-Clazz.declarePackage ("jalview.analysis.scoremodels");
-Clazz.load (["jalview.api.analysis.ScoreModelI", "$.ViewBasedAnalysisI"], "jalview.analysis.scoremodels.FeatureScoreModel", ["jalview.util.Comparison", "java.util.ArrayList", "$.Arrays", "$.Hashtable"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.fr = null;
-Clazz.instantialize (this, arguments);
-}, jalview.analysis.scoremodels, "FeatureScoreModel", null, [jalview.api.analysis.ScoreModelI, jalview.api.analysis.ViewBasedAnalysisI]);
-Clazz.overrideMethod (c$, "configureFromAlignmentView",
-function (view) {
-this.fr = view.cloneFeatureRenderer ();
-return true;
-}, "jalview.api.AlignmentViewPanel");
-Clazz.overrideMethod (c$, "findDistances",
-function (seqData) {
-var nofeats = 0;
-var dft = java.util.Arrays.asList (this.fr.getDisplayedFeatureTypes ());
-if (dft != null) {
-nofeats = dft.size ();
-}var sequenceString = seqData.getVisibleAlignment (jalview.util.Comparison.GapChars.charAt (0)).getSequencesArray ();
-var noseqs = sequenceString.length;
-var cpwidth = seqData.getWidth ();
-var distance = Clazz.newFloatArray (noseqs, noseqs, 0);
-if (nofeats == 0) {
-for (var d, $d = 0, $$d = distance; $d < $$d.length && ((d = $$d[$d]) || true); $d++) {
-for (var i = 0; i < d.length; d[i++] = 0) {
-;}
-}
-return distance;
-}var max = 0;
-for (var cpos = 0; cpos < cpwidth; cpos++) {
-var sfap = new java.util.ArrayList ();
-for (var i = 0; i < noseqs; i++) {
-var types = new java.util.Hashtable ();
-var sfs = this.fr.findFeaturesAtRes (sequenceString[i], sequenceString[i].findPosition (cpos));
-for (var sf, $sf = sfs.iterator (); $sf.hasNext () && ((sf = $sf.next ()) || true);) {
-types.put (sf.getType (), sf);
-}
-sfap.add (types);
-}
-for (var i = 0; i < (noseqs - 1); i++) {
-if (cpos == 0) {
-distance[i][i] = 0;
-}for (var j = i + 1; j < noseqs; j++) {
-var sfcommon = 0;
-var fi = sfap.get (i);
-var fk;
-var fj = sfap.get (j);
-if (fi.size () > fj.size ()) {
-fk = fj;
-} else {
-fk = fi;
-fi = fj;
-}for (var k, $k = fi.keySet ().iterator (); $k.hasNext () && ((k = $k.next ()) || true);) {
-var sfj = fk.get (k);
-if (sfj != null) {
-sfcommon++;
-}}
-distance[i][j] += (fi.size () + fk.size () - 2 * sfcommon);
-distance[j][i] += distance[i][j];
-}
-}
-}
-for (var i = 0; i < noseqs; i++) {
-for (var j = i + 1; j < noseqs; j++) {
-distance[i][j] /= cpwidth;
-distance[j][i] = distance[i][j];
-}
-}
-return distance;
-}, "jalview.datamodel.AlignmentView");
-Clazz.overrideMethod (c$, "getName",
-function () {
-return "Sequence Feature Similarity";
-});
-Clazz.overrideMethod (c$, "isDNA",
-function () {
-return true;
-});
-Clazz.overrideMethod (c$, "isProtein",
-function () {
-return true;
-});
-Clazz.overrideMethod (c$, "toString",
-function () {
-return "Score between sequences based on hamming distance between binary vectors marking features displayed at each column";
-});
-});
+Clazz.declarePackage ("jalview.analysis.scoremodels");\r
+Clazz.load (["jalview.api.analysis.ScoreModelI", "$.ViewBasedAnalysisI"], "jalview.analysis.scoremodels.FeatureScoreModel", ["jalview.util.Comparison", "java.util.ArrayList", "$.Arrays", "$.Hashtable"], function () {\r
+c$ = Clazz.decorateAsClass (function () {\r
+this.fr = null;\r
+Clazz.instantialize (this, arguments);\r
+}, jalview.analysis.scoremodels, "FeatureScoreModel", null, [jalview.api.analysis.ScoreModelI, jalview.api.analysis.ViewBasedAnalysisI]);\r
+Clazz.overrideMethod (c$, "configureFromAlignmentView", \r
+function (view) {\r
+this.fr = view.cloneFeatureRenderer ();\r
+return true;\r
+}, "jalview.api.AlignmentViewPanel");\r
+Clazz.overrideMethod (c$, "findDistances", \r
+function (seqData) {\r
+var nofeats = 0;\r
+var dft = java.util.Arrays.asList (this.fr.getDisplayedFeatureTypes ());\r
+if (dft != null) {\r
+nofeats = dft.size ();\r
+}var sequenceString = seqData.getVisibleAlignment (jalview.util.Comparison.GapChars.charAt (0)).getSequencesArray ();\r
+var noseqs = sequenceString.length;\r
+var cpwidth = seqData.getWidth ();\r
+var distance = Clazz.newFloatArray (noseqs, noseqs, 0);\r
+if (nofeats == 0) {\r
+for (var d, $d = 0, $$d = distance; $d < $$d.length && ((d = $$d[$d]) || true); $d++) {\r
+for (var i = 0; i < d.length; d[i++] = 0) {\r
+;}\r
+}\r
+return distance;\r
+}var max = 0;\r
+for (var cpos = 0; cpos < cpwidth; cpos++) {\r
+var sfap = new java.util.ArrayList ();\r
+for (var i = 0; i < noseqs; i++) {\r
+var types = new java.util.Hashtable ();\r
+var sfs = this.fr.findFeaturesAtRes (sequenceString[i], sequenceString[i].findPosition (cpos));\r
+for (var sf, $sf = sfs.iterator (); $sf.hasNext () && ((sf = $sf.next ()) || true);) {\r
+types.put (sf.getType (), sf);\r
+}\r
+sfap.add (types);\r
+}\r
+for (var i = 0; i < (noseqs - 1); i++) {\r
+if (cpos == 0) {\r
+distance[i][i] = 0;\r
+}for (var j = i + 1; j < noseqs; j++) {\r
+var sfcommon = 0;\r
+var fi = sfap.get (i);\r
+var fk;\r
+var fj = sfap.get (j);\r
+if (fi.size () > fj.size ()) {\r
+fk = fj;\r
+} else {\r
+fk = fi;\r
+fi = fj;\r
+}for (var k, $k = fi.keySet ().iterator (); $k.hasNext () && ((k = $k.next ()) || true);) {\r
+var sfj = fk.get (k);\r
+if (sfj != null) {\r
+sfcommon++;\r
+}}\r
+distance[i][j] += (fi.size () + fk.size () - 2 * sfcommon);\r
+distance[j][i] += distance[i][j];\r
+}\r
+}\r
+}\r
+for (var i = 0; i < noseqs; i++) {\r
+for (var j = i + 1; j < noseqs; j++) {\r
+distance[i][j] /= cpwidth;\r
+distance[j][i] = distance[i][j];\r
+}\r
+}\r
+return distance;\r
+}, "jalview.datamodel.AlignmentView");\r
+Clazz.overrideMethod (c$, "getName", \r
+function () {\r
+return "Sequence Feature Similarity";\r
+});\r
+Clazz.overrideMethod (c$, "isDNA", \r
+function () {\r
+return true;\r
+});\r
+Clazz.overrideMethod (c$, "isProtein", \r
+function () {\r
+return true;\r
+});\r
+Clazz.overrideMethod (c$, "toString", \r
+function () {\r
+return "Score between sequences based on hamming distance between binary vectors marking features displayed at each column";\r
+});\r
+});\r
git://source.jalview.org / jalviewjs.git / blobdiff