) {
-return;
-}var alHeight = this.alignment.getHeight ();
-var tmp =  new Array (alHeight + this.getSize ());
-var deletionIndex = this.adjustForHiddenSeqs (seqIndex);
-for (var i = 0; i < this.hiddenSequences.length; i++) {
-if (this.hiddenSequences[i] == null) {
-continue;
-}if (i > deletionIndex) {
-tmp[i - 1] = this.hiddenSequences[i];
-} else {
-tmp[i] = this.hiddenSequences[i];
-}}
-this.hiddenSequences = tmp;
-}, "~N");
-Clazz.defineMethod (c$, "adjustHeightSequenceAdded", 
-function () {
-if (this.hiddenSequences == null) {
-return;
-}var alHeight = this.alignment.getHeight ();
-var tmp =  new Array (alHeight + this.getSize ());
-System.arraycopy (this.hiddenSequences, 0, tmp, 0, this.hiddenSequences.length);
-this.hiddenSequences = tmp;
-});
-Clazz.defineMethod (c$, "hideSequence", 
-function (sequence) {
-if (this.hiddenSequences == null) {
-this.hiddenSequences =  new Array (this.alignment.getHeight ());
-}var alignmentIndex = this.alignment.findIndex (sequence);
-alignmentIndex = this.adjustForHiddenSeqs (alignmentIndex);
-if (this.hiddenSequences[alignmentIndex] != null) {
-System.out.println ("ERROR!!!!!!!!!!!");
-}this.hiddenSequences[alignmentIndex] = sequence;
-this.alignment.deleteSequence (sequence);
-}, "jalview.datamodel.SequenceI");
-Clazz.defineMethod (c$, "showAll", 
-function (hiddenRepSequences) {
-var revealedSeqs =  new java.util.ArrayList ();
-for (var i = 0; i < this.hiddenSequences.length; i++) {
-if (this.hiddenSequences[i] != null) {
-var tmp = this.showSequence (i, hiddenRepSequences);
-for (var seq, $seq = tmp.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) {
-revealedSeqs.add (seq);
-}
-}}
-return revealedSeqs;
-}, "java.util.Map");
-Clazz.defineMethod (c$, "showSequence", 
-function (alignmentIndex, hiddenRepSequences) {
-var revealedSeqs =  new java.util.ArrayList ();
-var repSequence = this.alignment.getSequenceAt (alignmentIndex);
-if (repSequence != null && hiddenRepSequences != null && hiddenRepSequences.containsKey (repSequence)) {
-hiddenRepSequences.remove (repSequence);
-revealedSeqs.add (repSequence);
-}var start = this.adjustForHiddenSeqs (alignmentIndex - 1);
-var end = this.adjustForHiddenSeqs (alignmentIndex);
-if (end >= this.hiddenSequences.length) {
-end = this.hiddenSequences.length - 1;
-}var asequences;
-{
-for (var index = end; index > start; index--) {
-var seq = this.hiddenSequences[index];
-this.hiddenSequences[index] = null;
-if (seq != null) {
-if (seq.getLength () > 0) {
-revealedSeqs.add (seq);
-asequences.add (alignmentIndex, seq);
-} else {
-System.out.println (seq.getName () + " has been deleted whilst hidden");
-}}}
-}return revealedSeqs;
-}, "~N,java.util.Map");
-Clazz.defineMethod (c$, "getHiddenSequence", 
-function (alignmentIndex) {
-return this.hiddenSequences[alignmentIndex];
-}, "~N");
-Clazz.defineMethod (c$, "findIndexWithoutHiddenSeqs", 
-function (alignmentIndex) {
-var index = 0;
-var hiddenSeqs = 0;
-if (this.hiddenSequences.length <= alignmentIndex) {
-alignmentIndex = this.hiddenSequences.length - 1;
-}while (index <= alignmentIndex) {
-if (this.hiddenSequences[index] != null) {
-hiddenSeqs++;
-}index++;
-}
-;return (alignmentIndex - hiddenSeqs);
-}, "~N");
-Clazz.defineMethod (c$, "adjustForHiddenSeqs", 
-function (alignmentIndex) {
-var index = 0;
-var hSize = this.hiddenSequences.length;
-while (index <= alignmentIndex && index < hSize) {
-if (this.hiddenSequences[index] != null) {
-alignmentIndex++;
-}index++;
-}
-;return alignmentIndex;
-}, "~N");
-Clazz.defineMethod (c$, "getFullAlignment", 
-function () {
-var isize = this.hiddenSequences.length;
-var seq =  new Array (isize);
-var index = 0;
-for (var i = 0; i < this.hiddenSequences.length; i++) {
-if (this.hiddenSequences[i] != null) {
-seq[i] = this.hiddenSequences[i];
-} else {
-seq[i] = this.alignment.getSequenceAt (index);
-index++;
-}}
-var fAlignmt =  new jalview.datamodel.Alignment (seq);
-fAlignmt.annotations = this.alignment.getAlignmentAnnotation ();
-fAlignmt.alignmentProperties = this.alignment.getProperties ();
-fAlignmt.groups = this.alignment.getGroups ();
-fAlignmt.$hasRNAStructure = this.alignment.hasRNAStructure ();
-return fAlignmt;
-});
-Clazz.defineMethod (c$, "isHidden", 
-function (seq) {
-if (this.hiddenSequences != null) {
-for (var i = 0; i < this.hiddenSequences.length; i++) {
-if (this.hiddenSequences[i] != null && this.hiddenSequences[i] === seq) {
-return true;
-}}
-}return false;
-}, "jalview.datamodel.SequenceI");
-});
+Clazz.declarePackage ("jalview.datamodel");
+Clazz.load (null, "jalview.datamodel.HiddenSequences", ["jalview.datamodel.Alignment", "java.util.ArrayList"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.hiddenSequences = null;
+this.alignment = null;
+Clazz.instantialize (this, arguments);
+}, jalview.datamodel, "HiddenSequences");
+Clazz.makeConstructor (c$, 
+function (al) {
+this.alignment = al;
+}, "jalview.datamodel.AlignmentI");
+Clazz.defineMethod (c$, "getSize", 
+function () {
+if (this.hiddenSequences == null) {
+return 0;
+}var count = 0;
+for (var i = 0; i < this.hiddenSequences.length; i++) {
+if (this.hiddenSequences[i] != null) {
+count++;
+}}
+return count;
+});
+Clazz.defineMethod (c$, "getWidth", 
+function () {
+var width = 0;
+for (var i = 0; i < this.hiddenSequences.length; i++) {
+if (this.hiddenSequences[i] != null && this.hiddenSequences[i].getLength () > width) {
+width = this.hiddenSequences[i].getLength ();
+}}
+return width;
+});
+Clazz.defineMethod (c$, "adjustHeightSequenceDeleted", 
+function (seqIndex) {
+if (this.hiddenSequences == null) {
+return;
+}var alHeight = this.alignment.getHeight ();
+var tmp =  new Array (alHeight + this.getSize ());
+var deletionIndex = this.adjustForHiddenSeqs (seqIndex);
+for (var i = 0; i < this.hiddenSequences.length; i++) {
+if (this.hiddenSequences[i] == null) {
+continue;
+}if (i > deletionIndex) {
+tmp[i - 1] = this.hiddenSequences[i];
+} else {
+tmp[i] = this.hiddenSequences[i];
+}}
+this.hiddenSequences = tmp;
+}, "~N");
+Clazz.defineMethod (c$, "adjustHeightSequenceAdded", 
+function () {
+if (this.hiddenSequences == null) {
+return;
+}var alHeight = this.alignment.getHeight ();
+var tmp =  new Array (alHeight + this.getSize ());
+System.arraycopy (this.hiddenSequences, 0, tmp, 0, this.hiddenSequences.length);
+this.hiddenSequences = tmp;
+});
+Clazz.defineMethod (c$, "hideSequence", 
+function (sequence) {
+if (this.hiddenSequences == null) {
+this.hiddenSequences =  new Array (this.alignment.getHeight ());
+}var alignmentIndex = this.alignment.findIndex (sequence);
+alignmentIndex = this.adjustForHiddenSeqs (alignmentIndex);
+if (this.hiddenSequences[alignmentIndex] != null) {
+System.out.println ("ERROR!!!!!!!!!!!");
+}this.hiddenSequences[alignmentIndex] = sequence;
+this.alignment.deleteSequence (sequence);
+}, "jalview.datamodel.SequenceI");
+Clazz.defineMethod (c$, "showAll", 
+function (hiddenRepSequences) {
+var revealedSeqs =  new java.util.ArrayList ();
+for (var i = 0; i < this.hiddenSequences.length; i++) {
+if (this.hiddenSequences[i] != null) {
+var tmp = this.showSequence (i, hiddenRepSequences);
+for (var seq, $seq = tmp.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) {
+revealedSeqs.add (seq);
+}
+}}
+return revealedSeqs;
+}, "java.util.Map");
+Clazz.defineMethod (c$, "showSequence", 
+function (alignmentIndex, hiddenRepSequences) {
+var revealedSeqs =  new java.util.ArrayList ();
+var repSequence = this.alignment.getSequenceAt (alignmentIndex);
+if (repSequence != null && hiddenRepSequences != null && hiddenRepSequences.containsKey (repSequence)) {
+hiddenRepSequences.remove (repSequence);
+revealedSeqs.add (repSequence);
+}var start = this.adjustForHiddenSeqs (alignmentIndex - 1);
+var end = this.adjustForHiddenSeqs (alignmentIndex);
+if (end >= this.hiddenSequences.length) {
+end = this.hiddenSequences.length - 1;
+}var asequences;
+{
+for (var index = end; index > start; index--) {
+var seq = this.hiddenSequences[index];
+this.hiddenSequences[index] = null;
+if (seq != null) {
+if (seq.getLength () > 0) {
+revealedSeqs.add (seq);
+asequences.add (alignmentIndex, seq);
+} else {
+System.out.println (seq.getName () + " has been deleted whilst hidden");
+}}}
+}return revealedSeqs;
+}, "~N,java.util.Map");
+Clazz.defineMethod (c$, "getHiddenSequence", 
+function (alignmentIndex) {
+return this.hiddenSequences[alignmentIndex];
+}, "~N");
+Clazz.defineMethod (c$, "findIndexWithoutHiddenSeqs", 
+function (alignmentIndex) {
+var index = 0;
+var hiddenSeqs = 0;
+if (this.hiddenSequences.length <= alignmentIndex) {
+alignmentIndex = this.hiddenSequences.length - 1;
+}while (index <= alignmentIndex) {
+if (this.hiddenSequences[index] != null) {
+hiddenSeqs++;
+}index++;
+}
+;return (alignmentIndex - hiddenSeqs);
+}, "~N");
+Clazz.defineMethod (c$, "adjustForHiddenSeqs", 
+function (alignmentIndex) {
+var index = 0;
+var hSize = this.hiddenSequences.length;
+while (index <= alignmentIndex && index < hSize) {
+if (this.hiddenSequences[index] != null) {
+alignmentIndex++;
+}index++;
+}
+;return alignmentIndex;
+}, "~N");
+Clazz.defineMethod (c$, "getFullAlignment", 
+function () {
+var isize = this.hiddenSequences.length;
+var seq =  new Array (isize);
+var index = 0;
+for (var i = 0; i < this.hiddenSequences.length; i++) {
+if (this.hiddenSequences[i] != null) {
+seq[i] = this.hiddenSequences[i];
+} else {
+seq[i] = this.alignment.getSequenceAt (index);
+index++;
+}}
+var fAlignmt =  new jalview.datamodel.Alignment (seq);
+fAlignmt.annotations = this.alignment.getAlignmentAnnotation ();
+fAlignmt.alignmentProperties = this.alignment.getProperties ();
+fAlignmt.groups = this.alignment.getGroups ();
+fAlignmt.$hasRNAStructure = this.alignment.hasRNAStructure ();
+return fAlignmt;
+});
+Clazz.defineMethod (c$, "isHidden", 
+function (seq) {
+if (this.hiddenSequences != null) {
+for (var i = 0; i < this.hiddenSequences.length; i++) {
+if (this.hiddenSequences[i] != null && this.hiddenSequences[i] === seq) {
+return true;
+}}
+}return false;
+}, "jalview.datamodel.SequenceI");
+});