-Clazz.declarePackage ("jalview.schemes");\r
-Clazz.load (null, "jalview.schemes.ColourSchemeProperty", ["jalview.schemes.Blosum62ColourScheme", "$.BuriedColourScheme", "$.ClustalxColourScheme", "$.HelixColourScheme", "$.HydrophobicColourScheme", "$.NucleotideColourScheme", "$.PIDColourScheme", "$.PurinePyrimidineColourScheme", "$.RNAHelicesColour", "$.StrandColourScheme", "$.TCoffeeColourScheme", "$.TaylorColourScheme", "$.TurnColourScheme", "$.UserColourScheme", "$.ZappoColourScheme", "jalview.util.ColorUtils", "java.awt.Color"], function () {\r
-c$ = Clazz.declareType (jalview.schemes, "ColourSchemeProperty");\r
-c$.getColourIndexFromName = Clazz.defineMethod (c$, "getColourIndexFromName", \r
-function (name) {\r
-var ret = -1;\r
-if (name.equalsIgnoreCase ("Clustal")) {\r
-ret = 2;\r
-} else if (name.equalsIgnoreCase ("Blosum62")) {\r
-ret = 3;\r
-} else if (name.equalsIgnoreCase ("% Identity")) {\r
-ret = 4;\r
-} else if (name.equalsIgnoreCase ("Zappo")) {\r
-ret = 5;\r
-} else if (name.equalsIgnoreCase ("Taylor")) {\r
-ret = 6;\r
-} else if (name.equalsIgnoreCase ("Hydrophobic")) {\r
-ret = 7;\r
-} else if (name.equalsIgnoreCase ("Helix Propensity")) {\r
-ret = 8;\r
-} else if (name.equalsIgnoreCase ("Strand Propensity")) {\r
-ret = 9;\r
-} else if (name.equalsIgnoreCase ("Turn Propensity")) {\r
-ret = 10;\r
-} else if (name.equalsIgnoreCase ("Buried Index")) {\r
-ret = 11;\r
-} else if (name.equalsIgnoreCase ("Nucleotide")) {\r
-ret = 12;\r
-} else if (name.equalsIgnoreCase ("T-Coffee Scores")) {\r
-ret = 15;\r
-} else if (name.equalsIgnoreCase ("User Defined")) {\r
-ret = 0;\r
-} else if (name.equalsIgnoreCase ("None")) {\r
-ret = 1;\r
-} else if (name.equalsIgnoreCase ("Purine/Pyrimidine")) {\r
-ret = 13;\r
-} else if (name.equalsIgnoreCase ("RNA Interaction type")) {\r
-ret = 17;\r
-} else if (name.equalsIgnoreCase ("RNA Helices")) {\r
-ret = 16;\r
-}return ret;\r
-}, "~S");\r
-c$.getColourName = Clazz.defineMethod (c$, "getColourName", \r
-function (cs) {\r
-var index = 1;\r
-if (Clazz.instanceOf (cs, jalview.schemes.ClustalxColourScheme)) {\r
-index = 2;\r
-} else if (Clazz.instanceOf (cs, jalview.schemes.Blosum62ColourScheme)) {\r
-index = 3;\r
-} else if (Clazz.instanceOf (cs, jalview.schemes.PIDColourScheme)) {\r
-index = 4;\r
-} else if (Clazz.instanceOf (cs, jalview.schemes.ZappoColourScheme)) {\r
-index = 5;\r
-} else if (Clazz.instanceOf (cs, jalview.schemes.TaylorColourScheme)) {\r
-index = 6;\r
-} else if (Clazz.instanceOf (cs, jalview.schemes.HydrophobicColourScheme)) {\r
-index = 7;\r
-} else if (Clazz.instanceOf (cs, jalview.schemes.HelixColourScheme)) {\r
-index = 8;\r
-} else if (Clazz.instanceOf (cs, jalview.schemes.StrandColourScheme)) {\r
-index = 9;\r
-} else if (Clazz.instanceOf (cs, jalview.schemes.TurnColourScheme)) {\r
-index = 10;\r
-} else if (Clazz.instanceOf (cs, jalview.schemes.BuriedColourScheme)) {\r
-index = 11;\r
-} else if (Clazz.instanceOf (cs, jalview.schemes.NucleotideColourScheme)) {\r
-index = 12;\r
-} else if (Clazz.instanceOf (cs, jalview.schemes.PurinePyrimidineColourScheme)) {\r
-index = 13;\r
-} else if (Clazz.instanceOf (cs, jalview.schemes.TCoffeeColourScheme)) {\r
-index = 15;\r
-} else if (Clazz.instanceOf (cs, jalview.schemes.RNAHelicesColour)) {\r
-index = 16;\r
-} else if (Clazz.instanceOf (cs, jalview.schemes.UserColourScheme)) {\r
-if (((cs).getName () != null) && ((cs).getName ().length > 0)) {\r
-return (cs).getName ();\r
-}index = 0;\r
-}return jalview.schemes.ColourSchemeProperty.getColourName (index);\r
-}, "jalview.schemes.ColourSchemeI");\r
-c$.getColourName = Clazz.defineMethod (c$, "getColourName", \r
-function (index) {\r
-var ret = null;\r
-switch (index) {\r
-case 2:\r
-ret = "Clustal";\r
-break;\r
-case 3:\r
-ret = "Blosum62";\r
-break;\r
-case 4:\r
-ret = "% Identity";\r
-break;\r
-case 5:\r
-ret = "Zappo";\r
-break;\r
-case 6:\r
-ret = "Taylor";\r
-break;\r
-case 7:\r
-ret = "Hydrophobic";\r
-break;\r
-case 8:\r
-ret = "Helix Propensity";\r
-break;\r
-case 9:\r
-ret = "Strand Propensity";\r
-break;\r
-case 10:\r
-ret = "Turn Propensity";\r
-break;\r
-case 11:\r
-ret = "Buried Index";\r
-break;\r
-case 12:\r
-ret = "Nucleotide";\r
-break;\r
-case 13:\r
-ret = "Purine/Pyrimidine";\r
-break;\r
-case 15:\r
-ret = "T-Coffee Scores";\r
-break;\r
-case 17:\r
-ret = "RNA Interaction type";\r
-break;\r
-case 16:\r
-ret = "RNA Helices";\r
-break;\r
-case 0:\r
-ret = "User Defined";\r
-break;\r
-default:\r
-ret = "None";\r
-break;\r
-}\r
-return ret;\r
-}, "~N");\r
-c$.getColour = Clazz.defineMethod (c$, "getColour", \r
-function (alignment, name) {\r
-var colindex = jalview.schemes.ColourSchemeProperty.getColourIndexFromName (name);\r
-if (colindex == -1) {\r
-if (name.indexOf ('=') == -1) {\r
-try {\r
-return new jalview.schemes.UserColourScheme (name);\r
-} catch (e) {\r
-if (Clazz.exceptionOf (e, Exception)) {\r
-} else {\r
-throw e;\r
-}\r
-}\r
-} else {\r
-try {\r
-var ucs = new jalview.schemes.UserColourScheme ("white");\r
-ucs.parseAppletParameter (name);\r
-} catch (e) {\r
-if (Clazz.exceptionOf (e, Exception)) {\r
-} else {\r
-throw e;\r
-}\r
-}\r
-}}return jalview.schemes.ColourSchemeProperty.getColour (alignment, jalview.schemes.ColourSchemeProperty.getColourIndexFromName (name));\r
-}, "jalview.datamodel.AnnotatedCollectionI,~S");\r
-c$.getColour = Clazz.defineMethod (c$, "getColour", \r
-function (coll, index) {\r
-var cs = null;\r
-switch (index) {\r
-case 2:\r
-cs = new jalview.schemes.ClustalxColourScheme (coll, null);\r
-break;\r
-case 3:\r
-cs = new jalview.schemes.Blosum62ColourScheme ();\r
-break;\r
-case 4:\r
-cs = new jalview.schemes.PIDColourScheme ();\r
-break;\r
-case 5:\r
-cs = new jalview.schemes.ZappoColourScheme ();\r
-break;\r
-case 6:\r
-cs = new jalview.schemes.TaylorColourScheme ();\r
-break;\r
-case 7:\r
-cs = new jalview.schemes.HydrophobicColourScheme ();\r
-break;\r
-case 8:\r
-cs = new jalview.schemes.HelixColourScheme ();\r
-break;\r
-case 9:\r
-cs = new jalview.schemes.StrandColourScheme ();\r
-break;\r
-case 10:\r
-cs = new jalview.schemes.TurnColourScheme ();\r
-break;\r
-case 11:\r
-cs = new jalview.schemes.BuriedColourScheme ();\r
-break;\r
-case 12:\r
-cs = new jalview.schemes.NucleotideColourScheme ();\r
-break;\r
-case 13:\r
-cs = new jalview.schemes.PurinePyrimidineColourScheme ();\r
-break;\r
-case 15:\r
-cs = new jalview.schemes.TCoffeeColourScheme (coll);\r
-break;\r
-case 16:\r
-cs = new jalview.schemes.RNAHelicesColour (coll);\r
-break;\r
-case 0:\r
-var col = new Array (24);\r
-for (var i = 0; i < 24; i++) {\r
-col[i] = java.awt.Color.white;\r
-}\r
-cs = new jalview.schemes.UserColourScheme (col);\r
-break;\r
-default:\r
-break;\r
-}\r
-return cs;\r
-}, "jalview.datamodel.AnnotatedCollectionI,~N");\r
-c$.getAWTColorFromName = Clazz.defineMethod (c$, "getAWTColorFromName", \r
-function (name) {\r
-var col = null;\r
-name = name.toLowerCase ();\r
-if (name.equals ("black")) {\r
-col = java.awt.Color.black;\r
-} else if (name.equals ("blue")) {\r
-col = java.awt.Color.blue;\r
-} else if (name.equals ("cyan")) {\r
-col = java.awt.Color.cyan;\r
-} else if (name.equals ("darkGray")) {\r
-col = java.awt.Color.darkGray;\r
-} else if (name.equals ("gray")) {\r
-col = java.awt.Color.gray;\r
-} else if (name.equals ("green")) {\r
-col = java.awt.Color.green;\r
-} else if (name.equals ("lightGray")) {\r
-col = java.awt.Color.lightGray;\r
-} else if (name.equals ("magenta")) {\r
-col = java.awt.Color.magenta;\r
-} else if (name.equals ("orange")) {\r
-col = java.awt.Color.orange;\r
-} else if (name.equals ("pink")) {\r
-col = java.awt.Color.pink;\r
-} else if (name.equals ("red")) {\r
-col = java.awt.Color.red;\r
-} else if (name.equals ("white")) {\r
-col = java.awt.Color.white;\r
-} else if (name.equals ("yellow")) {\r
-col = java.awt.Color.yellow;\r
-}return col;\r
-}, "~S");\r
-c$.initRnaHelicesShading = Clazz.defineMethod (c$, "initRnaHelicesShading", \r
-function (n) {\r
-var j = 0;\r
-if (jalview.schemes.ColourSchemeProperty.rnaHelices == null) {\r
-jalview.schemes.ColourSchemeProperty.rnaHelices = new Array (n + 1);\r
-} else if (jalview.schemes.ColourSchemeProperty.rnaHelices != null && jalview.schemes.ColourSchemeProperty.rnaHelices.length <= n) {\r
-var t = new Array (n + 1);\r
-System.arraycopy (jalview.schemes.ColourSchemeProperty.rnaHelices, 0, t, 0, jalview.schemes.ColourSchemeProperty.rnaHelices.length);\r
-j = jalview.schemes.ColourSchemeProperty.rnaHelices.length;\r
-jalview.schemes.ColourSchemeProperty.rnaHelices = t;\r
-} else {\r
-return;\r
-}for (; j <= n; j++) {\r
-jalview.schemes.ColourSchemeProperty.rnaHelices[j] = jalview.util.ColorUtils.generateRandomColor (java.awt.Color.white);\r
-}\r
-}, "~N");\r
-Clazz.defineStatics (c$,\r
-"UNDEFINED", -1,\r
-"USER_DEFINED", 0,\r
-"NONE", 1,\r
-"CLUSTAL", 2,\r
-"BLOSUM", 3,\r
-"PID", 4,\r
-"ZAPPO", 5,\r
-"TAYLOR", 6,\r
-"HYDROPHOBIC", 7,\r
-"HELIX", 8,\r
-"STRAND", 9,\r
-"TURN", 10,\r
-"BURIED", 11,\r
-"NUCLEOTIDE", 12,\r
-"PURINEPYRIMIDINE", 13,\r
-"COVARIATION", 14,\r
-"TCOFFEE", 15,\r
-"RNAHELIX", 16,\r
-"RNAINTERACTION", 17,\r
-"FIRST_COLOUR", 1,\r
-"LAST_COLOUR", 17,\r
-"rnaHelices", null);\r
-});\r
+Clazz.declarePackage ("jalview.schemes");
+Clazz.load (null, "jalview.schemes.ColourSchemeProperty", ["jalview.schemes.Blosum62ColourScheme", "$.BuriedColourScheme", "$.ClustalxColourScheme", "$.HelixColourScheme", "$.HydrophobicColourScheme", "$.NucleotideColourScheme", "$.PIDColourScheme", "$.PurinePyrimidineColourScheme", "$.RNAHelicesColour", "$.StrandColourScheme", "$.TCoffeeColourScheme", "$.TaylorColourScheme", "$.TurnColourScheme", "$.UserColourScheme", "$.ZappoColourScheme", "jalview.util.ColorUtils", "java.awt.Color"], function () {
+c$ = Clazz.declareType (jalview.schemes, "ColourSchemeProperty");
+c$.getColourIndexFromName = Clazz.defineMethod (c$, "getColourIndexFromName",
+function (name) {
+var ret = -1;
+if (name.equalsIgnoreCase ("Clustal")) {
+ret = 2;
+} else if (name.equalsIgnoreCase ("Blosum62")) {
+ret = 3;
+} else if (name.equalsIgnoreCase ("% Identity")) {
+ret = 4;
+} else if (name.equalsIgnoreCase ("Zappo")) {
+ret = 5;
+} else if (name.equalsIgnoreCase ("Taylor")) {
+ret = 6;
+} else if (name.equalsIgnoreCase ("Hydrophobic")) {
+ret = 7;
+} else if (name.equalsIgnoreCase ("Helix Propensity")) {
+ret = 8;
+} else if (name.equalsIgnoreCase ("Strand Propensity")) {
+ret = 9;
+} else if (name.equalsIgnoreCase ("Turn Propensity")) {
+ret = 10;
+} else if (name.equalsIgnoreCase ("Buried Index")) {
+ret = 11;
+} else if (name.equalsIgnoreCase ("Nucleotide")) {
+ret = 12;
+} else if (name.equalsIgnoreCase ("T-Coffee Scores")) {
+ret = 15;
+} else if (name.equalsIgnoreCase ("User Defined")) {
+ret = 0;
+} else if (name.equalsIgnoreCase ("None")) {
+ret = 1;
+} else if (name.equalsIgnoreCase ("Purine/Pyrimidine")) {
+ret = 13;
+} else if (name.equalsIgnoreCase ("RNA Interaction type")) {
+ret = 17;
+} else if (name.equalsIgnoreCase ("RNA Helices")) {
+ret = 16;
+}return ret;
+}, "~S");
+c$.getColourName = Clazz.defineMethod (c$, "getColourName",
+function (cs) {
+var index = 1;
+if (Clazz.instanceOf (cs, jalview.schemes.ClustalxColourScheme)) {
+index = 2;
+} else if (Clazz.instanceOf (cs, jalview.schemes.Blosum62ColourScheme)) {
+index = 3;
+} else if (Clazz.instanceOf (cs, jalview.schemes.PIDColourScheme)) {
+index = 4;
+} else if (Clazz.instanceOf (cs, jalview.schemes.ZappoColourScheme)) {
+index = 5;
+} else if (Clazz.instanceOf (cs, jalview.schemes.TaylorColourScheme)) {
+index = 6;
+} else if (Clazz.instanceOf (cs, jalview.schemes.HydrophobicColourScheme)) {
+index = 7;
+} else if (Clazz.instanceOf (cs, jalview.schemes.HelixColourScheme)) {
+index = 8;
+} else if (Clazz.instanceOf (cs, jalview.schemes.StrandColourScheme)) {
+index = 9;
+} else if (Clazz.instanceOf (cs, jalview.schemes.TurnColourScheme)) {
+index = 10;
+} else if (Clazz.instanceOf (cs, jalview.schemes.BuriedColourScheme)) {
+index = 11;
+} else if (Clazz.instanceOf (cs, jalview.schemes.NucleotideColourScheme)) {
+index = 12;
+} else if (Clazz.instanceOf (cs, jalview.schemes.PurinePyrimidineColourScheme)) {
+index = 13;
+} else if (Clazz.instanceOf (cs, jalview.schemes.TCoffeeColourScheme)) {
+index = 15;
+} else if (Clazz.instanceOf (cs, jalview.schemes.RNAHelicesColour)) {
+index = 16;
+} else if (Clazz.instanceOf (cs, jalview.schemes.UserColourScheme)) {
+if (((cs).getName () != null) && ((cs).getName ().length > 0)) {
+return (cs).getName ();
+}index = 0;
+}return jalview.schemes.ColourSchemeProperty.getColourName (index);
+}, "jalview.schemes.ColourSchemeI");
+c$.getColourName = Clazz.defineMethod (c$, "getColourName",
+function (index) {
+var ret = null;
+switch (index) {
+case 2:
+ret = "Clustal";
+break;
+case 3:
+ret = "Blosum62";
+break;
+case 4:
+ret = "% Identity";
+break;
+case 5:
+ret = "Zappo";
+break;
+case 6:
+ret = "Taylor";
+break;
+case 7:
+ret = "Hydrophobic";
+break;
+case 8:
+ret = "Helix Propensity";
+break;
+case 9:
+ret = "Strand Propensity";
+break;
+case 10:
+ret = "Turn Propensity";
+break;
+case 11:
+ret = "Buried Index";
+break;
+case 12:
+ret = "Nucleotide";
+break;
+case 13:
+ret = "Purine/Pyrimidine";
+break;
+case 15:
+ret = "T-Coffee Scores";
+break;
+case 17:
+ret = "RNA Interaction type";
+break;
+case 16:
+ret = "RNA Helices";
+break;
+case 0:
+ret = "User Defined";
+break;
+default:
+ret = "None";
+break;
+}
+return ret;
+}, "~N");
+c$.getColour = Clazz.defineMethod (c$, "getColour",
+function (alignment, name) {
+var colindex = jalview.schemes.ColourSchemeProperty.getColourIndexFromName (name);
+if (colindex == -1) {
+if (name.indexOf ('=') == -1) {
+try {
+return new jalview.schemes.UserColourScheme (name);
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+} else {
+throw e;
+}
+}
+} else {
+try {
+var ucs = new jalview.schemes.UserColourScheme ("white");
+ucs.parseAppletParameter (name);
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+} else {
+throw e;
+}
+}
+}}return jalview.schemes.ColourSchemeProperty.getColour (alignment, jalview.schemes.ColourSchemeProperty.getColourIndexFromName (name));
+}, "jalview.datamodel.AnnotatedCollectionI,~S");
+c$.getColour = Clazz.defineMethod (c$, "getColour",
+function (coll, index) {
+var cs = null;
+switch (index) {
+case 2:
+cs = new jalview.schemes.ClustalxColourScheme (coll, null);
+break;
+case 3:
+cs = new jalview.schemes.Blosum62ColourScheme ();
+break;
+case 4:
+cs = new jalview.schemes.PIDColourScheme ();
+break;
+case 5:
+cs = new jalview.schemes.ZappoColourScheme ();
+break;
+case 6:
+cs = new jalview.schemes.TaylorColourScheme ();
+break;
+case 7:
+cs = new jalview.schemes.HydrophobicColourScheme ();
+break;
+case 8:
+cs = new jalview.schemes.HelixColourScheme ();
+break;
+case 9:
+cs = new jalview.schemes.StrandColourScheme ();
+break;
+case 10:
+cs = new jalview.schemes.TurnColourScheme ();
+break;
+case 11:
+cs = new jalview.schemes.BuriedColourScheme ();
+break;
+case 12:
+cs = new jalview.schemes.NucleotideColourScheme ();
+break;
+case 13:
+cs = new jalview.schemes.PurinePyrimidineColourScheme ();
+break;
+case 15:
+cs = new jalview.schemes.TCoffeeColourScheme (coll);
+break;
+case 16:
+cs = new jalview.schemes.RNAHelicesColour (coll);
+break;
+case 0:
+var col = new Array (24);
+for (var i = 0; i < 24; i++) {
+col[i] = java.awt.Color.white;
+}
+cs = new jalview.schemes.UserColourScheme (col);
+break;
+default:
+break;
+}
+return cs;
+}, "jalview.datamodel.AnnotatedCollectionI,~N");
+c$.getAWTColorFromName = Clazz.defineMethod (c$, "getAWTColorFromName",
+function (name) {
+var col = null;
+name = name.toLowerCase ();
+if (name.equals ("black")) {
+col = java.awt.Color.black;
+} else if (name.equals ("blue")) {
+col = java.awt.Color.blue;
+} else if (name.equals ("cyan")) {
+col = java.awt.Color.cyan;
+} else if (name.equals ("darkGray")) {
+col = java.awt.Color.darkGray;
+} else if (name.equals ("gray")) {
+col = java.awt.Color.gray;
+} else if (name.equals ("green")) {
+col = java.awt.Color.green;
+} else if (name.equals ("lightGray")) {
+col = java.awt.Color.lightGray;
+} else if (name.equals ("magenta")) {
+col = java.awt.Color.magenta;
+} else if (name.equals ("orange")) {
+col = java.awt.Color.orange;
+} else if (name.equals ("pink")) {
+col = java.awt.Color.pink;
+} else if (name.equals ("red")) {
+col = java.awt.Color.red;
+} else if (name.equals ("white")) {
+col = java.awt.Color.white;
+} else if (name.equals ("yellow")) {
+col = java.awt.Color.yellow;
+}return col;
+}, "~S");
+c$.initRnaHelicesShading = Clazz.defineMethod (c$, "initRnaHelicesShading",
+function (n) {
+var j = 0;
+if (jalview.schemes.ColourSchemeProperty.rnaHelices == null) {
+jalview.schemes.ColourSchemeProperty.rnaHelices = new Array (n + 1);
+} else if (jalview.schemes.ColourSchemeProperty.rnaHelices != null && jalview.schemes.ColourSchemeProperty.rnaHelices.length <= n) {
+var t = new Array (n + 1);
+System.arraycopy (jalview.schemes.ColourSchemeProperty.rnaHelices, 0, t, 0, jalview.schemes.ColourSchemeProperty.rnaHelices.length);
+j = jalview.schemes.ColourSchemeProperty.rnaHelices.length;
+jalview.schemes.ColourSchemeProperty.rnaHelices = t;
+} else {
+return;
+}for (; j <= n; j++) {
+jalview.schemes.ColourSchemeProperty.rnaHelices[j] = jalview.util.ColorUtils.generateRandomColor (java.awt.Color.white);
+}
+}, "~N");
+Clazz.defineStatics (c$,
+"UNDEFINED", -1,
+"USER_DEFINED", 0,
+"NONE", 1,
+"CLUSTAL", 2,
+"BLOSUM", 3,
+"PID", 4,
+"ZAPPO", 5,
+"TAYLOR", 6,
+"HYDROPHOBIC", 7,
+"HELIX", 8,
+"STRAND", 9,
+"TURN", 10,
+"BURIED", 11,
+"NUCLEOTIDE", 12,
+"PURINEPYRIMIDINE", 13,
+"COVARIATION", 14,
+"TCOFFEE", 15,
+"RNAHELIX", 16,
+"RNAINTERACTION", 17,
+"FIRST_COLOUR", 1,
+"LAST_COLOUR", 17,
+"rnaHelices", null);
+});
git://source.jalview.org / jalviewjs.git / blobdiff