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