X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fschemes%2FResidueColourScheme.js;h=9b2382f1daa860a662e72b29aee8851b8b226fde;hp=aaf6ef5d24700214a85b3c40c50c77f6ffb2b8b1;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6

diff --git a/site/j2s/jalview/schemes/ResidueColourScheme.js b/site/j2s/jalview/schemes/ResidueColourScheme.js
index aaf6ef5..9b2382f 100644
--- a/site/j2s/jalview/schemes/ResidueColourScheme.js
+++ b/site/j2s/jalview/schemes/ResidueColourScheme.js
@@ -1,146 +1,146 @@
-Clazz.declarePackage ("jalview.schemes");
-Clazz.load (["jalview.schemes.ColourSchemeI"], "jalview.schemes.ResidueColourScheme", ["jalview.util.Comparison", "$.MessageManager", "java.awt.Color", "java.lang.Error"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.symbolIndex = null;
-this.conservationColouring = false;
-this.colors = null;
-this.threshold = 0;
-this.ignoreGaps = "G";
-this.consensus = null;
-this.conservation = null;
-this.conservationLength = 0;
-this.inc = 30;
-Clazz.instantialize (this, arguments);
-}, jalview.schemes, "ResidueColourScheme", null, jalview.schemes.ColourSchemeI);
-Clazz.makeConstructor (c$, 
-function (aaOrnaIndex, colours, threshold) {
-this.symbolIndex = aaOrnaIndex;
-this.colors = colours;
-this.threshold = threshold;
-}, "~A,~A,~N");
-Clazz.makeConstructor (c$, 
-function (aaOrNaIndex) {
-this.symbolIndex = aaOrNaIndex;
-}, "~A");
-Clazz.makeConstructor (c$, 
-function () {
-this.symbolIndex = null;
-});
-Clazz.defineMethod (c$, "findColour", 
-function (c) {
-return this.colors == null ? java.awt.Color.white : this.colors[this.symbolIndex[c.charCodeAt (0)]];
-}, "~S");
-Clazz.defineMethod (c$, "findColour", 
-function (c, j, seq) {
-var currentColour;
-if (this.colors != null && this.symbolIndex != null && (this.threshold == 0) || this.aboveThreshold (c, j)) {
-currentColour = this.colors[this.symbolIndex[c.charCodeAt (0)]];
-} else {
-currentColour = java.awt.Color.white;
-}if (this.conservationColouring) {
-currentColour = this.applyConservation (currentColour, j);
-}return currentColour;
-}, "~S,~N,jalview.datamodel.SequenceI");
-Clazz.overrideMethod (c$, "getThreshold", 
-function () {
-return this.threshold;
-});
-Clazz.overrideMethod (c$, "setThreshold", 
-function (ct, ignoreGaps) {
-this.threshold = ct;
-if (ignoreGaps) {
-this.ignoreGaps = "N";
-} else {
-this.ignoreGaps = "G";
-}}, "~N,~B");
-Clazz.defineMethod (c$, "aboveThreshold", 
-function (c, j) {
-if ('a' <= c && c <= 'z') {
-c = String.fromCharCode (c.charCodeAt (0) - (32));
-}if (this.consensus == null || this.consensus.length < j || this.consensus[j] == null) {
-return false;
-}if (((this.consensus[j].get ("C")).intValue () != -1) && this.consensus[j].contains (String.valueOf (c))) {
-if ((this.consensus[j].get (this.ignoreGaps)).floatValue () >= this.threshold) {
-return true;
-}}return false;
-}, "~S,~N");
-Clazz.overrideMethod (c$, "conservationApplied", 
-function () {
-return this.conservationColouring;
-});
-Clazz.overrideMethod (c$, "setConservationApplied", 
-function (conservationApplied) {
-this.conservationColouring = conservationApplied;
-}, "~B");
-Clazz.overrideMethod (c$, "setConservationInc", 
-function (i) {
-this.inc = i;
-}, "~N");
-Clazz.overrideMethod (c$, "getConservationInc", 
-function () {
-return this.inc;
-});
-Clazz.overrideMethod (c$, "setConsensus", 
-function (consensus) {
-if (consensus == null) {
-return;
-}this.consensus = consensus;
-}, "~A");
-Clazz.overrideMethod (c$, "setConservation", 
-function (cons) {
-if (cons == null) {
-this.conservationColouring = false;
-this.conservation = null;
-} else {
-this.conservationColouring = true;
-var i;
-var iSize = cons.getConsSequence ().getLength ();
-this.conservation =  Clazz.newCharArray (iSize, '\0');
-for (i = 0; i < iSize; i++) {
-this.conservation[i] = cons.getConsSequence ().getCharAt (i);
-}
-this.conservationLength = this.conservation.length;
-}}, "jalview.analysis.Conservation");
-Clazz.defineMethod (c$, "applyConservation", 
-function (currentColour, i) {
-if ((this.conservationLength > i) && (this.conservation[i] != '*') && (this.conservation[i] != '+')) {
-if (jalview.util.Comparison.isGap (this.conservation[i])) {
-currentColour = java.awt.Color.white;
-} else {
-var t = 11 - ((this.conservation[i]).charCodeAt (0) - 48);
-if (t == 0) {
-return java.awt.Color.white;
-}var red = currentColour.getRed ();
-var green = currentColour.getGreen ();
-var blue = currentColour.getBlue ();
-var dr = 255 - red;
-var dg = 255 - green;
-var db = 255 - blue;
-dr *= t / 10;
-dg *= t / 10;
-db *= t / 10;
-red += (this.inc / 20) * dr;
-green += (this.inc / 20) * dg;
-blue += (this.inc / 20) * db;
-if (red > 255 || green > 255 || blue > 255) {
-currentColour = java.awt.Color.white;
-} else {
-currentColour =  new java.awt.Color (red, green, blue);
-}}}return currentColour;
-}, "java.awt.Color,~N");
-Clazz.overrideMethod (c$, "alignmentChanged", 
-function (alignment, hiddenReps) {
-}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
-Clazz.overrideMethod (c$, "applyTo", 
-function (sg, hiddenRepSequences) {
-try {
-return this.getClass ().newInstance ();
-} catch (q) {
-if (Clazz.exceptionOf (q, Exception)) {
-throw  new Error (jalview.util.MessageManager.formatMessage ("error.implementation_error_cannot_duplicate_colour_scheme",  Clazz.newArray (-1, [this.getClass ().getName ()])), q);
-} else {
-throw q;
-}
-}
-}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
-});
+Clazz.declarePackage ("jalview.schemes");
+Clazz.load (["jalview.schemes.ColourSchemeI"], "jalview.schemes.ResidueColourScheme", ["jalview.util.Comparison", "$.MessageManager", "java.awt.Color", "java.lang.Error"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.symbolIndex = null;
+this.conservationColouring = false;
+this.colors = null;
+this.threshold = 0;
+this.ignoreGaps = "G";
+this.consensus = null;
+this.conservation = null;
+this.conservationLength = 0;
+this.inc = 30;
+Clazz.instantialize (this, arguments);
+}, jalview.schemes, "ResidueColourScheme", null, jalview.schemes.ColourSchemeI);
+Clazz.makeConstructor (c$, 
+function (aaOrnaIndex, colours, threshold) {
+this.symbolIndex = aaOrnaIndex;
+this.colors = colours;
+this.threshold = threshold;
+}, "~A,~A,~N");
+Clazz.makeConstructor (c$, 
+function (aaOrNaIndex) {
+this.symbolIndex = aaOrNaIndex;
+}, "~A");
+Clazz.makeConstructor (c$, 
+function () {
+this.symbolIndex = null;
+});
+Clazz.defineMethod (c$, "findColour", 
+function (c) {
+return this.colors == null ? java.awt.Color.white : this.colors[this.symbolIndex[c.charCodeAt (0)]];
+}, "~S");
+Clazz.defineMethod (c$, "findColour", 
+function (c, j, seq) {
+var currentColour;
+if (this.colors != null && this.symbolIndex != null && (this.threshold == 0) || this.aboveThreshold (c, j)) {
+currentColour = this.colors[this.symbolIndex[c.charCodeAt (0)]];
+} else {
+currentColour = java.awt.Color.white;
+}if (this.conservationColouring) {
+currentColour = this.applyConservation (currentColour, j);
+}return currentColour;
+}, "~S,~N,jalview.datamodel.SequenceI");
+Clazz.overrideMethod (c$, "getThreshold", 
+function () {
+return this.threshold;
+});
+Clazz.overrideMethod (c$, "setThreshold", 
+function (ct, ignoreGaps) {
+this.threshold = ct;
+if (ignoreGaps) {
+this.ignoreGaps = "N";
+} else {
+this.ignoreGaps = "G";
+}}, "~N,~B");
+Clazz.defineMethod (c$, "aboveThreshold", 
+function (c, j) {
+if ('a' <= c && c <= 'z') {
+c = String.fromCharCode (c.charCodeAt (0) - (32));
+}if (this.consensus == null || this.consensus.length < j || this.consensus[j] == null) {
+return false;
+}if (((this.consensus[j].get ("C")).intValue () != -1) && this.consensus[j].contains (String.valueOf (c))) {
+if ((this.consensus[j].get (this.ignoreGaps)).floatValue () >= this.threshold) {
+return true;
+}}return false;
+}, "~S,~N");
+Clazz.overrideMethod (c$, "conservationApplied", 
+function () {
+return this.conservationColouring;
+});
+Clazz.overrideMethod (c$, "setConservationApplied", 
+function (conservationApplied) {
+this.conservationColouring = conservationApplied;
+}, "~B");
+Clazz.overrideMethod (c$, "setConservationInc", 
+function (i) {
+this.inc = i;
+}, "~N");
+Clazz.overrideMethod (c$, "getConservationInc", 
+function () {
+return this.inc;
+});
+Clazz.overrideMethod (c$, "setConsensus", 
+function (consensus) {
+if (consensus == null) {
+return;
+}this.consensus = consensus;
+}, "~A");
+Clazz.overrideMethod (c$, "setConservation", 
+function (cons) {
+if (cons == null) {
+this.conservationColouring = false;
+this.conservation = null;
+} else {
+this.conservationColouring = true;
+var i;
+var iSize = cons.getConsSequence ().getLength ();
+this.conservation =  Clazz.newCharArray (iSize, '\0');
+for (i = 0; i < iSize; i++) {
+this.conservation[i] = cons.getConsSequence ().getCharAt (i);
+}
+this.conservationLength = this.conservation.length;
+}}, "jalview.analysis.Conservation");
+Clazz.defineMethod (c$, "applyConservation", 
+function (currentColour, i) {
+if ((this.conservationLength > i) && (this.conservation[i] != '*') && (this.conservation[i] != '+')) {
+if (jalview.util.Comparison.isGap (this.conservation[i])) {
+currentColour = java.awt.Color.white;
+} else {
+var t = 11 - ((this.conservation[i]).charCodeAt (0) - 48);
+if (t == 0) {
+return java.awt.Color.white;
+}var red = currentColour.getRed ();
+var green = currentColour.getGreen ();
+var blue = currentColour.getBlue ();
+var dr = 255 - red;
+var dg = 255 - green;
+var db = 255 - blue;
+dr *= t / 10;
+dg *= t / 10;
+db *= t / 10;
+red += (this.inc / 20) * dr;
+green += (this.inc / 20) * dg;
+blue += (this.inc / 20) * db;
+if (red > 255 || green > 255 || blue > 255) {
+currentColour = java.awt.Color.white;
+} else {
+currentColour =  new java.awt.Color (red, green, blue);
+}}}return currentColour;
+}, "java.awt.Color,~N");
+Clazz.overrideMethod (c$, "alignmentChanged", 
+function (alignment, hiddenReps) {
+}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
+Clazz.overrideMethod (c$, "applyTo", 
+function (sg, hiddenRepSequences) {
+try {
+return this.getClass ().newInstance ();
+} catch (q) {
+if (Clazz.exceptionOf (q, Exception)) {
+throw  new Error (jalview.util.MessageManager.formatMessage ("error.implementation_error_cannot_duplicate_colour_scheme",  Clazz.newArray (-1, [this.getClass ().getName ()])), q);
+} else {
+throw q;
+}
+}
+}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
+});