-Clazz.declarePackage ("jalview.analysis");
-Clazz.load (null, "jalview.analysis.ParseProperties", ["jalview.datamodel.AlignmentAnnotation", "jalview.jsdev.RegExp", "java.lang.Double"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.al = null;
-Clazz.instantialize (this, arguments);
-}, jalview.analysis, "ParseProperties");
-Clazz.makeConstructor (c$,
-function (al) {
-this.al = al;
-}, "jalview.datamodel.AlignmentI");
-Clazz.defineMethod (c$, "getScoresFromDescription",
-function (ScoreName, ScoreDescriptions, regex, repeat) {
-return this.getScoresFromDescription ( Clazz.newArray (-1, [ScoreName]), Clazz.newArray (-1, [ScoreDescriptions]), regex, repeat);
-}, "~S,~S,~S,~B");
-Clazz.defineMethod (c$, "getScoresFromDescription",
-function (ScoreNames, ScoreDescriptions, regex, repeat) {
-return this.getScoresFromDescription (this.al.getSequencesArray (), ScoreNames, ScoreDescriptions, regex, repeat);
-}, "~A,~A,~S,~B");
-Clazz.defineMethod (c$, "getScoresFromDescription",
-function (seqs, ScoreNames, ScoreDescriptions, regex, repeat) {
-var count = 0;
-var pattern = jalview.jsdev.RegExp.newRegex ([regex]);
-if (pattern.numSubs () > ScoreNames.length) {
-var onamelen = ScoreNames.length;
-var tnames = new Array (pattern.numSubs () + 1);
-System.arraycopy (ScoreNames, 0, tnames, 0, ScoreNames.length);
-var base = tnames[ScoreNames.length - 1];
-ScoreNames = tnames;
-var descrbase = ScoreDescriptions[onamelen - 1];
-if (descrbase == null) {
-descrbase = "Score parsed from (" + regex + ")";
-}tnames = new Array (pattern.numSubs () + 1);
-System.arraycopy (ScoreDescriptions, 0, tnames, 0, ScoreDescriptions.length);
-ScoreDescriptions = tnames;
-for (var i = onamelen; i < ScoreNames.length; i++) {
-ScoreNames[i] = base + "_" + i;
-ScoreDescriptions[i] = descrbase + " (column " + i + ")";
-}
-}for (var i = 0; i < seqs.length; i++) {
-var descr = seqs[i].getDescription ();
-if (descr == null) {
-continue;
-}var pos = 0;
-var added = false;
-var reps = 0;
-while ((repeat || pos == 0) && pattern.searchFrom (descr, pos)) {
-pos = pattern.matchedTo ();
-for (var cols = 0; cols < pattern.numSubs (); cols++) {
-var sstring = pattern.stringMatchedI (cols + 1);
-var score = NaN;
-try {
-score = new Double (sstring).doubleValue ();
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-continue;
-} else {
-throw e;
-}
-}
-var an = new jalview.datamodel.AlignmentAnnotation (ScoreNames[cols] + ((reps > 0) ? "_" + reps : ""), ScoreDescriptions[cols], null);
-an.setScore (score);
-System.out.println (seqs[i].getName () + " score: '" + ScoreNames[cols] + "' = " + score);
-an.setSequenceRef (seqs[i]);
-seqs[i].addAlignmentAnnotation (an);
-this.al.addAnnotation (an);
-added = true;
-}
-reps++;
-}
-if (added) {
-count++;
-}}
-return count;
-}, "~A,~A,~A,~S,~B");
-});
+Clazz.declarePackage ("jalview.analysis");\r
+Clazz.load (null, "jalview.analysis.ParseProperties", ["jalview.datamodel.AlignmentAnnotation", "jalview.jsdev.RegExp", "java.lang.Double"], function () {\r
+c$ = Clazz.decorateAsClass (function () {\r
+this.al = null;\r
+Clazz.instantialize (this, arguments);\r
+}, jalview.analysis, "ParseProperties");\r
+Clazz.makeConstructor (c$, \r
+function (al) {\r
+this.al = al;\r
+}, "jalview.datamodel.AlignmentI");\r
+Clazz.defineMethod (c$, "getScoresFromDescription", \r
+function (ScoreName, ScoreDescriptions, regex, repeat) {\r
+return this.getScoresFromDescription ( Clazz.newArray (-1, [ScoreName]), Clazz.newArray (-1, [ScoreDescriptions]), regex, repeat);\r
+}, "~S,~S,~S,~B");\r
+Clazz.defineMethod (c$, "getScoresFromDescription", \r
+function (ScoreNames, ScoreDescriptions, regex, repeat) {\r
+return this.getScoresFromDescription (this.al.getSequencesArray (), ScoreNames, ScoreDescriptions, regex, repeat);\r
+}, "~A,~A,~S,~B");\r
+Clazz.defineMethod (c$, "getScoresFromDescription", \r
+function (seqs, ScoreNames, ScoreDescriptions, regex, repeat) {\r
+var count = 0;\r
+var pattern = jalview.jsdev.RegExp.newRegex ([regex]);\r
+if (pattern.numSubs () > ScoreNames.length) {\r
+var onamelen = ScoreNames.length;\r
+var tnames = new Array (pattern.numSubs () + 1);\r
+System.arraycopy (ScoreNames, 0, tnames, 0, ScoreNames.length);\r
+var base = tnames[ScoreNames.length - 1];\r
+ScoreNames = tnames;\r
+var descrbase = ScoreDescriptions[onamelen - 1];\r
+if (descrbase == null) {\r
+descrbase = "Score parsed from (" + regex + ")";\r
+}tnames = new Array (pattern.numSubs () + 1);\r
+System.arraycopy (ScoreDescriptions, 0, tnames, 0, ScoreDescriptions.length);\r
+ScoreDescriptions = tnames;\r
+for (var i = onamelen; i < ScoreNames.length; i++) {\r
+ScoreNames[i] = base + "_" + i;\r
+ScoreDescriptions[i] = descrbase + " (column " + i + ")";\r
+}\r
+}for (var i = 0; i < seqs.length; i++) {\r
+var descr = seqs[i].getDescription ();\r
+if (descr == null) {\r
+continue;\r
+}var pos = 0;\r
+var added = false;\r
+var reps = 0;\r
+while ((repeat || pos == 0) && pattern.searchFrom (descr, pos)) {\r
+pos = pattern.matchedTo ();\r
+for (var cols = 0; cols < pattern.numSubs (); cols++) {\r
+var sstring = pattern.stringMatchedI (cols + 1);\r
+var score = NaN;\r
+try {\r
+score = new Double (sstring).doubleValue ();\r
+} catch (e) {\r
+if (Clazz.exceptionOf (e, Exception)) {\r
+continue;\r
+} else {\r
+throw e;\r
+}\r
+}\r
+var an = new jalview.datamodel.AlignmentAnnotation (ScoreNames[cols] + ((reps > 0) ? "_" + reps : ""), ScoreDescriptions[cols], null);\r
+an.setScore (score);\r
+System.out.println (seqs[i].getName () + " score: '" + ScoreNames[cols] + "' = " + score);\r
+an.setSequenceRef (seqs[i]);\r
+seqs[i].addAlignmentAnnotation (an);\r
+this.al.addAnnotation (an);\r
+added = true;\r
+}\r
+reps++;\r
+}\r
+if (added) {\r
+count++;\r
+}}\r
+return count;\r
+}, "~A,~A,~A,~S,~B");\r
+});\r
git://source.jalview.org / jalviewjs.git / blobdiff