X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fschemes%2FScoreMatrix.js;h=401ab4190133a6c5efddf0a6ba4a0e4324b17110;hp=a12c842e7f6644e7ad242f4216c0ddb9441d41ae;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/schemes/ScoreMatrix.js b/bin/jalview/schemes/ScoreMatrix.js
index a12c842..401ab41 100644
--- a/bin/jalview/schemes/ScoreMatrix.js
+++ b/bin/jalview/schemes/ScoreMatrix.js
@@ -1,86 +1,86 @@
-Clazz.declarePackage ("jalview.schemes");
-Clazz.load (["jalview.analysis.scoremodels.PairwiseSeqScoreModel", "jalview.api.analysis.ScoreModelI"], "jalview.schemes.ScoreMatrix", ["jalview.schemes.ResidueProperties", "java.lang.StringBuffer"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.name = null;
-this.matrix = null;
-this.type = 0;
-Clazz.instantialize (this, arguments);
-}, jalview.schemes, "ScoreMatrix", jalview.analysis.scoremodels.PairwiseSeqScoreModel, jalview.api.analysis.ScoreModelI);
-Clazz.overrideMethod (c$, "getName", 
-function () {
-return this.name;
-});
-Clazz.makeConstructor (c$, 
-function (name, matrix, type) {
-Clazz.superConstructor (this, jalview.schemes.ScoreMatrix, []);
-this.matrix = matrix;
-this.type = type;
-this.name = name;
-}, "~S,~A,~N");
-Clazz.overrideMethod (c$, "isDNA", 
-function () {
-return this.type == 1;
-});
-Clazz.overrideMethod (c$, "isProtein", 
-function () {
-return this.type == 0;
-});
-Clazz.overrideMethod (c$, "getMatrix", 
-function () {
-return this.matrix;
-});
-Clazz.defineMethod (c$, "getPairwiseScore", 
-function (A1, A2) {
-return this.getPairwiseScore (A1.charAt (0), A2.charAt (0));
-}, "~S,~S");
-Clazz.defineMethod (c$, "getPairwiseScore", 
-function (c, d) {
-var pog = 0;
-try {
-var a = (this.type == 0) ? jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)] : jalview.schemes.ResidueProperties.nucleotideIndex[c.charCodeAt (0)];
-var b = (this.type == 0) ? jalview.schemes.ResidueProperties.aaIndex[d.charCodeAt (0)] : jalview.schemes.ResidueProperties.nucleotideIndex[d.charCodeAt (0)];
-pog = this.matrix[a][b];
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-} else {
-throw e;
-}
-}
-return pog;
-}, "~S,~S");
-Clazz.overrideMethod (c$, "toString", 
-function () {
-return this.outputMatrix (false);
-});
-Clazz.defineMethod (c$, "outputMatrix", 
-function (html) {
-var sb =  new StringBuffer ();
-var symbols = (this.type == 0) ? jalview.schemes.ResidueProperties.aaIndex : jalview.schemes.ResidueProperties.nucleotideIndex;
-var symMax = (this.type == 0) ? 23 : 10;
-var header = true;
-if (html) {
-sb.append ("<table border=\"1\">");
-}for (var sym = 'A'; sym <= 'Z'; sym = String.fromCharCode (sym.charCodeAt (0) + 1)) {
-if (symbols[sym.charCodeAt (0)] >= 0 && symbols[sym.charCodeAt (0)] < symMax) {
-if (header) {
-sb.append (html ? "<tr><td></td>" : "");
-for (var sym2 = 'A'; sym2 <= 'Z'; sym2 = String.fromCharCode (sym2.charCodeAt (0) + 1)) {
-if (symbols[sym2.charCodeAt (0)] >= 0 && symbols[sym2.charCodeAt (0)] < symMax) {
-sb.append ((html ? "<td>&nbsp;" : "\t") + sym2 + (html ? "&nbsp;</td>" : ""));
-}}
-header = false;
-sb.append (html ? "</tr>\n" : "\n");
-}if (html) {
-sb.append ("<tr>");
-}sb.append ((html ? "<td>" : "") + sym + (html ? "</td>" : ""));
-for (var sym2 = 'A'; sym2 <= 'Z'; sym2 = String.fromCharCode (sym2.charCodeAt (0) + 1)) {
-if (symbols[sym2.charCodeAt (0)] >= 0 && symbols[sym2.charCodeAt (0)] < symMax) {
-sb.append ((html ? "<td>" : "\t") + this.matrix[symbols[sym.charCodeAt (0)]][symbols[sym2.charCodeAt (0)]] + (html ? "</td>" : ""));
-}}
-sb.append (html ? "</tr>\n" : "\n");
-}}
-if (html) {
-sb.append ("</table>");
-}return sb.toString ();
-}, "~B");
-});
+Clazz.declarePackage ("jalview.schemes");
+Clazz.load (["jalview.analysis.scoremodels.PairwiseSeqScoreModel", "jalview.api.analysis.ScoreModelI"], "jalview.schemes.ScoreMatrix", ["jalview.schemes.ResidueProperties", "java.lang.StringBuffer"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.name = null;
+this.matrix = null;
+this.type = 0;
+Clazz.instantialize (this, arguments);
+}, jalview.schemes, "ScoreMatrix", jalview.analysis.scoremodels.PairwiseSeqScoreModel, jalview.api.analysis.ScoreModelI);
+Clazz.overrideMethod (c$, "getName", 
+function () {
+return this.name;
+});
+Clazz.makeConstructor (c$, 
+function (name, matrix, type) {
+Clazz.superConstructor (this, jalview.schemes.ScoreMatrix, []);
+this.matrix = matrix;
+this.type = type;
+this.name = name;
+}, "~S,~A,~N");
+Clazz.overrideMethod (c$, "isDNA", 
+function () {
+return this.type == 1;
+});
+Clazz.overrideMethod (c$, "isProtein", 
+function () {
+return this.type == 0;
+});
+Clazz.overrideMethod (c$, "getMatrix", 
+function () {
+return this.matrix;
+});
+Clazz.defineMethod (c$, "getPairwiseScore", 
+function (A1, A2) {
+return this.getPairwiseScore (A1.charAt (0), A2.charAt (0));
+}, "~S,~S");
+Clazz.defineMethod (c$, "getPairwiseScore", 
+function (c, d) {
+var pog = 0;
+try {
+var a = (this.type == 0) ? jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)] : jalview.schemes.ResidueProperties.nucleotideIndex[c.charCodeAt (0)];
+var b = (this.type == 0) ? jalview.schemes.ResidueProperties.aaIndex[d.charCodeAt (0)] : jalview.schemes.ResidueProperties.nucleotideIndex[d.charCodeAt (0)];
+pog = this.matrix[a][b];
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+} else {
+throw e;
+}
+}
+return pog;
+}, "~S,~S");
+Clazz.overrideMethod (c$, "toString", 
+function () {
+return this.outputMatrix (false);
+});
+Clazz.defineMethod (c$, "outputMatrix", 
+function (html) {
+var sb =  new StringBuffer ();
+var symbols = (this.type == 0) ? jalview.schemes.ResidueProperties.aaIndex : jalview.schemes.ResidueProperties.nucleotideIndex;
+var symMax = (this.type == 0) ? 23 : 10;
+var header = true;
+if (html) {
+sb.append ("<table border=\"1\">");
+}for (var sym = 'A'; sym <= 'Z'; sym = String.fromCharCode (sym.charCodeAt (0) + 1)) {
+if (symbols[sym.charCodeAt (0)] >= 0 && symbols[sym.charCodeAt (0)] < symMax) {
+if (header) {
+sb.append (html ? "<tr><td></td>" : "");
+for (var sym2 = 'A'; sym2 <= 'Z'; sym2 = String.fromCharCode (sym2.charCodeAt (0) + 1)) {
+if (symbols[sym2.charCodeAt (0)] >= 0 && symbols[sym2.charCodeAt (0)] < symMax) {
+sb.append ((html ? "<td>&nbsp;" : "\t") + sym2 + (html ? "&nbsp;</td>" : ""));
+}}
+header = false;
+sb.append (html ? "</tr>\n" : "\n");
+}if (html) {
+sb.append ("<tr>");
+}sb.append ((html ? "<td>" : "") + sym + (html ? "</td>" : ""));
+for (var sym2 = 'A'; sym2 <= 'Z'; sym2 = String.fromCharCode (sym2.charCodeAt (0) + 1)) {
+if (symbols[sym2.charCodeAt (0)] >= 0 && symbols[sym2.charCodeAt (0)] < symMax) {
+sb.append ((html ? "<td>" : "\t") + this.matrix[symbols[sym.charCodeAt (0)]][symbols[sym2.charCodeAt (0)]] + (html ? "</td>" : ""));
+}}
+sb.append (html ? "</tr>\n" : "\n");
+}}
+if (html) {
+sb.append ("</table>");
+}return sb.toString ();
+}, "~B");
+});