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