JAL-1807 test

[jalviewjs.git] / bin / jalview / analysis / ParseProperties.js

diff --git a/bin/jalview/analysis/ParseProperties.js b/bin/jalview/analysis/ParseProperties.js
index d18979d..c117d07 100644 (file)
--- a/bin/jalview/analysis/ParseProperties.js
+++ b/bin/jalview/analysis/ParseProperties.js
@@ -1,75 +1,75 @@
-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
+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");
+});