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