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