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