X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fdatamodel%2FCigarArray.js;h=e850f41a378e769baaff93487001e318180c7b4e;hp=7925e733408bac48b2eb7324e460f15597add4d3;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/datamodel/CigarArray.js b/site/j2s/jalview/datamodel/CigarArray.js
index 7925e73..e850f41 100644
--- a/site/j2s/jalview/datamodel/CigarArray.js
+++ b/site/j2s/jalview/datamodel/CigarArray.js
@@ -1,188 +1,188 @@
-Clazz.declarePackage ("jalview.datamodel");
-Clazz.load (["jalview.datamodel.CigarBase"], "jalview.datamodel.CigarArray", ["jalview.datamodel.CigarCigar", "$.SeqCigar", "java.lang.StringBuffer", "java.util.Vector"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.refCigars = null;
-this.seqcigararray = false;
-Clazz.instantialize (this, arguments);
-}, jalview.datamodel, "CigarArray", jalview.datamodel.CigarBase);
-Clazz.defineMethod (c$, "isSeqCigarArray", 
-function () {
-return this.seqcigararray;
-});
-Clazz.makeConstructor (c$, 
-function (cigars) {
-Clazz.superConstructor (this, jalview.datamodel.CigarArray);
-this.seqcigararray = true;
-if (cigars != null && cigars.length > 0) {
-this.refCigars =  new Array (cigars.length);
-for (var c = 0; c < cigars.length; c++) {
-this.refCigars[c] = cigars[c];
-if (!((Clazz.instanceOf (cigars[c], jalview.datamodel.SeqCigar)) || Clazz.instanceOf (cigars[c], jalview.datamodel.CigarCigar))) {
-this.seqcigararray = false;
-}}
-}}, "~A");
-Clazz.makeConstructor (c$, 
-function (alignment, columnSelection, selectionGroup) {
-this.construct (jalview.datamodel.CigarArray.constructSeqCigarArray (alignment, selectionGroup));
-this.constructFromAlignment (alignment, columnSelection != null ? columnSelection.getHiddenColumns () : null, selectionGroup);
-}, "jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,jalview.datamodel.SequenceGroup");
-c$._calcStartEndBounds = Clazz.defineMethod (c$, "_calcStartEndBounds", 
- function (alignment, selectionGroup) {
-var startend =  Clazz.newIntArray (-1, [0, 0, 0]);
-if (selectionGroup != null) {
-startend[0] = selectionGroup.getSize ();
-startend[1] = selectionGroup.getStartRes ();
-startend[2] = selectionGroup.getEndRes ();
-} else {
-startend[0] = alignment.getHeight ();
-startend[2] = alignment.getWidth () - 1;
-}return startend;
-}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup");
-c$.constructSeqCigarArray = Clazz.defineMethod (c$, "constructSeqCigarArray", 
-function (alignment, selectionGroup) {
-var seqs = null;
-var i;
-var iSize;
-var _startend = jalview.datamodel.CigarArray._calcStartEndBounds (alignment, selectionGroup);
-var start = _startend[1];
-var end = _startend[2];
-if (selectionGroup != null) {
-iSize = selectionGroup.getSize ();
-seqs = selectionGroup.getSequencesInOrder (alignment);
-start = selectionGroup.getStartRes ();
-end = selectionGroup.getEndRes ();
-} else {
-iSize = alignment.getHeight ();
-seqs = alignment.getSequencesArray ();
-end = alignment.getWidth () - 1;
-}var selseqs =  new Array (iSize);
-for (i = 0; i < iSize; i++) {
-selseqs[i] =  new jalview.datamodel.SeqCigar (seqs[i], start, end);
-}
-return selseqs;
-}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup");
-Clazz.defineMethod (c$, "constructFromAlignment", 
- function (alignment, list, selectionGroup) {
-var _startend = jalview.datamodel.CigarArray._calcStartEndBounds (alignment, selectionGroup);
-var start = _startend[1];
-var end = _startend[2];
-if (list != null) {
-var region;
-var hideStart;
-var hideEnd;
-var last = start;
-for (var j = 0;  new Boolean (last < end & j < list.size ()).valueOf (); j++) {
-region = list.get (j);
-hideStart = region[0];
-hideEnd = region[1];
-if (hideStart < last) {
-if (hideEnd > last) {
-hideStart = last;
-} else {
-continue;
-}}if (hideStart > end) {
-break;
-}if (hideEnd > end) {
-hideEnd = end;
-}if (hideStart > hideEnd) {
-break;
-}if (last < hideStart) {
-this.addOperation ('M', hideStart - last);
-}this.addOperation ('D', 1 + hideEnd - hideStart);
-last = hideEnd + 1;
-}
-if (last < end) {
-this.addOperation ('M', end - last + 1);
-}} else {
-this.addOperation ('M', end - start + 1);
-}}, "jalview.datamodel.AlignmentI,java.util.List,jalview.datamodel.SequenceGroup");
-Clazz.defineMethod (c$, "getArrayofSequenceAndDeletions", 
-function (GapChar) {
-if (this.refCigars == null || this.refCigars.length == 0 || this.length == 0) {
-return null;
-}var sqanddels =  new Array (this.refCigars.length);
-for (var c = 0; c < this.refCigars.length; c++) {
-var refString = this.refCigars[c].getSequenceString (GapChar);
-if (refString != null) {
-sqanddels[c] = this.getSequenceAndDeletions (refString, GapChar);
-} else {
-sqanddels[c] = null;
-}}
-return sqanddels;
-}, "~S");
-Clazz.defineMethod (c$, "getSequenceString", 
-function (GapChar) {
-if (this.length == 0 || this.refCigars == null) {
-return "";
-}var seqStrings =  new StringBuffer ();
-var sqanddels = this.getArrayofSequenceAndDeletions (GapChar);
-for (var c = 0; c < this.refCigars.length; c++) {
-if (sqanddels[c] != null) {
-seqStrings.append (sqanddels[c][0]);
-sqanddels[c][0] = null;
-}seqStrings.append ('\n');
-}
-return seqStrings.toString ();
-}, "~S");
-Clazz.defineMethod (c$, "getSequenceStrings", 
-function (GapChar) {
-if (this.length == 0 || this.refCigars == null || this.refCigars.length == 0) {
-return null;
-}var sqanddels = this.getArrayofSequenceAndDeletions (GapChar);
-var seqs =  new Array (sqanddels.length);
-for (var c = 0; c < this.refCigars.length; c++) {
-seqs[c] = sqanddels[c][0];
-}
-return seqs;
-}, "~S");
-Clazz.defineMethod (c$, "applyDeletions", 
-function () {
-var delpos = null;
-if (this.length == 0) {
-return null;
-}var cursor = 0;
-var vcursor = 0;
-var offset = 0;
-var i = 0;
-while (i < this.length) {
-if (this.operation[i] != 'D') {
-if (this.operation[i] == 'M') {
-cursor += this.range[i];
-}vcursor += this.range[i++];
-} else {
-if (delpos == null) {
-delpos =  new java.util.Vector ();
-}var delstart = cursor;
-var delend = cursor + this.range[i] - 1;
-delpos.addElement ( Clazz.newIntArray (-1, [vcursor + offset, this.range[i]]));
-offset += this.range[i] - 1;
-System.arraycopy (this.operation, i + 1, this.operation, i, this.length - i);
-System.arraycopy (this.range, i + 1, this.range, i, this.length - i);
-this.length--;
-for (var s = 0; s < this.refCigars.length; s++) {
-var d = this.refCigars[s].deleteRange (delstart, delend);
-}
-}}
-if (delpos != null) {
-var pos =  Clazz.newIntArray (delpos.size () * 2, 0);
-for (var k = 0, l = delpos.size (); k < l; k++) {
-var dr = (delpos.elementAt (k));
-pos[k * 2] = dr[0];
-pos[k * 2 + 1] = dr[1];
-delpos.setElementAt (null, k);
-}
-delpos = null;
-return pos;
-}return null;
-});
-Clazz.defineMethod (c$, "getSeqCigarArray", 
-function () {
-if (!this.isSeqCigarArray ()) {
-return null;
-}var sa =  new Array (this.refCigars.length);
-for (var i = 0; i < this.refCigars.length; i++) {
-sa[i] = this.refCigars[i];
-}
-return sa;
-});
-});
+Clazz.declarePackage ("jalview.datamodel");
+Clazz.load (["jalview.datamodel.CigarBase"], "jalview.datamodel.CigarArray", ["jalview.datamodel.CigarCigar", "$.SeqCigar", "java.lang.StringBuffer", "java.util.Vector"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.refCigars = null;
+this.seqcigararray = false;
+Clazz.instantialize (this, arguments);
+}, jalview.datamodel, "CigarArray", jalview.datamodel.CigarBase);
+Clazz.defineMethod (c$, "isSeqCigarArray", 
+function () {
+return this.seqcigararray;
+});
+Clazz.makeConstructor (c$, 
+function (cigars) {
+Clazz.superConstructor (this, jalview.datamodel.CigarArray);
+this.seqcigararray = true;
+if (cigars != null && cigars.length > 0) {
+this.refCigars =  new Array (cigars.length);
+for (var c = 0; c < cigars.length; c++) {
+this.refCigars[c] = cigars[c];
+if (!((Clazz.instanceOf (cigars[c], jalview.datamodel.SeqCigar)) || Clazz.instanceOf (cigars[c], jalview.datamodel.CigarCigar))) {
+this.seqcigararray = false;
+}}
+}}, "~A");
+Clazz.makeConstructor (c$, 
+function (alignment, columnSelection, selectionGroup) {
+this.construct (jalview.datamodel.CigarArray.constructSeqCigarArray (alignment, selectionGroup));
+this.constructFromAlignment (alignment, columnSelection != null ? columnSelection.getHiddenColumns () : null, selectionGroup);
+}, "jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,jalview.datamodel.SequenceGroup");
+c$._calcStartEndBounds = Clazz.defineMethod (c$, "_calcStartEndBounds", 
+ function (alignment, selectionGroup) {
+var startend =  Clazz.newIntArray (-1, [0, 0, 0]);
+if (selectionGroup != null) {
+startend[0] = selectionGroup.getSize ();
+startend[1] = selectionGroup.getStartRes ();
+startend[2] = selectionGroup.getEndRes ();
+} else {
+startend[0] = alignment.getHeight ();
+startend[2] = alignment.getWidth () - 1;
+}return startend;
+}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup");
+c$.constructSeqCigarArray = Clazz.defineMethod (c$, "constructSeqCigarArray", 
+function (alignment, selectionGroup) {
+var seqs = null;
+var i;
+var iSize;
+var _startend = jalview.datamodel.CigarArray._calcStartEndBounds (alignment, selectionGroup);
+var start = _startend[1];
+var end = _startend[2];
+if (selectionGroup != null) {
+iSize = selectionGroup.getSize ();
+seqs = selectionGroup.getSequencesInOrder (alignment);
+start = selectionGroup.getStartRes ();
+end = selectionGroup.getEndRes ();
+} else {
+iSize = alignment.getHeight ();
+seqs = alignment.getSequencesArray ();
+end = alignment.getWidth () - 1;
+}var selseqs =  new Array (iSize);
+for (i = 0; i < iSize; i++) {
+selseqs[i] =  new jalview.datamodel.SeqCigar (seqs[i], start, end);
+}
+return selseqs;
+}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup");
+Clazz.defineMethod (c$, "constructFromAlignment", 
+ function (alignment, list, selectionGroup) {
+var _startend = jalview.datamodel.CigarArray._calcStartEndBounds (alignment, selectionGroup);
+var start = _startend[1];
+var end = _startend[2];
+if (list != null) {
+var region;
+var hideStart;
+var hideEnd;
+var last = start;
+for (var j = 0;  new Boolean (last < end & j < list.size ()).valueOf (); j++) {
+region = list.get (j);
+hideStart = region[0];
+hideEnd = region[1];
+if (hideStart < last) {
+if (hideEnd > last) {
+hideStart = last;
+} else {
+continue;
+}}if (hideStart > end) {
+break;
+}if (hideEnd > end) {
+hideEnd = end;
+}if (hideStart > hideEnd) {
+break;
+}if (last < hideStart) {
+this.addOperation ('M', hideStart - last);
+}this.addOperation ('D', 1 + hideEnd - hideStart);
+last = hideEnd + 1;
+}
+if (last < end) {
+this.addOperation ('M', end - last + 1);
+}} else {
+this.addOperation ('M', end - start + 1);
+}}, "jalview.datamodel.AlignmentI,java.util.List,jalview.datamodel.SequenceGroup");
+Clazz.defineMethod (c$, "getArrayofSequenceAndDeletions", 
+function (GapChar) {
+if (this.refCigars == null || this.refCigars.length == 0 || this.length == 0) {
+return null;
+}var sqanddels =  new Array (this.refCigars.length);
+for (var c = 0; c < this.refCigars.length; c++) {
+var refString = this.refCigars[c].getSequenceString (GapChar);
+if (refString != null) {
+sqanddels[c] = this.getSequenceAndDeletions (refString, GapChar);
+} else {
+sqanddels[c] = null;
+}}
+return sqanddels;
+}, "~S");
+Clazz.defineMethod (c$, "getSequenceString", 
+function (GapChar) {
+if (this.length == 0 || this.refCigars == null) {
+return "";
+}var seqStrings =  new StringBuffer ();
+var sqanddels = this.getArrayofSequenceAndDeletions (GapChar);
+for (var c = 0; c < this.refCigars.length; c++) {
+if (sqanddels[c] != null) {
+seqStrings.append (sqanddels[c][0]);
+sqanddels[c][0] = null;
+}seqStrings.append ('\n');
+}
+return seqStrings.toString ();
+}, "~S");
+Clazz.defineMethod (c$, "getSequenceStrings", 
+function (GapChar) {
+if (this.length == 0 || this.refCigars == null || this.refCigars.length == 0) {
+return null;
+}var sqanddels = this.getArrayofSequenceAndDeletions (GapChar);
+var seqs =  new Array (sqanddels.length);
+for (var c = 0; c < this.refCigars.length; c++) {
+seqs[c] = sqanddels[c][0];
+}
+return seqs;
+}, "~S");
+Clazz.defineMethod (c$, "applyDeletions", 
+function () {
+var delpos = null;
+if (this.length == 0) {
+return null;
+}var cursor = 0;
+var vcursor = 0;
+var offset = 0;
+var i = 0;
+while (i < this.length) {
+if (this.operation[i] != 'D') {
+if (this.operation[i] == 'M') {
+cursor += this.range[i];
+}vcursor += this.range[i++];
+} else {
+if (delpos == null) {
+delpos =  new java.util.Vector ();
+}var delstart = cursor;
+var delend = cursor + this.range[i] - 1;
+delpos.addElement ( Clazz.newIntArray (-1, [vcursor + offset, this.range[i]]));
+offset += this.range[i] - 1;
+System.arraycopy (this.operation, i + 1, this.operation, i, this.length - i);
+System.arraycopy (this.range, i + 1, this.range, i, this.length - i);
+this.length--;
+for (var s = 0; s < this.refCigars.length; s++) {
+var d = this.refCigars[s].deleteRange (delstart, delend);
+}
+}}
+if (delpos != null) {
+var pos =  Clazz.newIntArray (delpos.size () * 2, 0);
+for (var k = 0, l = delpos.size (); k < l; k++) {
+var dr = (delpos.elementAt (k));
+pos[k * 2] = dr[0];
+pos[k * 2 + 1] = dr[1];
+delpos.setElementAt (null, k);
+}
+delpos = null;
+return pos;
+}return null;
+});
+Clazz.defineMethod (c$, "getSeqCigarArray", 
+function () {
+if (!this.isSeqCigarArray ()) {
+return null;
+}var sa =  new Array (this.refCigars.length);
+for (var i = 0; i < this.refCigars.length; i++) {
+sa[i] = this.refCigars[i];
+}
+return sa;
+});
+});