X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fschemes%2FColourSchemeProperty.js;h=eb55454db5967c7a6900bdcddf193dd3e3651603;hp=352a3730a39f433a7402530ffcb7eb0c757aa90c;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/schemes/ColourSchemeProperty.js b/bin/jalview/schemes/ColourSchemeProperty.js
index 352a373..eb55454 100644
--- a/bin/jalview/schemes/ColourSchemeProperty.js
+++ b/bin/jalview/schemes/ColourSchemeProperty.js
@@ -1,292 +1,292 @@
-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$,
-"UNDEFINED", -1,
-"USER_DEFINED", 0,
-"NONE", 1,
-"CLUSTAL", 2,
-"BLOSUM", 3,
-"PID", 4,
-"ZAPPO", 5,
-"TAYLOR", 6,
-"HYDROPHOBIC", 7,
-"HELIX", 8,
-"STRAND", 9,
-"TURN", 10,
-"BURIED", 11,
-"NUCLEOTIDE", 12,
-"PURINEPYRIMIDINE", 13,
-"COVARIATION", 14,
-"TCOFFEE", 15,
-"RNAHELIX", 16,
-"RNAINTERACTION", 17,
-"FIRST_COLOUR", 1,
-"LAST_COLOUR", 17,
-"rnaHelices", null);
-});
+Clazz.declarePackage ("jalview.schemes");
+Clazz.load (null, "jalview.schemes.ColourSchemeProperty", ["jalview.schemes.Blosum62ColourScheme", "$.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);
+});