X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fschemes%2FUserColourScheme.js;fp=site%2Fj2s%2Fjalview%2Fschemes%2FUserColourScheme.js;h=ee8398745fd5a88472e6340f13bea2a44ae2d476;hp=dcf5f866b05f329f72f591786be5a000f8e475c2;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/schemes/UserColourScheme.js b/site/j2s/jalview/schemes/UserColourScheme.js
index dcf5f86..ee83987 100644
--- a/site/j2s/jalview/schemes/UserColourScheme.js
+++ b/site/j2s/jalview/schemes/UserColourScheme.js
@@ -1,165 +1,165 @@
-Clazz.declarePackage ("jalview.schemes");
-Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.UserColourScheme", ["jalview.schemes.ColourSchemeProperty", "$.ResidueProperties", "java.awt.Color", "java.util.StringTokenizer"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.lowerCaseColours = null;
-this.schemeName = null;
-Clazz.instantialize (this, arguments);
-}, jalview.schemes, "UserColourScheme", jalview.schemes.ResidueColourScheme);
-Clazz.makeConstructor (c$, 
-function () {
-Clazz.superConstructor (this, jalview.schemes.UserColourScheme, [jalview.schemes.ResidueProperties.aaIndex]);
-});
-Clazz.makeConstructor (c$, 
-function (newColors) {
-Clazz.superConstructor (this, jalview.schemes.UserColourScheme, [jalview.schemes.ResidueProperties.aaIndex]);
-this.colors = newColors;
-}, "~A");
-Clazz.overrideMethod (c$, "applyTo", 
-function (sg, hiddenRepSequences) {
-var usc =  new jalview.schemes.UserColourScheme (this.colors);
-if (this.lowerCaseColours != null) {
-usc.schemeName =  String.instantialize (this.schemeName);
-usc.lowerCaseColours =  new Array (this.lowerCaseColours.length);
-System.arraycopy (this.lowerCaseColours, 0, usc.lowerCaseColours, 0, this.lowerCaseColours.length);
-}return usc;
-}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
-Clazz.makeConstructor (c$, 
-function (colour) {
-Clazz.superConstructor (this, jalview.schemes.UserColourScheme, [jalview.schemes.ResidueProperties.aaIndex]);
-var col = this.getColourFromString (colour);
-if (col == null) {
-System.out.println ("Unknown colour!! " + colour);
-col = this.createColourFromName (colour);
-}this.colors =  new Array (24);
-for (var i = 0; i < 24; i++) {
-this.colors[i] = col;
-}
-this.schemeName = colour;
-}, "~S");
-Clazz.defineMethod (c$, "getColours", 
-function () {
-return this.colors;
-});
-Clazz.defineMethod (c$, "getLowerCaseColours", 
-function () {
-return this.lowerCaseColours;
-});
-Clazz.defineMethod (c$, "setName", 
-function (name) {
-this.schemeName = name;
-}, "~S");
-Clazz.defineMethod (c$, "getName", 
-function () {
-return this.schemeName;
-});
-Clazz.defineMethod (c$, "getColourFromString", 
-function (colour) {
-colour = colour.trim ();
-var col = null;
-try {
-var value = Integer.parseInt (colour, 16);
-col =  new java.awt.Color (value);
-} catch (ex) {
-if (Clazz.exceptionOf (ex, NumberFormatException)) {
-} else {
-throw ex;
-}
-}
-if (col == null) {
-col = jalview.schemes.ColourSchemeProperty.getAWTColorFromName (colour);
-}if (col == null) {
-try {
-var st =  new java.util.StringTokenizer (colour, ",");
-var r = Integer.parseInt (st.nextToken ());
-var g = Integer.parseInt (st.nextToken ());
-var b = Integer.parseInt (st.nextToken ());
-col =  new java.awt.Color (r, g, b);
-} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-} else {
-throw ex;
-}
-}
-}return col;
-}, "~S");
-Clazz.defineMethod (c$, "createColourFromName", 
-function (name) {
-var r;
-var g;
-var b;
-var lsize = name.length;
-var start = 0;
-var end = Clazz.doubleToInt (lsize / 3);
-var rgbOffset = Math.abs (name.hashCode () % 10) * 15;
-r = Math.abs (name.substring (start, end).hashCode () + rgbOffset) % 210 + 20;
-start = end;
-end += Clazz.doubleToInt (lsize / 3);
-if (end > lsize) {
-end = lsize;
-}g = Math.abs (name.substring (start, end).hashCode () + rgbOffset) % 210 + 20;
-b = Math.abs (name.substring (end).hashCode () + rgbOffset) % 210 + 20;
-var color =  new java.awt.Color (r, g, b);
-return color;
-}, "~S");
-Clazz.defineMethod (c$, "parseAppletParameter", 
-function (paramValue) {
-var st =  new java.util.StringTokenizer (paramValue, ";");
-var st2;
-var token = null;
-var colour;
-var residues;
-try {
-while (st.hasMoreElements ()) {
-token = st.nextToken ().trim ();
-residues = token.substring (0, token.indexOf ("="));
-colour = token.substring (token.indexOf ("=") + 1);
-st2 =  new java.util.StringTokenizer (residues, " ,");
-while (st2.hasMoreTokens ()) {
-token = st2.nextToken ();
-if (jalview.schemes.ResidueProperties.aaIndex[token.charCodeAt (0)] == -1) {
-continue;
-}var colIndex = jalview.schemes.ResidueProperties.aaIndex[token.charCodeAt (0)];
-if (token.equalsIgnoreCase ("lowerCase")) {
-if (this.lowerCaseColours == null) {
-this.lowerCaseColours =  new Array (23);
-}for (var i = 0; i < 23; i++) {
-if (this.lowerCaseColours[i] == null) {
-this.lowerCaseColours[i] = this.getColourFromString (colour);
-}}
-continue;
-}if (token.equals (token.toLowerCase ())) {
-if (this.lowerCaseColours == null) {
-this.lowerCaseColours =  new Array (23);
-}this.lowerCaseColours[colIndex] = this.getColourFromString (colour);
-} else {
-this.colors[colIndex] = this.getColourFromString (colour);
-}}
-}
-} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-System.out.println ("Error parsing userDefinedColours:\n" + token + "\n" + ex);
-} else {
-throw ex;
-}
-}
-}, "~S");
-Clazz.defineMethod (c$, "findColour", 
-function (c, j, seq) {
-var currentColour;
-var index = jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)];
-if ((this.threshold == 0) || this.aboveThreshold (c, j)) {
-if (this.lowerCaseColours != null && 'a' <= c && c <= 'z') {
-currentColour = this.lowerCaseColours[index];
-} else {
-currentColour = this.colors[index];
-}} else {
-currentColour = java.awt.Color.white;
-}if (this.conservationColouring) {
-currentColour = this.applyConservation (currentColour, j);
-}return currentColour;
-}, "~S,~N,jalview.datamodel.SequenceI");
-Clazz.defineMethod (c$, "setLowerCaseColours", 
-function (lcolours) {
-this.lowerCaseColours = lcolours;
-}, "~A");
-});
+Clazz.declarePackage ("jalview.schemes");
+Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.UserColourScheme", ["jalview.schemes.ColourSchemeProperty", "$.ResidueProperties", "java.awt.Color", "java.util.StringTokenizer"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.lowerCaseColours = null;
+this.schemeName = null;
+Clazz.instantialize (this, arguments);
+}, jalview.schemes, "UserColourScheme", jalview.schemes.ResidueColourScheme);
+Clazz.makeConstructor (c$, 
+function () {
+Clazz.superConstructor (this, jalview.schemes.UserColourScheme, [jalview.schemes.ResidueProperties.aaIndex]);
+});
+Clazz.makeConstructor (c$, 
+function (newColors) {
+Clazz.superConstructor (this, jalview.schemes.UserColourScheme, [jalview.schemes.ResidueProperties.aaIndex]);
+this.colors = newColors;
+}, "~A");
+Clazz.overrideMethod (c$, "applyTo", 
+function (sg, hiddenRepSequences) {
+var usc =  new jalview.schemes.UserColourScheme (this.colors);
+if (this.lowerCaseColours != null) {
+usc.schemeName =  String.instantialize (this.schemeName);
+usc.lowerCaseColours =  new Array (this.lowerCaseColours.length);
+System.arraycopy (this.lowerCaseColours, 0, usc.lowerCaseColours, 0, this.lowerCaseColours.length);
+}return usc;
+}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
+Clazz.makeConstructor (c$, 
+function (colour) {
+Clazz.superConstructor (this, jalview.schemes.UserColourScheme, [jalview.schemes.ResidueProperties.aaIndex]);
+var col = this.getColourFromString (colour);
+if (col == null) {
+System.out.println ("Unknown colour!! " + colour);
+col = this.createColourFromName (colour);
+}this.colors =  new Array (24);
+for (var i = 0; i < 24; i++) {
+this.colors[i] = col;
+}
+this.schemeName = colour;
+}, "~S");
+Clazz.defineMethod (c$, "getColours", 
+function () {
+return this.colors;
+});
+Clazz.defineMethod (c$, "getLowerCaseColours", 
+function () {
+return this.lowerCaseColours;
+});
+Clazz.defineMethod (c$, "setName", 
+function (name) {
+this.schemeName = name;
+}, "~S");
+Clazz.defineMethod (c$, "getName", 
+function () {
+return this.schemeName;
+});
+Clazz.defineMethod (c$, "getColourFromString", 
+function (colour) {
+colour = colour.trim ();
+var col = null;
+try {
+var value = Integer.parseInt (colour, 16);
+col =  new java.awt.Color (value);
+} catch (ex) {
+if (Clazz.exceptionOf (ex, NumberFormatException)) {
+} else {
+throw ex;
+}
+}
+if (col == null) {
+col = jalview.schemes.ColourSchemeProperty.getAWTColorFromName (colour);
+}if (col == null) {
+try {
+var st =  new java.util.StringTokenizer (colour, ",");
+var r = Integer.parseInt (st.nextToken ());
+var g = Integer.parseInt (st.nextToken ());
+var b = Integer.parseInt (st.nextToken ());
+col =  new java.awt.Color (r, g, b);
+} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+} else {
+throw ex;
+}
+}
+}return col;
+}, "~S");
+Clazz.defineMethod (c$, "createColourFromName", 
+function (name) {
+var r;
+var g;
+var b;
+var lsize = name.length;
+var start = 0;
+var end = Clazz.doubleToInt (lsize / 3);
+var rgbOffset = Math.abs (name.hashCode () % 10) * 15;
+r = Math.abs (name.substring (start, end).hashCode () + rgbOffset) % 210 + 20;
+start = end;
+end += Clazz.doubleToInt (lsize / 3);
+if (end > lsize) {
+end = lsize;
+}g = Math.abs (name.substring (start, end).hashCode () + rgbOffset) % 210 + 20;
+b = Math.abs (name.substring (end).hashCode () + rgbOffset) % 210 + 20;
+var color =  new java.awt.Color (r, g, b);
+return color;
+}, "~S");
+Clazz.defineMethod (c$, "parseAppletParameter", 
+function (paramValue) {
+var st =  new java.util.StringTokenizer (paramValue, ";");
+var st2;
+var token = null;
+var colour;
+var residues;
+try {
+while (st.hasMoreElements ()) {
+token = st.nextToken ().trim ();
+residues = token.substring (0, token.indexOf ("="));
+colour = token.substring (token.indexOf ("=") + 1);
+st2 =  new java.util.StringTokenizer (residues, " ,");
+while (st2.hasMoreTokens ()) {
+token = st2.nextToken ();
+if (jalview.schemes.ResidueProperties.aaIndex[token.charCodeAt (0)] == -1) {
+continue;
+}var colIndex = jalview.schemes.ResidueProperties.aaIndex[token.charCodeAt (0)];
+if (token.equalsIgnoreCase ("lowerCase")) {
+if (this.lowerCaseColours == null) {
+this.lowerCaseColours =  new Array (23);
+}for (var i = 0; i < 23; i++) {
+if (this.lowerCaseColours[i] == null) {
+this.lowerCaseColours[i] = this.getColourFromString (colour);
+}}
+continue;
+}if (token.equals (token.toLowerCase ())) {
+if (this.lowerCaseColours == null) {
+this.lowerCaseColours =  new Array (23);
+}this.lowerCaseColours[colIndex] = this.getColourFromString (colour);
+} else {
+this.colors[colIndex] = this.getColourFromString (colour);
+}}
+}
+} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+System.out.println ("Error parsing userDefinedColours:\n" + token + "\n" + ex);
+} else {
+throw ex;
+}
+}
+}, "~S");
+Clazz.defineMethod (c$, "findColour", 
+function (c, j, seq) {
+var currentColour;
+var index = jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)];
+if ((this.threshold == 0) || this.aboveThreshold (c, j)) {
+if (this.lowerCaseColours != null && 'a' <= c && c <= 'z') {
+currentColour = this.lowerCaseColours[index];
+} else {
+currentColour = this.colors[index];
+}} else {
+currentColour = java.awt.Color.white;
+}if (this.conservationColouring) {
+currentColour = this.applyConservation (currentColour, j);
+}return currentColour;
+}, "~S,~N,jalview.datamodel.SequenceI");
+Clazz.defineMethod (c$, "setLowerCaseColours", 
+function (lcolours) {
+this.lowerCaseColours = lcolours;
+}, "~A");
+});