X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fanalysis%2FFinder.js;h=5d20c2ce47620c76995b42dfbacc6111355717f4;hp=cf1d8f9318072aff786a23f48d91bff1f865aae4;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/analysis/Finder.js b/bin/jalview/analysis/Finder.js
index cf1d8f9..5d20c2c 100644
--- a/bin/jalview/analysis/Finder.js
+++ b/bin/jalview/analysis/Finder.js
@@ -1,182 +1,182 @@
-Clazz.declarePackage ("jalview.analysis");
-Clazz.load (null, "jalview.analysis.Finder", ["jalview.datamodel.SearchResults", "jalview.jsdev.RegExp", "jalview.util.Comparison", "java.lang.StringBuffer", "java.util.Vector"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.searchResults = null;
-this.alignment = null;
-this.selection = null;
-this.idMatch = null;
-this.caseSensitive = false;
-this.includeDescription = false;
-this.findAll = false;
-this.regex = null;
-this.seqIndex = 0;
-this.resIndex = -1;
-Clazz.instantialize (this, arguments);
-}, jalview.analysis, "Finder");
-Clazz.makeConstructor (c$, 
-function (alignment, selection) {
-this.alignment = alignment;
-this.selection = selection;
-}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup");
-Clazz.makeConstructor (c$, 
-function (alignment, selectionGroup, seqIndex, resIndex) {
-this.construct (alignment, selectionGroup);
-this.seqIndex = seqIndex;
-this.resIndex = resIndex;
-}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup,~N,~N");
-Clazz.defineMethod (c$, "find", 
-function (searchString) {
-var hasResults = false;
-if (!this.caseSensitive) {
-searchString = searchString.toUpperCase ();
-}this.regex = jalview.jsdev.RegExp.newRegex ([searchString]);
-this.regex.setIgnoreCase (!this.caseSensitive);
-this.searchResults =  new jalview.datamodel.SearchResults ();
-this.idMatch =  new java.util.Vector ();
-var seq;
-var item = null;
-var found = false;
-var end = this.alignment.getHeight ();
-if (this.selection != null) {
-if ((this.selection.getSize () < 1) || ((this.selection.getEndRes () - this.selection.getStartRes ()) < 2)) {
-this.selection = null;
-}}while (!found && (this.seqIndex < end)) {
-seq = this.alignment.getSequenceAt (this.seqIndex);
-if ((this.selection != null && this.selection.getSize () > 0) && !this.selection.getSequences (null).contains (seq)) {
-this.seqIndex++;
-this.resIndex = -1;
-continue;
-}if (this.resIndex < 0) {
-this.resIndex = 0;
-try {
-var res = Integer.parseInt (searchString);
-if (seq.getEnd () >= res) {
-this.searchResults.addResult (seq, res, res);
-hasResults = true;
-if (!this.findAll) {
-found = true;
-break;
-}}} catch (ex) {
-if (Clazz.exceptionOf (ex, NumberFormatException)) {
-} else {
-throw ex;
-}
-}
-if (this.regex.search (seq.getName ())) {
-this.idMatch.addElement (seq);
-hasResults = true;
-if (!this.findAll) {
-found = true;
-break;
-}}if (this.isIncludeDescription () && seq.getDescription () != null && this.regex.search (seq.getDescription ())) {
-this.idMatch.addElement (seq);
-hasResults = true;
-if (!this.findAll) {
-found = true;
-break;
-}}}item = seq.getSequenceAsString ();
-if ((this.selection != null) && (this.selection.getEndRes () < this.alignment.getWidth () - 1)) {
-item = item.substring (0, this.selection.getEndRes () + 1);
-}var noGapsSB =  new StringBuffer ();
-var insertCount = 0;
-var spaces =  new java.util.Vector ();
-for (var j = 0; j < item.length; j++) {
-if (!jalview.util.Comparison.isGap (item.charAt (j))) {
-noGapsSB.append (item.charAt (j));
-spaces.addElement ( new Integer (insertCount));
-} else {
-insertCount++;
-}}
-var noGaps = noGapsSB.toString ();
-for (var r = this.resIndex; r < noGaps.length; r++) {
-if (this.regex.searchFrom (noGaps, r)) {
-this.resIndex = this.regex.matchedFrom ();
-if ((this.selection != null && this.selection.getSize () > 0) && ((this.resIndex + Integer.parseInt (spaces.elementAt (this.resIndex).toString ())) < this.selection.getStartRes ())) {
-continue;
-}var sres = seq.findPosition (this.resIndex + Integer.parseInt (spaces.elementAt (this.resIndex).toString ()));
-var eres = seq.findPosition (this.regex.matchedTo () - 1 + Integer.parseInt (spaces.elementAt (this.regex.matchedTo () - 1).toString ()));
-this.searchResults.addResult (seq, sres, eres);
-hasResults = true;
-if (!this.findAll) {
-found = true;
-this.resIndex++;
-break;
-}r = this.resIndex;
-} else {
-break;
-}}
-if (!found) {
-this.seqIndex++;
-this.resIndex = -1;
-}}
-return hasResults;
-}, "~S");
-Clazz.defineMethod (c$, "getAlignment", 
-function () {
-return this.alignment;
-});
-Clazz.defineMethod (c$, "setAlignment", 
-function (alignment) {
-this.alignment = alignment;
-}, "jalview.datamodel.AlignmentI");
-Clazz.defineMethod (c$, "isCaseSensitive", 
-function () {
-return this.caseSensitive;
-});
-Clazz.defineMethod (c$, "setCaseSensitive", 
-function (caseSensitive) {
-this.caseSensitive = caseSensitive;
-}, "~B");
-Clazz.defineMethod (c$, "isFindAll", 
-function () {
-return this.findAll;
-});
-Clazz.defineMethod (c$, "setFindAll", 
-function (findAll) {
-this.findAll = findAll;
-}, "~B");
-Clazz.defineMethod (c$, "getSelection", 
-function () {
-return this.selection;
-});
-Clazz.defineMethod (c$, "setSelection", 
-function (selection) {
-this.selection = selection;
-}, "jalview.datamodel.SequenceGroup");
-Clazz.defineMethod (c$, "getIdMatch", 
-function () {
-return this.idMatch;
-});
-Clazz.defineMethod (c$, "getRegex", 
-function () {
-return this.regex;
-});
-Clazz.defineMethod (c$, "getSearchResults", 
-function () {
-return this.searchResults;
-});
-Clazz.defineMethod (c$, "getResIndex", 
-function () {
-return this.resIndex;
-});
-Clazz.defineMethod (c$, "setResIndex", 
-function (resIndex) {
-this.resIndex = resIndex;
-}, "~N");
-Clazz.defineMethod (c$, "getSeqIndex", 
-function () {
-return this.seqIndex;
-});
-Clazz.defineMethod (c$, "setSeqIndex", 
-function (seqIndex) {
-this.seqIndex = seqIndex;
-}, "~N");
-Clazz.defineMethod (c$, "isIncludeDescription", 
-function () {
-return this.includeDescription;
-});
-Clazz.defineMethod (c$, "setIncludeDescription", 
-function (includeDescription) {
-this.includeDescription = includeDescription;
-}, "~B");
-});
+Clazz.declarePackage ("jalview.analysis");
+Clazz.load (null, "jalview.analysis.Finder", ["jalview.datamodel.SearchResults", "jalview.jsdev.RegExp", "jalview.util.Comparison", "java.lang.StringBuffer", "java.util.Vector"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.searchResults = null;
+this.alignment = null;
+this.selection = null;
+this.idMatch = null;
+this.caseSensitive = false;
+this.includeDescription = false;
+this.findAll = false;
+this.regex = null;
+this.seqIndex = 0;
+this.resIndex = -1;
+Clazz.instantialize (this, arguments);
+}, jalview.analysis, "Finder");
+Clazz.makeConstructor (c$, 
+function (alignment, selection) {
+this.alignment = alignment;
+this.selection = selection;
+}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup");
+Clazz.makeConstructor (c$, 
+function (alignment, selectionGroup, seqIndex, resIndex) {
+this.construct (alignment, selectionGroup);
+this.seqIndex = seqIndex;
+this.resIndex = resIndex;
+}, "jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup,~N,~N");
+Clazz.defineMethod (c$, "find", 
+function (searchString) {
+var hasResults = false;
+if (!this.caseSensitive) {
+searchString = searchString.toUpperCase ();
+}this.regex = jalview.jsdev.RegExp.newRegex ([searchString]);
+this.regex.setIgnoreCase (!this.caseSensitive);
+this.searchResults =  new jalview.datamodel.SearchResults ();
+this.idMatch =  new java.util.Vector ();
+var seq;
+var item = null;
+var found = false;
+var end = this.alignment.getHeight ();
+if (this.selection != null) {
+if ((this.selection.getSize () < 1) || ((this.selection.getEndRes () - this.selection.getStartRes ()) < 2)) {
+this.selection = null;
+}}while (!found && (this.seqIndex < end)) {
+seq = this.alignment.getSequenceAt (this.seqIndex);
+if ((this.selection != null && this.selection.getSize () > 0) && !this.selection.getSequences (null).contains (seq)) {
+this.seqIndex++;
+this.resIndex = -1;
+continue;
+}if (this.resIndex < 0) {
+this.resIndex = 0;
+try {
+var res = Integer.parseInt (searchString);
+if (seq.getEnd () >= res) {
+this.searchResults.addResult (seq, res, res);
+hasResults = true;
+if (!this.findAll) {
+found = true;
+break;
+}}} catch (ex) {
+if (Clazz.exceptionOf (ex, NumberFormatException)) {
+} else {
+throw ex;
+}
+}
+if (this.regex.search (seq.getName ())) {
+this.idMatch.addElement (seq);
+hasResults = true;
+if (!this.findAll) {
+found = true;
+break;
+}}if (this.isIncludeDescription () && seq.getDescription () != null && this.regex.search (seq.getDescription ())) {
+this.idMatch.addElement (seq);
+hasResults = true;
+if (!this.findAll) {
+found = true;
+break;
+}}}item = seq.getSequenceAsString ();
+if ((this.selection != null) && (this.selection.getEndRes () < this.alignment.getWidth () - 1)) {
+item = item.substring (0, this.selection.getEndRes () + 1);
+}var noGapsSB =  new StringBuffer ();
+var insertCount = 0;
+var spaces =  new java.util.Vector ();
+for (var j = 0; j < item.length; j++) {
+if (!jalview.util.Comparison.isGap (item.charAt (j))) {
+noGapsSB.append (item.charAt (j));
+spaces.addElement ( new Integer (insertCount));
+} else {
+insertCount++;
+}}
+var noGaps = noGapsSB.toString ();
+for (var r = this.resIndex; r < noGaps.length; r++) {
+if (this.regex.searchFrom (noGaps, r)) {
+this.resIndex = this.regex.matchedFrom ();
+if ((this.selection != null && this.selection.getSize () > 0) && ((this.resIndex + Integer.parseInt (spaces.elementAt (this.resIndex).toString ())) < this.selection.getStartRes ())) {
+continue;
+}var sres = seq.findPosition (this.resIndex + Integer.parseInt (spaces.elementAt (this.resIndex).toString ()));
+var eres = seq.findPosition (this.regex.matchedTo () - 1 + Integer.parseInt (spaces.elementAt (this.regex.matchedTo () - 1).toString ()));
+this.searchResults.addResult (seq, sres, eres);
+hasResults = true;
+if (!this.findAll) {
+found = true;
+this.resIndex++;
+break;
+}r = this.resIndex;
+} else {
+break;
+}}
+if (!found) {
+this.seqIndex++;
+this.resIndex = -1;
+}}
+return hasResults;
+}, "~S");
+Clazz.defineMethod (c$, "getAlignment", 
+function () {
+return this.alignment;
+});
+Clazz.defineMethod (c$, "setAlignment", 
+function (alignment) {
+this.alignment = alignment;
+}, "jalview.datamodel.AlignmentI");
+Clazz.defineMethod (c$, "isCaseSensitive", 
+function () {
+return this.caseSensitive;
+});
+Clazz.defineMethod (c$, "setCaseSensitive", 
+function (caseSensitive) {
+this.caseSensitive = caseSensitive;
+}, "~B");
+Clazz.defineMethod (c$, "isFindAll", 
+function () {
+return this.findAll;
+});
+Clazz.defineMethod (c$, "setFindAll", 
+function (findAll) {
+this.findAll = findAll;
+}, "~B");
+Clazz.defineMethod (c$, "getSelection", 
+function () {
+return this.selection;
+});
+Clazz.defineMethod (c$, "setSelection", 
+function (selection) {
+this.selection = selection;
+}, "jalview.datamodel.SequenceGroup");
+Clazz.defineMethod (c$, "getIdMatch", 
+function () {
+return this.idMatch;
+});
+Clazz.defineMethod (c$, "getRegex", 
+function () {
+return this.regex;
+});
+Clazz.defineMethod (c$, "getSearchResults", 
+function () {
+return this.searchResults;
+});
+Clazz.defineMethod (c$, "getResIndex", 
+function () {
+return this.resIndex;
+});
+Clazz.defineMethod (c$, "setResIndex", 
+function (resIndex) {
+this.resIndex = resIndex;
+}, "~N");
+Clazz.defineMethod (c$, "getSeqIndex", 
+function () {
+return this.seqIndex;
+});
+Clazz.defineMethod (c$, "setSeqIndex", 
+function (seqIndex) {
+this.seqIndex = seqIndex;
+}, "~N");
+Clazz.defineMethod (c$, "isIncludeDescription", 
+function () {
+return this.includeDescription;
+});
+Clazz.defineMethod (c$, "setIncludeDescription", 
+function (includeDescription) {
+this.includeDescription = includeDescription;
+}, "~B");
+});