1 Clazz.declarePackage ("jalview.schemes");
2 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 () {
3 c$ = Clazz.declareType (jalview.schemes, "ColourSchemeProperty");
4 c$.getColourIndexFromName = Clazz.defineMethod (c$, "getColourIndexFromName",
7 if (name.equalsIgnoreCase ("Clustal")) {
9 } else if (name.equalsIgnoreCase ("Blosum62")) {
11 } else if (name.equalsIgnoreCase ("% Identity")) {
13 } else if (name.equalsIgnoreCase ("Zappo")) {
15 } else if (name.equalsIgnoreCase ("Taylor")) {
17 } else if (name.equalsIgnoreCase ("Hydrophobic")) {
19 } else if (name.equalsIgnoreCase ("Helix Propensity")) {
21 } else if (name.equalsIgnoreCase ("Strand Propensity")) {
23 } else if (name.equalsIgnoreCase ("Turn Propensity")) {
25 } else if (name.equalsIgnoreCase ("Buried Index")) {
27 } else if (name.equalsIgnoreCase ("Nucleotide")) {
29 } else if (name.equalsIgnoreCase ("T-Coffee Scores")) {
31 } else if (name.equalsIgnoreCase ("User Defined")) {
33 } else if (name.equalsIgnoreCase ("None")) {
35 } else if (name.equalsIgnoreCase ("Purine/Pyrimidine")) {
37 } else if (name.equalsIgnoreCase ("RNA Interaction type")) {
39 } else if (name.equalsIgnoreCase ("RNA Helices")) {
43 c$.getColourName = Clazz.defineMethod (c$, "getColourName",
46 if (Clazz.instanceOf (cs, jalview.schemes.ClustalxColourScheme)) {
48 } else if (Clazz.instanceOf (cs, jalview.schemes.Blosum62ColourScheme)) {
50 } else if (Clazz.instanceOf (cs, jalview.schemes.PIDColourScheme)) {
52 } else if (Clazz.instanceOf (cs, jalview.schemes.ZappoColourScheme)) {
54 } else if (Clazz.instanceOf (cs, jalview.schemes.TaylorColourScheme)) {
56 } else if (Clazz.instanceOf (cs, jalview.schemes.HydrophobicColourScheme)) {
58 } else if (Clazz.instanceOf (cs, jalview.schemes.HelixColourScheme)) {
60 } else if (Clazz.instanceOf (cs, jalview.schemes.StrandColourScheme)) {
62 } else if (Clazz.instanceOf (cs, jalview.schemes.TurnColourScheme)) {
64 } else if (Clazz.instanceOf (cs, jalview.schemes.BuriedColourScheme)) {
66 } else if (Clazz.instanceOf (cs, jalview.schemes.NucleotideColourScheme)) {
68 } else if (Clazz.instanceOf (cs, jalview.schemes.PurinePyrimidineColourScheme)) {
70 } else if (Clazz.instanceOf (cs, jalview.schemes.TCoffeeColourScheme)) {
72 } else if (Clazz.instanceOf (cs, jalview.schemes.RNAHelicesColour)) {
74 } else if (Clazz.instanceOf (cs, jalview.schemes.UserColourScheme)) {
75 if (((cs).getName () != null) && ((cs).getName ().length > 0)) {
76 return (cs).getName ();
78 }return jalview.schemes.ColourSchemeProperty.getColourName (index);
79 }, "jalview.schemes.ColourSchemeI");
80 c$.getColourName = Clazz.defineMethod (c$, "getColourName",
103 ret = "Helix Propensity";
106 ret = "Strand Propensity";
109 ret = "Turn Propensity";
112 ret = "Buried Index";
118 ret = "Purine/Pyrimidine";
121 ret = "T-Coffee Scores";
124 ret = "RNA Interaction type";
130 ret = "User Defined";
138 c$.getColour = Clazz.defineMethod (c$, "getColour",
139 function (alignment, name) {
140 var colindex = jalview.schemes.ColourSchemeProperty.getColourIndexFromName (name);
141 if (colindex == -1) {
142 if (name.indexOf ('=') == -1) {
144 return new jalview.schemes.UserColourScheme (name);
146 if (Clazz.exceptionOf (e, Exception)) {
153 var ucs = new jalview.schemes.UserColourScheme ("white");
154 ucs.parseAppletParameter (name);
156 if (Clazz.exceptionOf (e, Exception)) {
161 }}return jalview.schemes.ColourSchemeProperty.getColour (alignment, jalview.schemes.ColourSchemeProperty.getColourIndexFromName (name));
162 }, "jalview.datamodel.AnnotatedCollectionI,~S");
163 c$.getColour = Clazz.defineMethod (c$, "getColour",
164 function (coll, index) {
168 cs = new jalview.schemes.ClustalxColourScheme (coll, null);
171 cs = new jalview.schemes.Blosum62ColourScheme ();
174 cs = new jalview.schemes.PIDColourScheme ();
177 cs = new jalview.schemes.ZappoColourScheme ();
180 cs = new jalview.schemes.TaylorColourScheme ();
183 cs = new jalview.schemes.HydrophobicColourScheme ();
186 cs = new jalview.schemes.HelixColourScheme ();
189 cs = new jalview.schemes.StrandColourScheme ();
192 cs = new jalview.schemes.TurnColourScheme ();
195 cs = new jalview.schemes.BuriedColourScheme ();
198 cs = new jalview.schemes.NucleotideColourScheme ();
201 cs = new jalview.schemes.PurinePyrimidineColourScheme ();
204 cs = new jalview.schemes.TCoffeeColourScheme (coll);
207 cs = new jalview.schemes.RNAHelicesColour (coll);
210 var col = new Array (24);
211 for (var i = 0; i < 24; i++) {
212 col[i] = java.awt.Color.white;
214 cs = new jalview.schemes.UserColourScheme (col);
220 }, "jalview.datamodel.AnnotatedCollectionI,~N");
221 c$.getAWTColorFromName = Clazz.defineMethod (c$, "getAWTColorFromName",
224 name = name.toLowerCase ();
225 if (name.equals ("black")) {
226 col = java.awt.Color.black;
227 } else if (name.equals ("blue")) {
228 col = java.awt.Color.blue;
229 } else if (name.equals ("cyan")) {
230 col = java.awt.Color.cyan;
231 } else if (name.equals ("darkGray")) {
232 col = java.awt.Color.darkGray;
233 } else if (name.equals ("gray")) {
234 col = java.awt.Color.gray;
235 } else if (name.equals ("green")) {
236 col = java.awt.Color.green;
237 } else if (name.equals ("lightGray")) {
238 col = java.awt.Color.lightGray;
239 } else if (name.equals ("magenta")) {
240 col = java.awt.Color.magenta;
241 } else if (name.equals ("orange")) {
242 col = java.awt.Color.orange;
243 } else if (name.equals ("pink")) {
244 col = java.awt.Color.pink;
245 } else if (name.equals ("red")) {
246 col = java.awt.Color.red;
247 } else if (name.equals ("white")) {
248 col = java.awt.Color.white;
249 } else if (name.equals ("yellow")) {
250 col = java.awt.Color.yellow;
253 c$.initRnaHelicesShading = Clazz.defineMethod (c$, "initRnaHelicesShading",
256 if (jalview.schemes.ColourSchemeProperty.rnaHelices == null) {
257 jalview.schemes.ColourSchemeProperty.rnaHelices = new Array (n + 1);
258 } else if (jalview.schemes.ColourSchemeProperty.rnaHelices != null && jalview.schemes.ColourSchemeProperty.rnaHelices.length <= n) {
259 var t = new Array (n + 1);
260 System.arraycopy (jalview.schemes.ColourSchemeProperty.rnaHelices, 0, t, 0, jalview.schemes.ColourSchemeProperty.rnaHelices.length);
261 j = jalview.schemes.ColourSchemeProperty.rnaHelices.length;
262 jalview.schemes.ColourSchemeProperty.rnaHelices = t;
265 }for (; j <= n; j++) {
266 jalview.schemes.ColourSchemeProperty.rnaHelices[j] = jalview.util.ColorUtils.generateRandomColor (java.awt.Color.white);
269 Clazz.defineStatics (c$,
284 "PURINEPYRIMIDINE", 13,
288 "RNAINTERACTION", 17,