X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fanalysis%2Fscoremodels%2FFeatureScoreModel.js;h=7e483bdf011f5cb297aa8c736d905e68ece02949;hp=3e8e57d4fd4bfaeb065856004aff8366cb712a0a;hb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/analysis/scoremodels/FeatureScoreModel.js b/bin/jalview/analysis/scoremodels/FeatureScoreModel.js
index 3e8e57d..7e483bd 100644
--- a/bin/jalview/analysis/scoremodels/FeatureScoreModel.js
+++ b/bin/jalview/analysis/scoremodels/FeatureScoreModel.js
@@ -1,86 +1,86 @@
-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");
+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";
+});
+});