X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fdatamodel%2FSearchResults.js;h=08fc20be8cefe19b1472f884075c5c63bb0d7d18;hp=dc7f66d351c952aad6402a58c330e56674dbe518;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6

diff --git a/site/j2s/jalview/datamodel/SearchResults.js b/site/j2s/jalview/datamodel/SearchResults.js
index dc7f66d..08fc20b 100644
--- a/site/j2s/jalview/datamodel/SearchResults.js
+++ b/site/j2s/jalview/datamodel/SearchResults.js
@@ -1,137 +1,137 @@
-Clazz.declarePackage ("jalview.datamodel");
-Clazz.load (["java.util.ArrayList"], "jalview.datamodel.SearchResults", ["java.lang.StringBuilder", "java.util.Arrays"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.matches = null;
-if (!Clazz.isClassDefined ("jalview.datamodel.SearchResults.Match")) {
-jalview.datamodel.SearchResults.$SearchResults$Match$ ();
-}
-Clazz.instantialize (this, arguments);
-}, jalview.datamodel, "SearchResults");
-Clazz.prepareFields (c$, function () {
-this.matches =  new java.util.ArrayList ();
-});
-Clazz.defineMethod (c$, "addResult", 
-function (seq, start, end) {
-this.matches.add (Clazz.innerTypeInstance (jalview.datamodel.SearchResults.Match, this, null, seq, start, end));
-}, "jalview.datamodel.SequenceI,~N,~N");
-Clazz.defineMethod (c$, "involvesSequence", 
-function (sequence) {
-var ds = sequence.getDatasetSequence ();
-for (var m, $m = this.matches.iterator (); $m.hasNext () && ((m = $m.next ()) || true);) {
-if (m.sequence != null && (m.sequence === sequence || m.sequence === ds)) {
-return true;
-}}
-return false;
-}, "jalview.datamodel.SequenceI");
-Clazz.defineMethod (c$, "getResults", 
-function (sequence, start, end) {
-if (this.matches.isEmpty ()) {
-return null;
-}var result = null;
-var tmp = null;
-var resultLength;
-var matchStart = 0;
-var matchEnd = 0;
-var mfound;
-for (var m, $m = this.matches.iterator (); $m.hasNext () && ((m = $m.next ()) || true);) {
-mfound = false;
-if (m.sequence === sequence) {
-mfound = true;
-matchStart = sequence.findIndex (m.start) - 1;
-matchEnd = sequence.findIndex (m.end) - 1;
-} else if (m.sequence === sequence.getDatasetSequence ()) {
-mfound = true;
-matchStart = sequence.findIndex (m.start) - 1;
-matchEnd = sequence.findIndex (m.end) - 1;
-}if (mfound) {
-if (matchStart <= end && matchEnd >= start) {
-if (matchStart < start) {
-matchStart = start;
-}if (matchEnd > end) {
-matchEnd = end;
-}if (result == null) {
-result =  Clazz.newIntArray (-1, [matchStart, matchEnd]);
-} else {
-resultLength = result.length;
-tmp =  Clazz.newIntArray (resultLength + 2, 0);
-System.arraycopy (result, 0, tmp, 0, resultLength);
-result = tmp;
-result[resultLength] = matchStart;
-result[resultLength + 1] = matchEnd;
-}} else {
-}}}
-return result;
-}, "jalview.datamodel.SequenceI,~N,~N");
-Clazz.defineMethod (c$, "getSize", 
-function () {
-return this.matches.size ();
-});
-Clazz.defineMethod (c$, "getResultSequence", 
-function (index) {
-return this.matches.get (index).sequence;
-}, "~N");
-Clazz.defineMethod (c$, "getResultStart", 
-function (i) {
-return this.matches.get (i).start;
-}, "~N");
-Clazz.defineMethod (c$, "getResultEnd", 
-function (i) {
-return this.matches.get (i).end;
-}, "~N");
-Clazz.defineMethod (c$, "isEmpty", 
-function () {
-return this.matches.isEmpty ();
-});
-Clazz.defineMethod (c$, "getResults", 
-function () {
-return this.matches;
-});
-Clazz.overrideMethod (c$, "toString", 
-function () {
-var result =  new StringBuilder (256);
-for (var m, $m = this.matches.iterator (); $m.hasNext () && ((m = $m.next ()) || true);) {
-result.append (m.toString ());
-}
-return result.toString ();
-});
-c$.$SearchResults$Match$ = function () {
-Clazz.pu$h(self.c$);
-c$ = Clazz.decorateAsClass (function () {
-Clazz.prepareCallback (this, arguments);
-this.sequence = null;
-this.start = 0;
-this.end = 0;
-Clazz.instantialize (this, arguments);
-}, jalview.datamodel.SearchResults, "Match");
-Clazz.makeConstructor (c$, 
-function (a, b, c) {
-this.sequence = a;
-this.start = b;
-this.end = c;
-}, "jalview.datamodel.SequenceI,~N,~N");
-Clazz.defineMethod (c$, "getSequence", 
-function () {
-return this.sequence;
-});
-Clazz.defineMethod (c$, "getStart", 
-function () {
-return this.start;
-});
-Clazz.defineMethod (c$, "getEnd", 
-function () {
-return this.end;
-});
-Clazz.overrideMethod (c$, "toString", 
-function () {
-var a = this.sequence.getSequence ();
-var b = Math.max (this.start - 1, 0);
-var c = Math.min (this.end, a.length + 1);
-return String.valueOf (java.util.Arrays.copyOfRange (a, b, c));
-});
-Clazz.defineMethod (c$, "setSequence", 
-function (a) {
-this.sequence = a;
-}, "jalview.datamodel.SequenceI");
-c$ = Clazz.p0p ();
-};
-});
+Clazz.declarePackage ("jalview.datamodel");
+Clazz.load (["java.util.ArrayList"], "jalview.datamodel.SearchResults", ["java.lang.StringBuilder", "java.util.Arrays"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.matches = null;
+if (!Clazz.isClassDefined ("jalview.datamodel.SearchResults.Match")) {
+jalview.datamodel.SearchResults.$SearchResults$Match$ ();
+}
+Clazz.instantialize (this, arguments);
+}, jalview.datamodel, "SearchResults");
+Clazz.prepareFields (c$, function () {
+this.matches =  new java.util.ArrayList ();
+});
+Clazz.defineMethod (c$, "addResult", 
+function (seq, start, end) {
+this.matches.add (Clazz.innerTypeInstance (jalview.datamodel.SearchResults.Match, this, null, seq, start, end));
+}, "jalview.datamodel.SequenceI,~N,~N");
+Clazz.defineMethod (c$, "involvesSequence", 
+function (sequence) {
+var ds = sequence.getDatasetSequence ();
+for (var m, $m = this.matches.iterator (); $m.hasNext () && ((m = $m.next ()) || true);) {
+if (m.sequence != null && (m.sequence === sequence || m.sequence === ds)) {
+return true;
+}}
+return false;
+}, "jalview.datamodel.SequenceI");
+Clazz.defineMethod (c$, "getResults", 
+function (sequence, start, end) {
+if (this.matches.isEmpty ()) {
+return null;
+}var result = null;
+var tmp = null;
+var resultLength;
+var matchStart = 0;
+var matchEnd = 0;
+var mfound;
+for (var m, $m = this.matches.iterator (); $m.hasNext () && ((m = $m.next ()) || true);) {
+mfound = false;
+if (m.sequence === sequence) {
+mfound = true;
+matchStart = sequence.findIndex (m.start) - 1;
+matchEnd = sequence.findIndex (m.end) - 1;
+} else if (m.sequence === sequence.getDatasetSequence ()) {
+mfound = true;
+matchStart = sequence.findIndex (m.start) - 1;
+matchEnd = sequence.findIndex (m.end) - 1;
+}if (mfound) {
+if (matchStart <= end && matchEnd >= start) {
+if (matchStart < start) {
+matchStart = start;
+}if (matchEnd > end) {
+matchEnd = end;
+}if (result == null) {
+result =  Clazz.newIntArray (-1, [matchStart, matchEnd]);
+} else {
+resultLength = result.length;
+tmp =  Clazz.newIntArray (resultLength + 2, 0);
+System.arraycopy (result, 0, tmp, 0, resultLength);
+result = tmp;
+result[resultLength] = matchStart;
+result[resultLength + 1] = matchEnd;
+}} else {
+}}}
+return result;
+}, "jalview.datamodel.SequenceI,~N,~N");
+Clazz.defineMethod (c$, "getSize", 
+function () {
+return this.matches.size ();
+});
+Clazz.defineMethod (c$, "getResultSequence", 
+function (index) {
+return this.matches.get (index).sequence;
+}, "~N");
+Clazz.defineMethod (c$, "getResultStart", 
+function (i) {
+return this.matches.get (i).start;
+}, "~N");
+Clazz.defineMethod (c$, "getResultEnd", 
+function (i) {
+return this.matches.get (i).end;
+}, "~N");
+Clazz.defineMethod (c$, "isEmpty", 
+function () {
+return this.matches.isEmpty ();
+});
+Clazz.defineMethod (c$, "getResults", 
+function () {
+return this.matches;
+});
+Clazz.overrideMethod (c$, "toString", 
+function () {
+var result =  new StringBuilder (256);
+for (var m, $m = this.matches.iterator (); $m.hasNext () && ((m = $m.next ()) || true);) {
+result.append (m.toString ());
+}
+return result.toString ();
+});
+c$.$SearchResults$Match$ = function () {
+Clazz.pu$h(self.c$);
+c$ = Clazz.decorateAsClass (function () {
+Clazz.prepareCallback (this, arguments);
+this.sequence = null;
+this.start = 0;
+this.end = 0;
+Clazz.instantialize (this, arguments);
+}, jalview.datamodel.SearchResults, "Match");
+Clazz.makeConstructor (c$, 
+function (a, b, c) {
+this.sequence = a;
+this.start = b;
+this.end = c;
+}, "jalview.datamodel.SequenceI,~N,~N");
+Clazz.defineMethod (c$, "getSequence", 
+function () {
+return this.sequence;
+});
+Clazz.defineMethod (c$, "getStart", 
+function () {
+return this.start;
+});
+Clazz.defineMethod (c$, "getEnd", 
+function () {
+return this.end;
+});
+Clazz.overrideMethod (c$, "toString", 
+function () {
+var a = this.sequence.getSequence ();
+var b = Math.max (this.start - 1, 0);
+var c = Math.min (this.end, a.length + 1);
+return String.valueOf (java.util.Arrays.copyOfRange (a, b, c));
+});
+Clazz.defineMethod (c$, "setSequence", 
+function (a) {
+this.sequence = a;
+}, "jalview.datamodel.SequenceI");
+c$ = Clazz.p0p ();
+};
+});