1 Clazz.declarePackage ("jalview.schemes");
\r
2 Clazz.load (["jalview.analysis.scoremodels.FeatureScoreModel", "$.PIDScoreModel", "jalview.schemes.ScoreMatrix", "java.awt.Color", "java.util.ArrayList", "$.HashMap", "$.Hashtable", "$.Vector"], "jalview.schemes.ResidueProperties", ["java.lang.StringBuffer"], function () {
\r
3 c$ = Clazz.declareType (jalview.schemes, "ResidueProperties");
\r
4 c$.buildAmbiguityCodonSet = Clazz.defineMethod (c$, "buildAmbiguityCodonSet",
\r
6 if (jalview.schemes.ResidueProperties._ambiguityCodes.size () > 0) {
\r
7 System.err.println ("Ignoring multiple calls to buildAmbiguityCodonSet");
\r
9 }for (var acode, $acode = jalview.schemes.ResidueProperties.ambiguityCodes.entrySet ().iterator (); $acode.hasNext () && ((acode = $acode.next ()) || true);) {
\r
10 for (var r, $r = 0, $$r = acode.getValue (); $r < $$r.length && ((r = $$r[$r]) || true); $r++) {
\r
11 var codesfor = jalview.schemes.ResidueProperties._ambiguityCodes.get (r);
\r
12 if (codesfor == null) {
\r
13 jalview.schemes.ResidueProperties._ambiguityCodes.put (r, codesfor = new java.util.ArrayList ());
\r
14 }if (!codesfor.contains (acode.getKey ())) {
\r
15 codesfor.add (acode.getKey ());
\r
17 System.err.println ("Inconsistency in the IUBMB ambiguity code nomenclature table: collision for " + acode.getKey () + " in residue " + r);
\r
20 var unambcodons = jalview.schemes.ResidueProperties.codonHash2.keySet ().toArray ( new Array (jalview.schemes.ResidueProperties.codonHash2.size ()));
\r
21 for (var codon, $codon = 0, $$codon = unambcodons; $codon < $$codon.length && ((codon = $$codon[$codon]) || true); $codon++) {
\r
22 var residue = jalview.schemes.ResidueProperties.codonHash2.get (codon);
\r
23 var acodon = new Array (codon.length);
\r
24 for (var i = 0, iSize = codon.length; i < iSize; i++) {
\r
25 var _ac = "" + codon.charAt (i);
\r
26 var acodes = jalview.schemes.ResidueProperties._ambiguityCodes.get (_ac);
\r
27 if (acodes != null) {
\r
28 acodon[i] = acodes.toArray ( new Array (acodes.size ()));
\r
30 acodon[i] = Clazz.newArray (-1, []);
\r
32 var tpos = Clazz.newIntArray (codon.length, 0);
\r
33 var cpos = Clazz.newIntArray (codon.length, 0);
\r
34 for (var i = 0; i < tpos.length; i++) {
\r
37 tpos[acodon.length - 1] = 0;
\r
40 while (tpos[0] < acodon[0].length) {
\r
41 var allres = Clazz.newCharArray (tpos.length, '\0');
\r
44 for (ipos = 0; ipos < tpos.length; ipos++) {
\r
45 if (acodon[ipos].length == 0 || tpos[ipos] < 0) {
\r
46 _acodon += codon.charAt (ipos);
\r
47 allres[ipos] = Clazz.newCharArray (-1, [codon.charAt (ipos)]);
\r
49 _acodon += acodon[ipos][tpos[ipos]];
\r
50 var altbase = jalview.schemes.ResidueProperties.ambiguityCodes.get (acodon[ipos][tpos[ipos]]);
\r
51 allres[ipos] = Clazz.newCharArray (altbase.length, '\0');
\r
53 for (var ab, $ab = 0, $$ab = altbase; $ab < $$ab.length && ((ab = $$ab[$ab]) || true); $ab++) {
\r
54 allres[ipos][j++] = ab.charAt (0);
\r
57 for (ipos = 0; ipos < cpos.length; ipos++) {
\r
63 for (j = 0; j < cpos.length; j++) {
\r
64 _codon += allres[j][cpos[j]];
\r
66 var tr = jalview.schemes.ResidueProperties.codonHash2.get (_codon);
\r
67 if (valid = (tr != null && tr.equals (residue))) {
\r
68 ipos = acodon.length - 1;
\r
69 while (++cpos[ipos] >= allres[ipos].length && ipos > 0) {
\r
73 }} while (valid && cpos[0] < allres[0].length);
\r
75 jalview.schemes.ResidueProperties.codonHash2.put (_acodon, residue);
\r
77 }ipos = acodon.length - 1;
\r
78 while (++tpos[ipos] >= acodon[ipos].length && ipos > 0) {
\r
85 c$.getHydmax = Clazz.defineMethod (c$, "getHydmax",
\r
89 c$.getHydmin = Clazz.defineMethod (c$, "getHydmin",
\r
93 c$.getHyd = Clazz.defineMethod (c$, "getHyd",
\r
95 return jalview.schemes.ResidueProperties.hyd;
\r
97 c$.getAA3Hash = Clazz.defineMethod (c$, "getAA3Hash",
\r
99 return jalview.schemes.ResidueProperties.aa3Hash;
\r
101 c$.getDNA = Clazz.defineMethod (c$, "getDNA",
\r
103 return jalview.schemes.ResidueProperties.DNA;
\r
105 c$.getBLOSUM62 = Clazz.defineMethod (c$, "getBLOSUM62",
\r
107 return jalview.schemes.ResidueProperties.BLOSUM62;
\r
109 c$.getPAM250 = Clazz.defineMethod (c$, "getPAM250",
\r
110 function (A1, A2) {
\r
111 return jalview.schemes.ResidueProperties.getPAM250 (A1.charAt (0), A2.charAt (0));
\r
113 c$.getBLOSUM62 = Clazz.defineMethod (c$, "getBLOSUM62",
\r
114 function (c1, c2) {
\r
117 var a = jalview.schemes.ResidueProperties.aaIndex[c1.charCodeAt (0)];
\r
118 var b = jalview.schemes.ResidueProperties.aaIndex[c2.charCodeAt (0)];
\r
119 pog = jalview.schemes.ResidueProperties.BLOSUM62[a][b];
\r
121 if (Clazz.exceptionOf (e, Exception)) {
\r
128 c$.getCodons = Clazz.defineMethod (c$, "getCodons",
\r
130 if (jalview.schemes.ResidueProperties.codonHash.containsKey (res)) {
\r
131 return jalview.schemes.ResidueProperties.codonHash.get (res);
\r
134 c$.codonTranslate = Clazz.defineMethod (c$, "codonTranslate",
\r
135 function (lccodon) {
\r
137 return jalview.schemes.ResidueProperties._codonTranslate (lccodon);
\r
138 }var cdn = jalview.schemes.ResidueProperties.codonHash2.get (lccodon.toUpperCase ());
\r
139 if (cdn != null && cdn.equals ("*")) {
\r
143 c$._codonTranslate = Clazz.defineMethod (c$, "_codonTranslate",
\r
144 function (lccodon) {
\r
145 var codon = lccodon.toUpperCase ();
\r
146 if (codon.indexOf ('X') > -1 || codon.indexOf ('N') > -1) {
\r
148 }for (var key, $key = jalview.schemes.ResidueProperties.codonHash.keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) {
\r
149 if (jalview.schemes.ResidueProperties.codonHash.get (key).contains (codon)) {
\r
154 c$.getDefaultPeptideMatrix = Clazz.defineMethod (c$, "getDefaultPeptideMatrix",
\r
156 return jalview.schemes.ResidueProperties.getBLOSUM62 ();
\r
158 c$.getDefaultDnaMatrix = Clazz.defineMethod (c$, "getDefaultDnaMatrix",
\r
160 return jalview.schemes.ResidueProperties.getDNA ();
\r
162 c$.getScoreMatrix = Clazz.defineMethod (c$, "getScoreMatrix",
\r
163 function (pwtype) {
\r
164 var val = jalview.schemes.ResidueProperties.scoreMatrices.get (pwtype);
\r
165 if (val != null && Clazz.instanceOf (val, jalview.schemes.ScoreMatrix)) {
\r
169 c$.getScoreModel = Clazz.defineMethod (c$, "getScoreModel",
\r
170 function (pwtype) {
\r
171 return jalview.schemes.ResidueProperties.scoreMatrices.get (pwtype);
\r
173 c$.getPAM250 = Clazz.defineMethod (c$, "getPAM250",
\r
175 var a = jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)];
\r
176 var b = jalview.schemes.ResidueProperties.aaIndex[d.charCodeAt (0)];
\r
177 var pog = jalview.schemes.ResidueProperties.PAM250[a][b];
\r
180 c$.getDssp3state = Clazz.defineMethod (c$, "getDssp3state",
\r
181 function (ssstring) {
\r
182 if (ssstring == null) {
\r
184 }var ss = new StringBuffer ();
\r
185 for (var i = 0; i < ssstring.length; i++) {
\r
186 var ssc = ssstring.substring (i, i + 1);
\r
187 if (jalview.schemes.ResidueProperties.toDssp3State.containsKey (ssc)) {
\r
188 ss.append (jalview.schemes.ResidueProperties.toDssp3State.get (ssc));
\r
192 return ss.toString ();
\r
194 c$.getRNASecStrucState = Clazz.defineMethod (c$, "getRNASecStrucState",
\r
195 function (ssstring) {
\r
196 if (ssstring == null) {
\r
198 }var ss = new StringBuffer ();
\r
199 for (var i = 0; i < ssstring.length; i++) {
\r
200 var ssc = ssstring.substring (i, i + 1);
\r
201 if (jalview.schemes.ResidueProperties.toRNAssState.containsKey (ssc)) {
\r
206 return ss.toString ();
\r
208 c$.isCloseParenRNA = Clazz.defineMethod (c$, "isCloseParenRNA",
\r
210 return jalview.schemes.ResidueProperties.RNAcloseParen[dc.charCodeAt (0)];
\r
212 c$.getResidues = Clazz.defineMethod (c$, "getResidues",
\r
213 function (nucleotide, includeAmbiguous) {
\r
214 var result = new java.util.ArrayList ();
\r
216 for (var nuc, $nuc = jalview.schemes.ResidueProperties.nucleotideName.keySet ().iterator (); $nuc.hasNext () && ((nuc = $nuc.next ()) || true);) {
\r
217 var val = jalview.schemes.ResidueProperties.nucleotideIndex[nuc.charCodeAt (0)];
\r
218 if ((!includeAmbiguous && val > 4) || (val >= 10)) {
\r
220 }nuc = nuc.toUpperCase ();
\r
221 if (!result.contains (nuc)) {
\r
225 for (var res, $res = jalview.schemes.ResidueProperties.aa3Hash.keySet ().iterator (); $res.hasNext () && ((res = $res.next ()) || true);) {
\r
226 var index = jalview.schemes.ResidueProperties.aa3Hash.get (res).intValue ();
\r
227 if ((!includeAmbiguous && index >= 20) || index >= 23) {
\r
229 }res = res.toUpperCase ();
\r
230 if (!result.contains (res)) {
\r
235 c$.scoreMatrices = c$.prototype.scoreMatrices = new java.util.Hashtable ();
\r
236 Clazz.defineStatics (c$,
\r
238 "nucleotideIndex", null,
\r
239 "purinepyrimidineIndex", null);
\r
240 c$.aa3Hash = c$.prototype.aa3Hash = new java.util.HashMap ();
\r
241 c$.aa2Triplet = c$.prototype.aa2Triplet = new java.util.HashMap ();
\r
242 c$.nucleotideName = c$.prototype.nucleotideName = new java.util.HashMap ();
\r
244 jalview.schemes.ResidueProperties.aaIndex = Clazz.newIntArray (255, 0);
\r
245 for (var i = 0; i < 255; i++) {
\r
246 jalview.schemes.ResidueProperties.aaIndex[i] = 23;
\r
248 jalview.schemes.ResidueProperties.aaIndex['A'.charCodeAt (0)] = 0;
\r
249 jalview.schemes.ResidueProperties.aaIndex['R'.charCodeAt (0)] = 1;
\r
250 jalview.schemes.ResidueProperties.aaIndex['N'.charCodeAt (0)] = 2;
\r
251 jalview.schemes.ResidueProperties.aaIndex['D'.charCodeAt (0)] = 3;
\r
252 jalview.schemes.ResidueProperties.aaIndex['C'.charCodeAt (0)] = 4;
\r
253 jalview.schemes.ResidueProperties.aaIndex['Q'.charCodeAt (0)] = 5;
\r
254 jalview.schemes.ResidueProperties.aaIndex['E'.charCodeAt (0)] = 6;
\r
255 jalview.schemes.ResidueProperties.aaIndex['G'.charCodeAt (0)] = 7;
\r
256 jalview.schemes.ResidueProperties.aaIndex['H'.charCodeAt (0)] = 8;
\r
257 jalview.schemes.ResidueProperties.aaIndex['I'.charCodeAt (0)] = 9;
\r
258 jalview.schemes.ResidueProperties.aaIndex['L'.charCodeAt (0)] = 10;
\r
259 jalview.schemes.ResidueProperties.aaIndex['K'.charCodeAt (0)] = 11;
\r
260 jalview.schemes.ResidueProperties.aaIndex['M'.charCodeAt (0)] = 12;
\r
261 jalview.schemes.ResidueProperties.aaIndex['F'.charCodeAt (0)] = 13;
\r
262 jalview.schemes.ResidueProperties.aaIndex['P'.charCodeAt (0)] = 14;
\r
263 jalview.schemes.ResidueProperties.aaIndex['S'.charCodeAt (0)] = 15;
\r
264 jalview.schemes.ResidueProperties.aaIndex['T'.charCodeAt (0)] = 16;
\r
265 jalview.schemes.ResidueProperties.aaIndex['W'.charCodeAt (0)] = 17;
\r
266 jalview.schemes.ResidueProperties.aaIndex['Y'.charCodeAt (0)] = 18;
\r
267 jalview.schemes.ResidueProperties.aaIndex['V'.charCodeAt (0)] = 19;
\r
268 jalview.schemes.ResidueProperties.aaIndex['B'.charCodeAt (0)] = 20;
\r
269 jalview.schemes.ResidueProperties.aaIndex['Z'.charCodeAt (0)] = 21;
\r
270 jalview.schemes.ResidueProperties.aaIndex['X'.charCodeAt (0)] = 22;
\r
271 jalview.schemes.ResidueProperties.aaIndex['U'.charCodeAt (0)] = 22;
\r
272 jalview.schemes.ResidueProperties.aaIndex['a'.charCodeAt (0)] = 0;
\r
273 jalview.schemes.ResidueProperties.aaIndex['r'.charCodeAt (0)] = 1;
\r
274 jalview.schemes.ResidueProperties.aaIndex['n'.charCodeAt (0)] = 2;
\r
275 jalview.schemes.ResidueProperties.aaIndex['d'.charCodeAt (0)] = 3;
\r
276 jalview.schemes.ResidueProperties.aaIndex['c'.charCodeAt (0)] = 4;
\r
277 jalview.schemes.ResidueProperties.aaIndex['q'.charCodeAt (0)] = 5;
\r
278 jalview.schemes.ResidueProperties.aaIndex['e'.charCodeAt (0)] = 6;
\r
279 jalview.schemes.ResidueProperties.aaIndex['g'.charCodeAt (0)] = 7;
\r
280 jalview.schemes.ResidueProperties.aaIndex['h'.charCodeAt (0)] = 8;
\r
281 jalview.schemes.ResidueProperties.aaIndex['i'.charCodeAt (0)] = 9;
\r
282 jalview.schemes.ResidueProperties.aaIndex['l'.charCodeAt (0)] = 10;
\r
283 jalview.schemes.ResidueProperties.aaIndex['k'.charCodeAt (0)] = 11;
\r
284 jalview.schemes.ResidueProperties.aaIndex['m'.charCodeAt (0)] = 12;
\r
285 jalview.schemes.ResidueProperties.aaIndex['f'.charCodeAt (0)] = 13;
\r
286 jalview.schemes.ResidueProperties.aaIndex['p'.charCodeAt (0)] = 14;
\r
287 jalview.schemes.ResidueProperties.aaIndex['s'.charCodeAt (0)] = 15;
\r
288 jalview.schemes.ResidueProperties.aaIndex['t'.charCodeAt (0)] = 16;
\r
289 jalview.schemes.ResidueProperties.aaIndex['w'.charCodeAt (0)] = 17;
\r
290 jalview.schemes.ResidueProperties.aaIndex['y'.charCodeAt (0)] = 18;
\r
291 jalview.schemes.ResidueProperties.aaIndex['v'.charCodeAt (0)] = 19;
\r
292 jalview.schemes.ResidueProperties.aaIndex['b'.charCodeAt (0)] = 20;
\r
293 jalview.schemes.ResidueProperties.aaIndex['z'.charCodeAt (0)] = 21;
\r
294 jalview.schemes.ResidueProperties.aaIndex['x'.charCodeAt (0)] = 22;
\r
295 jalview.schemes.ResidueProperties.aaIndex['u'.charCodeAt (0)] = 22;
\r
296 }Clazz.defineStatics (c$,
\r
297 "maxProteinIndex", 23,
\r
298 "maxNucleotideIndex", 10);
\r
300 jalview.schemes.ResidueProperties.nucleotideIndex = Clazz.newIntArray (255, 0);
\r
301 for (var i = 0; i < 255; i++) {
\r
302 jalview.schemes.ResidueProperties.nucleotideIndex[i] = 10;
\r
304 jalview.schemes.ResidueProperties.nucleotideIndex['A'.charCodeAt (0)] = 0;
\r
305 jalview.schemes.ResidueProperties.nucleotideIndex['a'.charCodeAt (0)] = 0;
\r
306 jalview.schemes.ResidueProperties.nucleotideIndex['C'.charCodeAt (0)] = 1;
\r
307 jalview.schemes.ResidueProperties.nucleotideIndex['c'.charCodeAt (0)] = 1;
\r
308 jalview.schemes.ResidueProperties.nucleotideIndex['G'.charCodeAt (0)] = 2;
\r
309 jalview.schemes.ResidueProperties.nucleotideIndex['g'.charCodeAt (0)] = 2;
\r
310 jalview.schemes.ResidueProperties.nucleotideIndex['T'.charCodeAt (0)] = 3;
\r
311 jalview.schemes.ResidueProperties.nucleotideIndex['t'.charCodeAt (0)] = 3;
\r
312 jalview.schemes.ResidueProperties.nucleotideIndex['U'.charCodeAt (0)] = 4;
\r
313 jalview.schemes.ResidueProperties.nucleotideIndex['u'.charCodeAt (0)] = 4;
\r
314 jalview.schemes.ResidueProperties.nucleotideIndex['I'.charCodeAt (0)] = 5;
\r
315 jalview.schemes.ResidueProperties.nucleotideIndex['i'.charCodeAt (0)] = 5;
\r
316 jalview.schemes.ResidueProperties.nucleotideIndex['X'.charCodeAt (0)] = 6;
\r
317 jalview.schemes.ResidueProperties.nucleotideIndex['x'.charCodeAt (0)] = 6;
\r
318 jalview.schemes.ResidueProperties.nucleotideIndex['R'.charCodeAt (0)] = 7;
\r
319 jalview.schemes.ResidueProperties.nucleotideIndex['r'.charCodeAt (0)] = 7;
\r
320 jalview.schemes.ResidueProperties.nucleotideIndex['Y'.charCodeAt (0)] = 8;
\r
321 jalview.schemes.ResidueProperties.nucleotideIndex['y'.charCodeAt (0)] = 8;
\r
322 jalview.schemes.ResidueProperties.nucleotideIndex['N'.charCodeAt (0)] = 9;
\r
323 jalview.schemes.ResidueProperties.nucleotideIndex['n'.charCodeAt (0)] = 9;
\r
324 jalview.schemes.ResidueProperties.nucleotideName.put ("A", "Adenine");
\r
325 jalview.schemes.ResidueProperties.nucleotideName.put ("a", "Adenine");
\r
326 jalview.schemes.ResidueProperties.nucleotideName.put ("G", "Guanine");
\r
327 jalview.schemes.ResidueProperties.nucleotideName.put ("g", "Guanine");
\r
328 jalview.schemes.ResidueProperties.nucleotideName.put ("C", "Cytosine");
\r
329 jalview.schemes.ResidueProperties.nucleotideName.put ("c", "Cytosine");
\r
330 jalview.schemes.ResidueProperties.nucleotideName.put ("T", "Thymine");
\r
331 jalview.schemes.ResidueProperties.nucleotideName.put ("t", "Thymine");
\r
332 jalview.schemes.ResidueProperties.nucleotideName.put ("U", "Uracil");
\r
333 jalview.schemes.ResidueProperties.nucleotideName.put ("u", "Uracil");
\r
334 jalview.schemes.ResidueProperties.nucleotideName.put ("I", "Inosine");
\r
335 jalview.schemes.ResidueProperties.nucleotideName.put ("i", "Inosine");
\r
336 jalview.schemes.ResidueProperties.nucleotideName.put ("X", "Xanthine");
\r
337 jalview.schemes.ResidueProperties.nucleotideName.put ("x", "Xanthine");
\r
338 jalview.schemes.ResidueProperties.nucleotideName.put ("R", "Unknown Purine");
\r
339 jalview.schemes.ResidueProperties.nucleotideName.put ("r", "Unknown Purine");
\r
340 jalview.schemes.ResidueProperties.nucleotideName.put ("Y", "Unknown Pyrimidine");
\r
341 jalview.schemes.ResidueProperties.nucleotideName.put ("y", "Unknown Pyrimidine");
\r
342 jalview.schemes.ResidueProperties.nucleotideName.put ("N", "Unknown");
\r
343 jalview.schemes.ResidueProperties.nucleotideName.put ("n", "Unknown");
\r
344 jalview.schemes.ResidueProperties.nucleotideName.put ("W", "Weak nucleotide (A or T)");
\r
345 jalview.schemes.ResidueProperties.nucleotideName.put ("w", "Weak nucleotide (A or T)");
\r
346 jalview.schemes.ResidueProperties.nucleotideName.put ("S", "Strong nucleotide (G or C)");
\r
347 jalview.schemes.ResidueProperties.nucleotideName.put ("s", "Strong nucleotide (G or C)");
\r
348 jalview.schemes.ResidueProperties.nucleotideName.put ("M", "Amino (A or C)");
\r
349 jalview.schemes.ResidueProperties.nucleotideName.put ("m", "Amino (A or C)");
\r
350 jalview.schemes.ResidueProperties.nucleotideName.put ("K", "Keto (G or T)");
\r
351 jalview.schemes.ResidueProperties.nucleotideName.put ("k", "Keto (G or T)");
\r
352 jalview.schemes.ResidueProperties.nucleotideName.put ("B", "Not A (G or C or T)");
\r
353 jalview.schemes.ResidueProperties.nucleotideName.put ("b", "Not A (G or C or T)");
\r
354 jalview.schemes.ResidueProperties.nucleotideName.put ("H", "Not G (A or C or T)");
\r
355 jalview.schemes.ResidueProperties.nucleotideName.put ("h", "Not G (A or C or T)");
\r
356 jalview.schemes.ResidueProperties.nucleotideName.put ("D", "Not C (A or G or T)");
\r
357 jalview.schemes.ResidueProperties.nucleotideName.put ("d", "Not C (A or G or T)");
\r
358 jalview.schemes.ResidueProperties.nucleotideName.put ("V", "Not T (A or G or C");
\r
359 jalview.schemes.ResidueProperties.nucleotideName.put ("v", "Not T (A or G or C");
\r
361 jalview.schemes.ResidueProperties.purinepyrimidineIndex = Clazz.newIntArray (255, 0);
\r
362 for (var i = 0; i < 255; i++) {
\r
363 jalview.schemes.ResidueProperties.purinepyrimidineIndex[i] = 3;
\r
365 jalview.schemes.ResidueProperties.purinepyrimidineIndex['A'.charCodeAt (0)] = 0;
\r
366 jalview.schemes.ResidueProperties.purinepyrimidineIndex['a'.charCodeAt (0)] = 0;
\r
367 jalview.schemes.ResidueProperties.purinepyrimidineIndex['C'.charCodeAt (0)] = 1;
\r
368 jalview.schemes.ResidueProperties.purinepyrimidineIndex['c'.charCodeAt (0)] = 1;
\r
369 jalview.schemes.ResidueProperties.purinepyrimidineIndex['G'.charCodeAt (0)] = 0;
\r
370 jalview.schemes.ResidueProperties.purinepyrimidineIndex['g'.charCodeAt (0)] = 0;
\r
371 jalview.schemes.ResidueProperties.purinepyrimidineIndex['T'.charCodeAt (0)] = 1;
\r
372 jalview.schemes.ResidueProperties.purinepyrimidineIndex['t'.charCodeAt (0)] = 1;
\r
373 jalview.schemes.ResidueProperties.purinepyrimidineIndex['U'.charCodeAt (0)] = 1;
\r
374 jalview.schemes.ResidueProperties.purinepyrimidineIndex['u'.charCodeAt (0)] = 1;
\r
375 jalview.schemes.ResidueProperties.purinepyrimidineIndex['I'.charCodeAt (0)] = 2;
\r
376 jalview.schemes.ResidueProperties.purinepyrimidineIndex['i'.charCodeAt (0)] = 2;
\r
377 jalview.schemes.ResidueProperties.purinepyrimidineIndex['X'.charCodeAt (0)] = 2;
\r
378 jalview.schemes.ResidueProperties.purinepyrimidineIndex['x'.charCodeAt (0)] = 2;
\r
379 jalview.schemes.ResidueProperties.purinepyrimidineIndex['R'.charCodeAt (0)] = 0;
\r
380 jalview.schemes.ResidueProperties.purinepyrimidineIndex['r'.charCodeAt (0)] = 0;
\r
381 jalview.schemes.ResidueProperties.purinepyrimidineIndex['Y'.charCodeAt (0)] = 1;
\r
382 jalview.schemes.ResidueProperties.purinepyrimidineIndex['y'.charCodeAt (0)] = 1;
\r
383 jalview.schemes.ResidueProperties.purinepyrimidineIndex['N'.charCodeAt (0)] = 2;
\r
384 jalview.schemes.ResidueProperties.purinepyrimidineIndex['n'.charCodeAt (0)] = 2;
\r
386 jalview.schemes.ResidueProperties.aa3Hash.put ("ALA", new Integer (0));
\r
387 jalview.schemes.ResidueProperties.aa3Hash.put ("ARG", new Integer (1));
\r
388 jalview.schemes.ResidueProperties.aa3Hash.put ("ASN", new Integer (2));
\r
389 jalview.schemes.ResidueProperties.aa3Hash.put ("ASP", new Integer (3));
\r
390 jalview.schemes.ResidueProperties.aa3Hash.put ("CYS", new Integer (4));
\r
391 jalview.schemes.ResidueProperties.aa3Hash.put ("GLN", new Integer (5));
\r
392 jalview.schemes.ResidueProperties.aa3Hash.put ("GLU", new Integer (6));
\r
393 jalview.schemes.ResidueProperties.aa3Hash.put ("GLY", new Integer (7));
\r
394 jalview.schemes.ResidueProperties.aa3Hash.put ("HIS", new Integer (8));
\r
395 jalview.schemes.ResidueProperties.aa3Hash.put ("ILE", new Integer (9));
\r
396 jalview.schemes.ResidueProperties.aa3Hash.put ("LEU", new Integer (10));
\r
397 jalview.schemes.ResidueProperties.aa3Hash.put ("LYS", new Integer (11));
\r
398 jalview.schemes.ResidueProperties.aa3Hash.put ("MET", new Integer (12));
\r
399 jalview.schemes.ResidueProperties.aa3Hash.put ("PHE", new Integer (13));
\r
400 jalview.schemes.ResidueProperties.aa3Hash.put ("PRO", new Integer (14));
\r
401 jalview.schemes.ResidueProperties.aa3Hash.put ("SER", new Integer (15));
\r
402 jalview.schemes.ResidueProperties.aa3Hash.put ("THR", new Integer (16));
\r
403 jalview.schemes.ResidueProperties.aa3Hash.put ("TRP", new Integer (17));
\r
404 jalview.schemes.ResidueProperties.aa3Hash.put ("TYR", new Integer (18));
\r
405 jalview.schemes.ResidueProperties.aa3Hash.put ("VAL", new Integer (19));
\r
406 jalview.schemes.ResidueProperties.aa3Hash.put ("ASX", new Integer (20));
\r
407 jalview.schemes.ResidueProperties.aa3Hash.put ("GLX", new Integer (21));
\r
408 jalview.schemes.ResidueProperties.aa3Hash.put ("XAA", new Integer (22));
\r
409 jalview.schemes.ResidueProperties.aa3Hash.put ("-", new Integer (23));
\r
410 jalview.schemes.ResidueProperties.aa3Hash.put ("*", new Integer (23));
\r
411 jalview.schemes.ResidueProperties.aa3Hash.put (".", new Integer (23));
\r
412 jalview.schemes.ResidueProperties.aa3Hash.put (" ", new Integer (23));
\r
413 jalview.schemes.ResidueProperties.aa3Hash.put ("Gap", new Integer (23));
\r
415 jalview.schemes.ResidueProperties.aa2Triplet.put ("A", "ALA");
\r
416 jalview.schemes.ResidueProperties.aa2Triplet.put ("a", "ALA");
\r
417 jalview.schemes.ResidueProperties.aa2Triplet.put ("R", "ARG");
\r
418 jalview.schemes.ResidueProperties.aa2Triplet.put ("r", "ARG");
\r
419 jalview.schemes.ResidueProperties.aa2Triplet.put ("N", "ASN");
\r
420 jalview.schemes.ResidueProperties.aa2Triplet.put ("n", "ASN");
\r
421 jalview.schemes.ResidueProperties.aa2Triplet.put ("D", "ASP");
\r
422 jalview.schemes.ResidueProperties.aa2Triplet.put ("d", "ASP");
\r
423 jalview.schemes.ResidueProperties.aa2Triplet.put ("C", "CYS");
\r
424 jalview.schemes.ResidueProperties.aa2Triplet.put ("c", "CYS");
\r
425 jalview.schemes.ResidueProperties.aa2Triplet.put ("Q", "GLN");
\r
426 jalview.schemes.ResidueProperties.aa2Triplet.put ("q", "GLN");
\r
427 jalview.schemes.ResidueProperties.aa2Triplet.put ("E", "GLU");
\r
428 jalview.schemes.ResidueProperties.aa2Triplet.put ("e", "GLU");
\r
429 jalview.schemes.ResidueProperties.aa2Triplet.put ("G", "GLY");
\r
430 jalview.schemes.ResidueProperties.aa2Triplet.put ("g", "GLY");
\r
431 jalview.schemes.ResidueProperties.aa2Triplet.put ("H", "HIS");
\r
432 jalview.schemes.ResidueProperties.aa2Triplet.put ("h", "HIS");
\r
433 jalview.schemes.ResidueProperties.aa2Triplet.put ("I", "ILE");
\r
434 jalview.schemes.ResidueProperties.aa2Triplet.put ("i", "ILE");
\r
435 jalview.schemes.ResidueProperties.aa2Triplet.put ("L", "LEU");
\r
436 jalview.schemes.ResidueProperties.aa2Triplet.put ("l", "LEU");
\r
437 jalview.schemes.ResidueProperties.aa2Triplet.put ("K", "LYS");
\r
438 jalview.schemes.ResidueProperties.aa2Triplet.put ("k", "LYS");
\r
439 jalview.schemes.ResidueProperties.aa2Triplet.put ("M", "MET");
\r
440 jalview.schemes.ResidueProperties.aa2Triplet.put ("m", "MET");
\r
441 jalview.schemes.ResidueProperties.aa2Triplet.put ("F", "PHE");
\r
442 jalview.schemes.ResidueProperties.aa2Triplet.put ("f", "PHE");
\r
443 jalview.schemes.ResidueProperties.aa2Triplet.put ("P", "PRO");
\r
444 jalview.schemes.ResidueProperties.aa2Triplet.put ("p", "PRO");
\r
445 jalview.schemes.ResidueProperties.aa2Triplet.put ("S", "SER");
\r
446 jalview.schemes.ResidueProperties.aa2Triplet.put ("s", "SER");
\r
447 jalview.schemes.ResidueProperties.aa2Triplet.put ("T", "THR");
\r
448 jalview.schemes.ResidueProperties.aa2Triplet.put ("t", "THR");
\r
449 jalview.schemes.ResidueProperties.aa2Triplet.put ("W", "TRP");
\r
450 jalview.schemes.ResidueProperties.aa2Triplet.put ("w", "TRP");
\r
451 jalview.schemes.ResidueProperties.aa2Triplet.put ("Y", "TYR");
\r
452 jalview.schemes.ResidueProperties.aa2Triplet.put ("y", "TYR");
\r
453 jalview.schemes.ResidueProperties.aa2Triplet.put ("V", "VAL");
\r
454 jalview.schemes.ResidueProperties.aa2Triplet.put ("v", "VAL");
\r
455 }Clazz.defineStatics (c$,
\r
456 "aa", Clazz.newArray (-1, ["A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " "]));
\r
457 c$.midBlue = c$.prototype.midBlue = new java.awt.Color (100, 100, 255);
\r
458 c$.scaleColours = c$.prototype.scaleColours = new java.util.Vector ();
\r
460 jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (114, 0, 147));
\r
461 jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (156, 0, 98));
\r
462 jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (190, 0, 0));
\r
463 jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.red);
\r
464 jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (255, 125, 0));
\r
465 jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.orange);
\r
466 jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (255, 194, 85));
\r
467 jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.yellow);
\r
468 jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (255, 255, 181));
\r
469 jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.white);
\r
470 }c$.taylor = c$.prototype.taylor = Clazz.newArray (-1, [ new java.awt.Color (204, 255, 0), new java.awt.Color (0, 0, 255), new java.awt.Color (204, 0, 255), new java.awt.Color (255, 0, 0), new java.awt.Color (255, 255, 0), new java.awt.Color (255, 0, 204), new java.awt.Color (255, 0, 102), new java.awt.Color (255, 153, 0), new java.awt.Color (0, 102, 255), new java.awt.Color (102, 255, 0), new java.awt.Color (51, 255, 0), new java.awt.Color (102, 0, 255), new java.awt.Color (0, 255, 0), new java.awt.Color (0, 255, 102), new java.awt.Color (255, 204, 0), new java.awt.Color (255, 51, 0), new java.awt.Color (255, 102, 0), new java.awt.Color (0, 204, 255), new java.awt.Color (0, 255, 204), new java.awt.Color (153, 255, 0), java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white]);
\r
471 c$.nucleotide = c$.prototype.nucleotide = Clazz.newArray (-1, [ new java.awt.Color (100, 247, 63), new java.awt.Color (255, 179, 64), new java.awt.Color (235, 65, 60), new java.awt.Color (60, 136, 238), new java.awt.Color (60, 136, 238), java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white]);
\r
472 c$.purinepyrimidine = c$.prototype.purinepyrimidine = Clazz.newArray (-1, [ new java.awt.Color (255, 131, 250), new java.awt.Color (64, 224, 208), java.awt.Color.white, java.awt.Color.white]);
\r
473 c$.zappo = c$.prototype.zappo = Clazz.newArray (-1, [java.awt.Color.pink, jalview.schemes.ResidueProperties.midBlue, java.awt.Color.green, java.awt.Color.red, java.awt.Color.yellow, java.awt.Color.green, java.awt.Color.red, java.awt.Color.magenta, jalview.schemes.ResidueProperties.midBlue, java.awt.Color.pink, java.awt.Color.pink, jalview.schemes.ResidueProperties.midBlue, java.awt.Color.pink, java.awt.Color.orange, java.awt.Color.magenta, java.awt.Color.green, java.awt.Color.green, java.awt.Color.orange, java.awt.Color.orange, java.awt.Color.pink, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white]);
\r
474 Clazz.defineStatics (c$,
\r
475 "hyd2", Clazz.newDoubleArray (-1, [0.62, 0.29, -0.9, -0.74, 1.19, 0.48, -0.4, 1.38, -1.5, 1.06, 0.64, -0.78, 0.12, -0.85, -2.53, -0.18, -0.05, 1.08, 0.81, 0.0, 0.26, 0.0, 0.0]),
\r
476 "helix", Clazz.newDoubleArray (-1, [1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16, 1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0]),
\r
479 "strand", Clazz.newDoubleArray (-1, [0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74, 1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0]),
\r
482 "turn", Clazz.newDoubleArray (-1, [0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01, 0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0]),
\r
485 "buried", Clazz.newDoubleArray (-1, [1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2, 0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4, 0.3, 1.358, 0.00]),
\r
488 "hyd", Clazz.newDoubleArray (-1, [1.8, -4.5, -3.5, -3.5, 2.5, -3.5, -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9, 2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0]),
\r
491 "BLOSUM62", Clazz.newArray (-1, [ Clazz.newIntArray (-1, [4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0, -4]), Clazz.newIntArray (-1, [-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1, -4]), Clazz.newIntArray (-1, [-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1, -4]), Clazz.newIntArray (-1, [-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1, -4]), Clazz.newIntArray (-1, [0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2, -4]), Clazz.newIntArray (-1, [-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1, -4]), Clazz.newIntArray (-1, [-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4]), Clazz.newIntArray (-1, [0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1, -4]), Clazz.newIntArray (-1, [-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1, -4]), Clazz.newIntArray (-1, [-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1, -4]), Clazz.newIntArray (-1, [-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1, -4]), Clazz.newIntArray (-1, [-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1, -4]), Clazz.newIntArray (-1, [-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1, -4]), Clazz.newIntArray (-1, [-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1, -4]), Clazz.newIntArray (-1, [-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2, -4]), Clazz.newIntArray (-1, [1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0, -4]), Clazz.newIntArray (-1, [0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0, -4]), Clazz.newIntArray (-1, [-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2, -4]), Clazz.newIntArray (-1, [-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1, -4]), Clazz.newIntArray (-1, [0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1, -4]), Clazz.newIntArray (-1, [-2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1, -4]), Clazz.newIntArray (-1, [-1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4]), Clazz.newIntArray (-1, [0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1, -4]), Clazz.newIntArray (-1, [-4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1])]),
\r
492 "PAM250", Clazz.newArray (-1, [ Clazz.newIntArray (-1, [2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3, 0, 0, 0, 0, -8]), Clazz.newIntArray (-1, [-2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4, -2, -1, 0, -1, -8]), Clazz.newIntArray (-1, [0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2, 2, 1, 0, -8]), Clazz.newIntArray (-1, [0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4, -2, 3, 3, -1, -8]), Clazz.newIntArray (-1, [-2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2, -8, 0, -2, -4, -5, -3, -8]), Clazz.newIntArray (-1, [0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4, -2, 1, 3, -1, -8]), Clazz.newIntArray (-1, [0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4, -2, 3, 3, -1, -8]), Clazz.newIntArray (-1, [1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5, -1, 0, 0, -1, -8]), Clazz.newIntArray (-1, [-1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0, -2, 1, 2, -1, -8]), Clazz.newIntArray (-1, [-1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5, -1, 4, -2, -2, -1, -8]), Clazz.newIntArray (-1, [-2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2, -1, 2, -3, -3, -1, -8]), Clazz.newIntArray (-1, [-1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4, -2, 1, 0, -1, -8]), Clazz.newIntArray (-1, [-1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4, -2, 2, -2, -2, -1, -8]), Clazz.newIntArray (-1, [-3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0, 7, -1, -4, -5, -2, -8]), Clazz.newIntArray (-1, [1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5, -1, -1, 0, -1, -8]), Clazz.newIntArray (-1, [1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3, -1, 0, 0, 0, -8]), Clazz.newIntArray (-1, [1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3, 0, 0, -1, 0, -8]), Clazz.newIntArray (-1, [-6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5, 17, 0, -6, -5, -6, -4, -8]), Clazz.newIntArray (-1, [-3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0, 10, -2, -3, -4, -2, -8]), Clazz.newIntArray (-1, [0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6, -2, 4, -2, -2, -1, -8]), Clazz.newIntArray (-1, [0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3, -2, 3, 2, -1, -8]), Clazz.newIntArray (-1, [0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4, -2, 2, 3, -1, -8]), Clazz.newIntArray (-1, [0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4, -2, -1, -1, -1, -1, -8]), Clazz.newIntArray (-1, [-8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, 1])]));
\r
493 c$.ssHash = c$.prototype.ssHash = new java.util.Hashtable ();
\r
495 jalview.schemes.ResidueProperties.ssHash.put ("H", java.awt.Color.magenta);
\r
496 jalview.schemes.ResidueProperties.ssHash.put ("E", java.awt.Color.yellow);
\r
497 jalview.schemes.ResidueProperties.ssHash.put ("-", java.awt.Color.white);
\r
498 jalview.schemes.ResidueProperties.ssHash.put (".", java.awt.Color.white);
\r
499 jalview.schemes.ResidueProperties.ssHash.put ("S", java.awt.Color.cyan);
\r
500 jalview.schemes.ResidueProperties.ssHash.put ("T", java.awt.Color.blue);
\r
501 jalview.schemes.ResidueProperties.ssHash.put ("G", java.awt.Color.pink);
\r
502 jalview.schemes.ResidueProperties.ssHash.put ("I", java.awt.Color.pink);
\r
503 jalview.schemes.ResidueProperties.ssHash.put ("B", java.awt.Color.yellow);
\r
504 }Clazz.defineStatics (c$,
\r
505 "DNA", Clazz.newArray (-1, [ Clazz.newIntArray (-1, [10, -8, -8, -8, -8, 1, 1, 1, -8, 1, 1]), Clazz.newIntArray (-1, [-8, 10, -8, -8, -8, 1, 1, -8, 1, 1, 1]), Clazz.newIntArray (-1, [-8, -8, 10, -8, -8, 1, 1, 1, -8, 1, 1]), Clazz.newIntArray (-1, [-8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1]), Clazz.newIntArray (-1, [-8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1]), Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 10, 0, 0, 0, 1, 1]), Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 0, 10, 0, 0, 1, 1]), Clazz.newIntArray (-1, [1, -8, 1, -8, -8, 0, 0, 10, -8, 1, 1]), Clazz.newIntArray (-1, [-8, 1, -8, 1, 1, 0, 0, -8, 10, 1, 1]), Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 1]), Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1])]));
\r
507 jalview.schemes.ResidueProperties.scoreMatrices.put ("BLOSUM62", new jalview.schemes.ScoreMatrix ("BLOSUM62", jalview.schemes.ResidueProperties.BLOSUM62, 0));
\r
508 jalview.schemes.ResidueProperties.scoreMatrices.put ("PAM250", new jalview.schemes.ScoreMatrix ("PAM250", jalview.schemes.ResidueProperties.PAM250, 0));
\r
509 jalview.schemes.ResidueProperties.scoreMatrices.put ("DNA", new jalview.schemes.ScoreMatrix ("DNA", jalview.schemes.ResidueProperties.DNA, 1));
\r
510 }c$.pidColours = c$.prototype.pidColours = Clazz.newArray (-1, [jalview.schemes.ResidueProperties.midBlue, new java.awt.Color (153, 153, 255), new java.awt.Color (204, 204, 255)]);
\r
511 Clazz.defineStatics (c$,
\r
512 "pidThresholds", Clazz.newFloatArray (-1, [80, 60, 40]));
\r
513 c$.codonHash = c$.prototype.codonHash = new java.util.HashMap ();
\r
514 c$.Lys = c$.prototype.Lys = new java.util.ArrayList ();
\r
515 c$.Asn = c$.prototype.Asn = new java.util.ArrayList ();
\r
516 c$.Gln = c$.prototype.Gln = new java.util.ArrayList ();
\r
517 c$.His = c$.prototype.His = new java.util.ArrayList ();
\r
518 c$.Glu = c$.prototype.Glu = new java.util.ArrayList ();
\r
519 c$.Asp = c$.prototype.Asp = new java.util.ArrayList ();
\r
520 c$.Tyr = c$.prototype.Tyr = new java.util.ArrayList ();
\r
521 c$.Thr = c$.prototype.Thr = new java.util.ArrayList ();
\r
522 c$.Pro = c$.prototype.Pro = new java.util.ArrayList ();
\r
523 c$.Ala = c$.prototype.Ala = new java.util.ArrayList ();
\r
524 c$.Ser = c$.prototype.Ser = new java.util.ArrayList ();
\r
525 c$.Arg = c$.prototype.Arg = new java.util.ArrayList ();
\r
526 c$.Gly = c$.prototype.Gly = new java.util.ArrayList ();
\r
527 c$.Trp = c$.prototype.Trp = new java.util.ArrayList ();
\r
528 c$.Cys = c$.prototype.Cys = new java.util.ArrayList ();
\r
529 c$.Ile = c$.prototype.Ile = new java.util.ArrayList ();
\r
530 c$.Met = c$.prototype.Met = new java.util.ArrayList ();
\r
531 c$.Leu = c$.prototype.Leu = new java.util.ArrayList ();
\r
532 c$.Val = c$.prototype.Val = new java.util.ArrayList ();
\r
533 c$.Phe = c$.prototype.Phe = new java.util.ArrayList ();
\r
534 c$.STOP = c$.prototype.STOP = new java.util.ArrayList ();
\r
535 Clazz.defineStatics (c$,
\r
538 jalview.schemes.ResidueProperties.codonHash.put ("K", jalview.schemes.ResidueProperties.Lys);
\r
539 jalview.schemes.ResidueProperties.codonHash.put ("N", jalview.schemes.ResidueProperties.Asn);
\r
540 jalview.schemes.ResidueProperties.codonHash.put ("Q", jalview.schemes.ResidueProperties.Gln);
\r
541 jalview.schemes.ResidueProperties.codonHash.put ("H", jalview.schemes.ResidueProperties.His);
\r
542 jalview.schemes.ResidueProperties.codonHash.put ("E", jalview.schemes.ResidueProperties.Glu);
\r
543 jalview.schemes.ResidueProperties.codonHash.put ("D", jalview.schemes.ResidueProperties.Asp);
\r
544 jalview.schemes.ResidueProperties.codonHash.put ("Y", jalview.schemes.ResidueProperties.Tyr);
\r
545 jalview.schemes.ResidueProperties.codonHash.put ("T", jalview.schemes.ResidueProperties.Thr);
\r
546 jalview.schemes.ResidueProperties.codonHash.put ("P", jalview.schemes.ResidueProperties.Pro);
\r
547 jalview.schemes.ResidueProperties.codonHash.put ("A", jalview.schemes.ResidueProperties.Ala);
\r
548 jalview.schemes.ResidueProperties.codonHash.put ("S", jalview.schemes.ResidueProperties.Ser);
\r
549 jalview.schemes.ResidueProperties.codonHash.put ("R", jalview.schemes.ResidueProperties.Arg);
\r
550 jalview.schemes.ResidueProperties.codonHash.put ("G", jalview.schemes.ResidueProperties.Gly);
\r
551 jalview.schemes.ResidueProperties.codonHash.put ("W", jalview.schemes.ResidueProperties.Trp);
\r
552 jalview.schemes.ResidueProperties.codonHash.put ("C", jalview.schemes.ResidueProperties.Cys);
\r
553 jalview.schemes.ResidueProperties.codonHash.put ("I", jalview.schemes.ResidueProperties.Ile);
\r
554 jalview.schemes.ResidueProperties.codonHash.put ("M", jalview.schemes.ResidueProperties.Met);
\r
555 jalview.schemes.ResidueProperties.codonHash.put ("L", jalview.schemes.ResidueProperties.Leu);
\r
556 jalview.schemes.ResidueProperties.codonHash.put ("V", jalview.schemes.ResidueProperties.Val);
\r
557 jalview.schemes.ResidueProperties.codonHash.put ("F", jalview.schemes.ResidueProperties.Phe);
\r
558 jalview.schemes.ResidueProperties.codonHash.put ("STOP", jalview.schemes.ResidueProperties.STOP);
\r
559 }c$.ambiguityCodes = c$.prototype.ambiguityCodes = new java.util.Hashtable ();
\r
560 c$.codonHash2 = c$.prototype.codonHash2 = new java.util.Hashtable ();
\r
561 c$._ambiguityCodes = c$.prototype._ambiguityCodes = new java.util.Hashtable ();
\r
563 jalview.schemes.ResidueProperties.ambiguityCodes.put ("R", Clazz.newArray (-1, ["A", "G"]));
\r
564 jalview.schemes.ResidueProperties.ambiguityCodes.put ("Y", Clazz.newArray (-1, ["T", "C"]));
\r
565 jalview.schemes.ResidueProperties.ambiguityCodes.put ("W", Clazz.newArray (-1, ["A", "T"]));
\r
566 jalview.schemes.ResidueProperties.ambiguityCodes.put ("S", Clazz.newArray (-1, ["G", "C"]));
\r
567 jalview.schemes.ResidueProperties.ambiguityCodes.put ("M", Clazz.newArray (-1, ["A", "C"]));
\r
568 jalview.schemes.ResidueProperties.ambiguityCodes.put ("K", Clazz.newArray (-1, ["G", "T"]));
\r
569 jalview.schemes.ResidueProperties.ambiguityCodes.put ("H", Clazz.newArray (-1, ["A", "T", "C"]));
\r
570 jalview.schemes.ResidueProperties.ambiguityCodes.put ("B", Clazz.newArray (-1, ["G", "T", "C"]));
\r
571 jalview.schemes.ResidueProperties.ambiguityCodes.put ("V", Clazz.newArray (-1, ["G", "A", "C"]));
\r
572 jalview.schemes.ResidueProperties.ambiguityCodes.put ("D", Clazz.newArray (-1, ["G", "A", "T"]));
\r
573 jalview.schemes.ResidueProperties.ambiguityCodes.put ("N", Clazz.newArray (-1, ["G", "A", "T", "C"]));
\r
574 jalview.schemes.ResidueProperties.codonHash2.put ("AAA", "K");
\r
575 jalview.schemes.ResidueProperties.codonHash2.put ("AAG", "K");
\r
576 jalview.schemes.ResidueProperties.codonHash2.put ("AAC", "N");
\r
577 jalview.schemes.ResidueProperties.codonHash2.put ("AAT", "N");
\r
578 jalview.schemes.ResidueProperties.codonHash2.put ("CAA", "Q");
\r
579 jalview.schemes.ResidueProperties.codonHash2.put ("CAG", "Q");
\r
580 jalview.schemes.ResidueProperties.codonHash2.put ("CAC", "H");
\r
581 jalview.schemes.ResidueProperties.codonHash2.put ("CAT", "H");
\r
582 jalview.schemes.ResidueProperties.codonHash2.put ("GAA", "E");
\r
583 jalview.schemes.ResidueProperties.codonHash2.put ("GAG", "E");
\r
584 jalview.schemes.ResidueProperties.codonHash2.put ("GAC", "D");
\r
585 jalview.schemes.ResidueProperties.codonHash2.put ("GAT", "D");
\r
586 jalview.schemes.ResidueProperties.codonHash2.put ("TAC", "Y");
\r
587 jalview.schemes.ResidueProperties.codonHash2.put ("TAT", "Y");
\r
588 jalview.schemes.ResidueProperties.codonHash2.put ("ACA", "T");
\r
589 jalview.schemes.ResidueProperties.codonHash2.put ("ACC", "T");
\r
590 jalview.schemes.ResidueProperties.codonHash2.put ("ACT", "T");
\r
591 jalview.schemes.ResidueProperties.codonHash2.put ("ACG", "T");
\r
592 jalview.schemes.ResidueProperties.codonHash2.put ("CCA", "P");
\r
593 jalview.schemes.ResidueProperties.codonHash2.put ("CCG", "P");
\r
594 jalview.schemes.ResidueProperties.codonHash2.put ("CCC", "P");
\r
595 jalview.schemes.ResidueProperties.codonHash2.put ("CCT", "P");
\r
596 jalview.schemes.ResidueProperties.codonHash2.put ("GCA", "A");
\r
597 jalview.schemes.ResidueProperties.codonHash2.put ("GCG", "A");
\r
598 jalview.schemes.ResidueProperties.codonHash2.put ("GCC", "A");
\r
599 jalview.schemes.ResidueProperties.codonHash2.put ("GCT", "A");
\r
600 jalview.schemes.ResidueProperties.codonHash2.put ("TCA", "S");
\r
601 jalview.schemes.ResidueProperties.codonHash2.put ("TCG", "S");
\r
602 jalview.schemes.ResidueProperties.codonHash2.put ("TCC", "S");
\r
603 jalview.schemes.ResidueProperties.codonHash2.put ("TCT", "S");
\r
604 jalview.schemes.ResidueProperties.codonHash2.put ("AGC", "S");
\r
605 jalview.schemes.ResidueProperties.codonHash2.put ("AGT", "S");
\r
606 jalview.schemes.ResidueProperties.codonHash2.put ("AGA", "R");
\r
607 jalview.schemes.ResidueProperties.codonHash2.put ("AGG", "R");
\r
608 jalview.schemes.ResidueProperties.codonHash2.put ("CGA", "R");
\r
609 jalview.schemes.ResidueProperties.codonHash2.put ("CGG", "R");
\r
610 jalview.schemes.ResidueProperties.codonHash2.put ("CGC", "R");
\r
611 jalview.schemes.ResidueProperties.codonHash2.put ("CGT", "R");
\r
612 jalview.schemes.ResidueProperties.codonHash2.put ("GGA", "G");
\r
613 jalview.schemes.ResidueProperties.codonHash2.put ("GGG", "G");
\r
614 jalview.schemes.ResidueProperties.codonHash2.put ("GGC", "G");
\r
615 jalview.schemes.ResidueProperties.codonHash2.put ("GGT", "G");
\r
616 jalview.schemes.ResidueProperties.codonHash2.put ("TGA", "*");
\r
617 jalview.schemes.ResidueProperties.codonHash2.put ("TAA", "*");
\r
618 jalview.schemes.ResidueProperties.codonHash2.put ("TAG", "*");
\r
619 jalview.schemes.ResidueProperties.codonHash2.put ("TGG", "W");
\r
620 jalview.schemes.ResidueProperties.codonHash2.put ("TGC", "C");
\r
621 jalview.schemes.ResidueProperties.codonHash2.put ("TGT", "C");
\r
622 jalview.schemes.ResidueProperties.codonHash2.put ("ATA", "I");
\r
623 jalview.schemes.ResidueProperties.codonHash2.put ("ATC", "I");
\r
624 jalview.schemes.ResidueProperties.codonHash2.put ("ATT", "I");
\r
625 jalview.schemes.ResidueProperties.codonHash2.put ("ATG", "M");
\r
626 jalview.schemes.ResidueProperties.codonHash2.put ("CTA", "L");
\r
627 jalview.schemes.ResidueProperties.codonHash2.put ("CTG", "L");
\r
628 jalview.schemes.ResidueProperties.codonHash2.put ("CTC", "L");
\r
629 jalview.schemes.ResidueProperties.codonHash2.put ("CTT", "L");
\r
630 jalview.schemes.ResidueProperties.codonHash2.put ("TTA", "L");
\r
631 jalview.schemes.ResidueProperties.codonHash2.put ("TTG", "L");
\r
632 jalview.schemes.ResidueProperties.codonHash2.put ("GTA", "V");
\r
633 jalview.schemes.ResidueProperties.codonHash2.put ("GTG", "V");
\r
634 jalview.schemes.ResidueProperties.codonHash2.put ("GTC", "V");
\r
635 jalview.schemes.ResidueProperties.codonHash2.put ("GTT", "V");
\r
636 jalview.schemes.ResidueProperties.codonHash2.put ("TTC", "F");
\r
637 jalview.schemes.ResidueProperties.codonHash2.put ("TTT", "F");
\r
638 jalview.schemes.ResidueProperties.buildAmbiguityCodonSet ();
\r
640 jalview.schemes.ResidueProperties.Lys.add ("AAA");
\r
641 jalview.schemes.ResidueProperties.Lys.add ("AAG");
\r
642 jalview.schemes.ResidueProperties.Asn.add ("AAC");
\r
643 jalview.schemes.ResidueProperties.Asn.add ("AAT");
\r
644 jalview.schemes.ResidueProperties.Gln.add ("CAA");
\r
645 jalview.schemes.ResidueProperties.Gln.add ("CAG");
\r
646 jalview.schemes.ResidueProperties.His.add ("CAC");
\r
647 jalview.schemes.ResidueProperties.His.add ("CAT");
\r
648 jalview.schemes.ResidueProperties.Glu.add ("GAA");
\r
649 jalview.schemes.ResidueProperties.Glu.add ("GAG");
\r
650 jalview.schemes.ResidueProperties.Asp.add ("GAC");
\r
651 jalview.schemes.ResidueProperties.Asp.add ("GAT");
\r
652 jalview.schemes.ResidueProperties.Tyr.add ("TAC");
\r
653 jalview.schemes.ResidueProperties.Tyr.add ("TAT");
\r
654 jalview.schemes.ResidueProperties.Thr.add ("ACA");
\r
655 jalview.schemes.ResidueProperties.Thr.add ("ACG");
\r
656 jalview.schemes.ResidueProperties.Thr.add ("ACC");
\r
657 jalview.schemes.ResidueProperties.Thr.add ("ACT");
\r
658 jalview.schemes.ResidueProperties.Pro.add ("CCA");
\r
659 jalview.schemes.ResidueProperties.Pro.add ("CCG");
\r
660 jalview.schemes.ResidueProperties.Pro.add ("CCC");
\r
661 jalview.schemes.ResidueProperties.Pro.add ("CCT");
\r
662 jalview.schemes.ResidueProperties.Ala.add ("GCA");
\r
663 jalview.schemes.ResidueProperties.Ala.add ("GCG");
\r
664 jalview.schemes.ResidueProperties.Ala.add ("GCC");
\r
665 jalview.schemes.ResidueProperties.Ala.add ("GCT");
\r
666 jalview.schemes.ResidueProperties.Ser.add ("TCA");
\r
667 jalview.schemes.ResidueProperties.Ser.add ("TCG");
\r
668 jalview.schemes.ResidueProperties.Ser.add ("TCC");
\r
669 jalview.schemes.ResidueProperties.Ser.add ("TCT");
\r
670 jalview.schemes.ResidueProperties.Ser.add ("AGC");
\r
671 jalview.schemes.ResidueProperties.Ser.add ("AGT");
\r
672 jalview.schemes.ResidueProperties.Arg.add ("AGA");
\r
673 jalview.schemes.ResidueProperties.Arg.add ("AGG");
\r
674 jalview.schemes.ResidueProperties.Arg.add ("CGA");
\r
675 jalview.schemes.ResidueProperties.Arg.add ("CGG");
\r
676 jalview.schemes.ResidueProperties.Arg.add ("CGC");
\r
677 jalview.schemes.ResidueProperties.Arg.add ("CGT");
\r
678 jalview.schemes.ResidueProperties.Gly.add ("GGA");
\r
679 jalview.schemes.ResidueProperties.Gly.add ("GGG");
\r
680 jalview.schemes.ResidueProperties.Gly.add ("GGC");
\r
681 jalview.schemes.ResidueProperties.Gly.add ("GGT");
\r
682 jalview.schemes.ResidueProperties.STOP.add ("TGA");
\r
683 jalview.schemes.ResidueProperties.STOP.add ("TAA");
\r
684 jalview.schemes.ResidueProperties.STOP.add ("TAG");
\r
685 jalview.schemes.ResidueProperties.Trp.add ("TGG");
\r
686 jalview.schemes.ResidueProperties.Cys.add ("TGC");
\r
687 jalview.schemes.ResidueProperties.Cys.add ("TGT");
\r
688 jalview.schemes.ResidueProperties.Ile.add ("ATA");
\r
689 jalview.schemes.ResidueProperties.Ile.add ("ATC");
\r
690 jalview.schemes.ResidueProperties.Ile.add ("ATT");
\r
691 jalview.schemes.ResidueProperties.Met.add ("ATG");
\r
692 jalview.schemes.ResidueProperties.Leu.add ("CTA");
\r
693 jalview.schemes.ResidueProperties.Leu.add ("CTG");
\r
694 jalview.schemes.ResidueProperties.Leu.add ("CTC");
\r
695 jalview.schemes.ResidueProperties.Leu.add ("CTT");
\r
696 jalview.schemes.ResidueProperties.Leu.add ("TTA");
\r
697 jalview.schemes.ResidueProperties.Leu.add ("TTG");
\r
698 jalview.schemes.ResidueProperties.Val.add ("GTA");
\r
699 jalview.schemes.ResidueProperties.Val.add ("GTG");
\r
700 jalview.schemes.ResidueProperties.Val.add ("GTC");
\r
701 jalview.schemes.ResidueProperties.Val.add ("GTT");
\r
702 jalview.schemes.ResidueProperties.Phe.add ("TTC");
\r
703 jalview.schemes.ResidueProperties.Phe.add ("TTT");
\r
704 }c$.propHash = c$.prototype.propHash = new java.util.Hashtable ();
\r
705 c$.hydrophobic = c$.prototype.hydrophobic = new java.util.Hashtable ();
\r
706 c$.polar = c$.prototype.polar = new java.util.Hashtable ();
\r
707 c$.small = c$.prototype.small = new java.util.Hashtable ();
\r
708 c$.positive = c$.prototype.positive = new java.util.Hashtable ();
\r
709 c$.negative = c$.prototype.negative = new java.util.Hashtable ();
\r
710 c$.charged = c$.prototype.charged = new java.util.Hashtable ();
\r
711 c$.aromatic = c$.prototype.aromatic = new java.util.Hashtable ();
\r
712 c$.aliphatic = c$.prototype.aliphatic = new java.util.Hashtable ();
\r
713 c$.tiny = c$.prototype.tiny = new java.util.Hashtable ();
\r
714 c$.proline = c$.prototype.proline = new java.util.Hashtable ();
\r
716 jalview.schemes.ResidueProperties.hydrophobic.put ("I", new Integer (1));
\r
717 jalview.schemes.ResidueProperties.hydrophobic.put ("L", new Integer (1));
\r
718 jalview.schemes.ResidueProperties.hydrophobic.put ("V", new Integer (1));
\r
719 jalview.schemes.ResidueProperties.hydrophobic.put ("C", new Integer (1));
\r
720 jalview.schemes.ResidueProperties.hydrophobic.put ("A", new Integer (1));
\r
721 jalview.schemes.ResidueProperties.hydrophobic.put ("G", new Integer (1));
\r
722 jalview.schemes.ResidueProperties.hydrophobic.put ("M", new Integer (1));
\r
723 jalview.schemes.ResidueProperties.hydrophobic.put ("F", new Integer (1));
\r
724 jalview.schemes.ResidueProperties.hydrophobic.put ("Y", new Integer (1));
\r
725 jalview.schemes.ResidueProperties.hydrophobic.put ("W", new Integer (1));
\r
726 jalview.schemes.ResidueProperties.hydrophobic.put ("H", new Integer (1));
\r
727 jalview.schemes.ResidueProperties.hydrophobic.put ("K", new Integer (1));
\r
728 jalview.schemes.ResidueProperties.hydrophobic.put ("X", new Integer (1));
\r
729 jalview.schemes.ResidueProperties.hydrophobic.put ("-", new Integer (1));
\r
730 jalview.schemes.ResidueProperties.hydrophobic.put ("*", new Integer (1));
\r
731 jalview.schemes.ResidueProperties.hydrophobic.put ("R", new Integer (0));
\r
732 jalview.schemes.ResidueProperties.hydrophobic.put ("E", new Integer (0));
\r
733 jalview.schemes.ResidueProperties.hydrophobic.put ("Q", new Integer (0));
\r
734 jalview.schemes.ResidueProperties.hydrophobic.put ("D", new Integer (0));
\r
735 jalview.schemes.ResidueProperties.hydrophobic.put ("N", new Integer (0));
\r
736 jalview.schemes.ResidueProperties.hydrophobic.put ("S", new Integer (0));
\r
737 jalview.schemes.ResidueProperties.hydrophobic.put ("T", new Integer (0));
\r
738 jalview.schemes.ResidueProperties.hydrophobic.put ("P", new Integer (0));
\r
740 jalview.schemes.ResidueProperties.polar.put ("Y", new Integer (1));
\r
741 jalview.schemes.ResidueProperties.polar.put ("W", new Integer (1));
\r
742 jalview.schemes.ResidueProperties.polar.put ("H", new Integer (1));
\r
743 jalview.schemes.ResidueProperties.polar.put ("K", new Integer (1));
\r
744 jalview.schemes.ResidueProperties.polar.put ("R", new Integer (1));
\r
745 jalview.schemes.ResidueProperties.polar.put ("E", new Integer (1));
\r
746 jalview.schemes.ResidueProperties.polar.put ("Q", new Integer (1));
\r
747 jalview.schemes.ResidueProperties.polar.put ("D", new Integer (1));
\r
748 jalview.schemes.ResidueProperties.polar.put ("N", new Integer (1));
\r
749 jalview.schemes.ResidueProperties.polar.put ("S", new Integer (1));
\r
750 jalview.schemes.ResidueProperties.polar.put ("T", new Integer (1));
\r
751 jalview.schemes.ResidueProperties.polar.put ("X", new Integer (1));
\r
752 jalview.schemes.ResidueProperties.polar.put ("-", new Integer (1));
\r
753 jalview.schemes.ResidueProperties.polar.put ("*", new Integer (1));
\r
754 jalview.schemes.ResidueProperties.polar.put ("I", new Integer (0));
\r
755 jalview.schemes.ResidueProperties.polar.put ("L", new Integer (0));
\r
756 jalview.schemes.ResidueProperties.polar.put ("V", new Integer (0));
\r
757 jalview.schemes.ResidueProperties.polar.put ("C", new Integer (0));
\r
758 jalview.schemes.ResidueProperties.polar.put ("A", new Integer (0));
\r
759 jalview.schemes.ResidueProperties.polar.put ("G", new Integer (0));
\r
760 jalview.schemes.ResidueProperties.polar.put ("M", new Integer (0));
\r
761 jalview.schemes.ResidueProperties.polar.put ("F", new Integer (0));
\r
762 jalview.schemes.ResidueProperties.polar.put ("P", new Integer (0));
\r
764 jalview.schemes.ResidueProperties.small.put ("I", new Integer (0));
\r
765 jalview.schemes.ResidueProperties.small.put ("L", new Integer (0));
\r
766 jalview.schemes.ResidueProperties.small.put ("V", new Integer (1));
\r
767 jalview.schemes.ResidueProperties.small.put ("C", new Integer (1));
\r
768 jalview.schemes.ResidueProperties.small.put ("A", new Integer (1));
\r
769 jalview.schemes.ResidueProperties.small.put ("G", new Integer (1));
\r
770 jalview.schemes.ResidueProperties.small.put ("M", new Integer (0));
\r
771 jalview.schemes.ResidueProperties.small.put ("F", new Integer (0));
\r
772 jalview.schemes.ResidueProperties.small.put ("Y", new Integer (0));
\r
773 jalview.schemes.ResidueProperties.small.put ("W", new Integer (0));
\r
774 jalview.schemes.ResidueProperties.small.put ("H", new Integer (0));
\r
775 jalview.schemes.ResidueProperties.small.put ("K", new Integer (0));
\r
776 jalview.schemes.ResidueProperties.small.put ("R", new Integer (0));
\r
777 jalview.schemes.ResidueProperties.small.put ("E", new Integer (0));
\r
778 jalview.schemes.ResidueProperties.small.put ("Q", new Integer (0));
\r
779 jalview.schemes.ResidueProperties.small.put ("D", new Integer (1));
\r
780 jalview.schemes.ResidueProperties.small.put ("N", new Integer (1));
\r
781 jalview.schemes.ResidueProperties.small.put ("S", new Integer (1));
\r
782 jalview.schemes.ResidueProperties.small.put ("T", new Integer (1));
\r
783 jalview.schemes.ResidueProperties.small.put ("P", new Integer (1));
\r
784 jalview.schemes.ResidueProperties.small.put ("-", new Integer (1));
\r
785 jalview.schemes.ResidueProperties.small.put ("*", new Integer (1));
\r
787 jalview.schemes.ResidueProperties.positive.put ("I", new Integer (0));
\r
788 jalview.schemes.ResidueProperties.positive.put ("L", new Integer (0));
\r
789 jalview.schemes.ResidueProperties.positive.put ("V", new Integer (0));
\r
790 jalview.schemes.ResidueProperties.positive.put ("C", new Integer (0));
\r
791 jalview.schemes.ResidueProperties.positive.put ("A", new Integer (0));
\r
792 jalview.schemes.ResidueProperties.positive.put ("G", new Integer (0));
\r
793 jalview.schemes.ResidueProperties.positive.put ("M", new Integer (0));
\r
794 jalview.schemes.ResidueProperties.positive.put ("F", new Integer (0));
\r
795 jalview.schemes.ResidueProperties.positive.put ("Y", new Integer (0));
\r
796 jalview.schemes.ResidueProperties.positive.put ("W", new Integer (0));
\r
797 jalview.schemes.ResidueProperties.positive.put ("H", new Integer (1));
\r
798 jalview.schemes.ResidueProperties.positive.put ("K", new Integer (1));
\r
799 jalview.schemes.ResidueProperties.positive.put ("R", new Integer (1));
\r
800 jalview.schemes.ResidueProperties.positive.put ("E", new Integer (0));
\r
801 jalview.schemes.ResidueProperties.positive.put ("Q", new Integer (0));
\r
802 jalview.schemes.ResidueProperties.positive.put ("D", new Integer (0));
\r
803 jalview.schemes.ResidueProperties.positive.put ("N", new Integer (0));
\r
804 jalview.schemes.ResidueProperties.positive.put ("S", new Integer (0));
\r
805 jalview.schemes.ResidueProperties.positive.put ("T", new Integer (0));
\r
806 jalview.schemes.ResidueProperties.positive.put ("P", new Integer (0));
\r
807 jalview.schemes.ResidueProperties.positive.put ("-", new Integer (1));
\r
808 jalview.schemes.ResidueProperties.positive.put ("*", new Integer (1));
\r
810 jalview.schemes.ResidueProperties.negative.put ("I", new Integer (0));
\r
811 jalview.schemes.ResidueProperties.negative.put ("L", new Integer (0));
\r
812 jalview.schemes.ResidueProperties.negative.put ("V", new Integer (0));
\r
813 jalview.schemes.ResidueProperties.negative.put ("C", new Integer (0));
\r
814 jalview.schemes.ResidueProperties.negative.put ("A", new Integer (0));
\r
815 jalview.schemes.ResidueProperties.negative.put ("G", new Integer (0));
\r
816 jalview.schemes.ResidueProperties.negative.put ("M", new Integer (0));
\r
817 jalview.schemes.ResidueProperties.negative.put ("F", new Integer (0));
\r
818 jalview.schemes.ResidueProperties.negative.put ("Y", new Integer (0));
\r
819 jalview.schemes.ResidueProperties.negative.put ("W", new Integer (0));
\r
820 jalview.schemes.ResidueProperties.negative.put ("H", new Integer (0));
\r
821 jalview.schemes.ResidueProperties.negative.put ("K", new Integer (0));
\r
822 jalview.schemes.ResidueProperties.negative.put ("R", new Integer (0));
\r
823 jalview.schemes.ResidueProperties.negative.put ("E", new Integer (1));
\r
824 jalview.schemes.ResidueProperties.negative.put ("Q", new Integer (0));
\r
825 jalview.schemes.ResidueProperties.negative.put ("D", new Integer (1));
\r
826 jalview.schemes.ResidueProperties.negative.put ("N", new Integer (0));
\r
827 jalview.schemes.ResidueProperties.negative.put ("S", new Integer (0));
\r
828 jalview.schemes.ResidueProperties.negative.put ("T", new Integer (0));
\r
829 jalview.schemes.ResidueProperties.negative.put ("P", new Integer (0));
\r
830 jalview.schemes.ResidueProperties.negative.put ("-", new Integer (1));
\r
831 jalview.schemes.ResidueProperties.negative.put ("*", new Integer (1));
\r
833 jalview.schemes.ResidueProperties.charged.put ("I", new Integer (0));
\r
834 jalview.schemes.ResidueProperties.charged.put ("L", new Integer (0));
\r
835 jalview.schemes.ResidueProperties.charged.put ("V", new Integer (0));
\r
836 jalview.schemes.ResidueProperties.charged.put ("C", new Integer (0));
\r
837 jalview.schemes.ResidueProperties.charged.put ("A", new Integer (0));
\r
838 jalview.schemes.ResidueProperties.charged.put ("G", new Integer (0));
\r
839 jalview.schemes.ResidueProperties.charged.put ("M", new Integer (0));
\r
840 jalview.schemes.ResidueProperties.charged.put ("F", new Integer (0));
\r
841 jalview.schemes.ResidueProperties.charged.put ("Y", new Integer (0));
\r
842 jalview.schemes.ResidueProperties.charged.put ("W", new Integer (0));
\r
843 jalview.schemes.ResidueProperties.charged.put ("H", new Integer (1));
\r
844 jalview.schemes.ResidueProperties.charged.put ("K", new Integer (1));
\r
845 jalview.schemes.ResidueProperties.charged.put ("R", new Integer (1));
\r
846 jalview.schemes.ResidueProperties.charged.put ("E", new Integer (1));
\r
847 jalview.schemes.ResidueProperties.charged.put ("Q", new Integer (0));
\r
848 jalview.schemes.ResidueProperties.charged.put ("D", new Integer (1));
\r
849 jalview.schemes.ResidueProperties.charged.put ("N", new Integer (0));
\r
850 jalview.schemes.ResidueProperties.charged.put ("S", new Integer (0));
\r
851 jalview.schemes.ResidueProperties.charged.put ("T", new Integer (0));
\r
852 jalview.schemes.ResidueProperties.charged.put ("P", new Integer (0));
\r
853 jalview.schemes.ResidueProperties.charged.put ("-", new Integer (1));
\r
854 jalview.schemes.ResidueProperties.charged.put ("*", new Integer (1));
\r
856 jalview.schemes.ResidueProperties.aromatic.put ("I", new Integer (0));
\r
857 jalview.schemes.ResidueProperties.aromatic.put ("L", new Integer (0));
\r
858 jalview.schemes.ResidueProperties.aromatic.put ("V", new Integer (0));
\r
859 jalview.schemes.ResidueProperties.aromatic.put ("C", new Integer (0));
\r
860 jalview.schemes.ResidueProperties.aromatic.put ("A", new Integer (0));
\r
861 jalview.schemes.ResidueProperties.aromatic.put ("G", new Integer (0));
\r
862 jalview.schemes.ResidueProperties.aromatic.put ("M", new Integer (0));
\r
863 jalview.schemes.ResidueProperties.aromatic.put ("F", new Integer (1));
\r
864 jalview.schemes.ResidueProperties.aromatic.put ("Y", new Integer (1));
\r
865 jalview.schemes.ResidueProperties.aromatic.put ("W", new Integer (1));
\r
866 jalview.schemes.ResidueProperties.aromatic.put ("H", new Integer (1));
\r
867 jalview.schemes.ResidueProperties.aromatic.put ("K", new Integer (0));
\r
868 jalview.schemes.ResidueProperties.aromatic.put ("R", new Integer (0));
\r
869 jalview.schemes.ResidueProperties.aromatic.put ("E", new Integer (0));
\r
870 jalview.schemes.ResidueProperties.aromatic.put ("Q", new Integer (0));
\r
871 jalview.schemes.ResidueProperties.aromatic.put ("D", new Integer (0));
\r
872 jalview.schemes.ResidueProperties.aromatic.put ("N", new Integer (0));
\r
873 jalview.schemes.ResidueProperties.aromatic.put ("S", new Integer (0));
\r
874 jalview.schemes.ResidueProperties.aromatic.put ("T", new Integer (0));
\r
875 jalview.schemes.ResidueProperties.aromatic.put ("P", new Integer (0));
\r
876 jalview.schemes.ResidueProperties.aromatic.put ("-", new Integer (1));
\r
877 jalview.schemes.ResidueProperties.aromatic.put ("*", new Integer (1));
\r
879 jalview.schemes.ResidueProperties.aliphatic.put ("I", new Integer (1));
\r
880 jalview.schemes.ResidueProperties.aliphatic.put ("L", new Integer (1));
\r
881 jalview.schemes.ResidueProperties.aliphatic.put ("V", new Integer (1));
\r
882 jalview.schemes.ResidueProperties.aliphatic.put ("C", new Integer (0));
\r
883 jalview.schemes.ResidueProperties.aliphatic.put ("A", new Integer (0));
\r
884 jalview.schemes.ResidueProperties.aliphatic.put ("G", new Integer (0));
\r
885 jalview.schemes.ResidueProperties.aliphatic.put ("M", new Integer (0));
\r
886 jalview.schemes.ResidueProperties.aliphatic.put ("F", new Integer (0));
\r
887 jalview.schemes.ResidueProperties.aliphatic.put ("Y", new Integer (0));
\r
888 jalview.schemes.ResidueProperties.aliphatic.put ("W", new Integer (0));
\r
889 jalview.schemes.ResidueProperties.aliphatic.put ("H", new Integer (0));
\r
890 jalview.schemes.ResidueProperties.aliphatic.put ("K", new Integer (0));
\r
891 jalview.schemes.ResidueProperties.aliphatic.put ("R", new Integer (0));
\r
892 jalview.schemes.ResidueProperties.aliphatic.put ("E", new Integer (0));
\r
893 jalview.schemes.ResidueProperties.aliphatic.put ("Q", new Integer (0));
\r
894 jalview.schemes.ResidueProperties.aliphatic.put ("D", new Integer (0));
\r
895 jalview.schemes.ResidueProperties.aliphatic.put ("N", new Integer (0));
\r
896 jalview.schemes.ResidueProperties.aliphatic.put ("S", new Integer (0));
\r
897 jalview.schemes.ResidueProperties.aliphatic.put ("T", new Integer (0));
\r
898 jalview.schemes.ResidueProperties.aliphatic.put ("P", new Integer (0));
\r
899 jalview.schemes.ResidueProperties.aliphatic.put ("-", new Integer (1));
\r
900 jalview.schemes.ResidueProperties.aliphatic.put ("*", new Integer (1));
\r
902 jalview.schemes.ResidueProperties.tiny.put ("I", new Integer (0));
\r
903 jalview.schemes.ResidueProperties.tiny.put ("L", new Integer (0));
\r
904 jalview.schemes.ResidueProperties.tiny.put ("V", new Integer (0));
\r
905 jalview.schemes.ResidueProperties.tiny.put ("C", new Integer (0));
\r
906 jalview.schemes.ResidueProperties.tiny.put ("A", new Integer (1));
\r
907 jalview.schemes.ResidueProperties.tiny.put ("G", new Integer (1));
\r
908 jalview.schemes.ResidueProperties.tiny.put ("M", new Integer (0));
\r
909 jalview.schemes.ResidueProperties.tiny.put ("F", new Integer (0));
\r
910 jalview.schemes.ResidueProperties.tiny.put ("Y", new Integer (0));
\r
911 jalview.schemes.ResidueProperties.tiny.put ("W", new Integer (0));
\r
912 jalview.schemes.ResidueProperties.tiny.put ("H", new Integer (0));
\r
913 jalview.schemes.ResidueProperties.tiny.put ("K", new Integer (0));
\r
914 jalview.schemes.ResidueProperties.tiny.put ("R", new Integer (0));
\r
915 jalview.schemes.ResidueProperties.tiny.put ("E", new Integer (0));
\r
916 jalview.schemes.ResidueProperties.tiny.put ("Q", new Integer (0));
\r
917 jalview.schemes.ResidueProperties.tiny.put ("D", new Integer (0));
\r
918 jalview.schemes.ResidueProperties.tiny.put ("N", new Integer (0));
\r
919 jalview.schemes.ResidueProperties.tiny.put ("S", new Integer (1));
\r
920 jalview.schemes.ResidueProperties.tiny.put ("T", new Integer (0));
\r
921 jalview.schemes.ResidueProperties.tiny.put ("P", new Integer (0));
\r
922 jalview.schemes.ResidueProperties.tiny.put ("-", new Integer (1));
\r
923 jalview.schemes.ResidueProperties.tiny.put ("*", new Integer (1));
\r
925 jalview.schemes.ResidueProperties.proline.put ("I", new Integer (0));
\r
926 jalview.schemes.ResidueProperties.proline.put ("L", new Integer (0));
\r
927 jalview.schemes.ResidueProperties.proline.put ("V", new Integer (0));
\r
928 jalview.schemes.ResidueProperties.proline.put ("C", new Integer (0));
\r
929 jalview.schemes.ResidueProperties.proline.put ("A", new Integer (0));
\r
930 jalview.schemes.ResidueProperties.proline.put ("G", new Integer (0));
\r
931 jalview.schemes.ResidueProperties.proline.put ("M", new Integer (0));
\r
932 jalview.schemes.ResidueProperties.proline.put ("F", new Integer (0));
\r
933 jalview.schemes.ResidueProperties.proline.put ("Y", new Integer (0));
\r
934 jalview.schemes.ResidueProperties.proline.put ("W", new Integer (0));
\r
935 jalview.schemes.ResidueProperties.proline.put ("H", new Integer (0));
\r
936 jalview.schemes.ResidueProperties.proline.put ("K", new Integer (0));
\r
937 jalview.schemes.ResidueProperties.proline.put ("R", new Integer (0));
\r
938 jalview.schemes.ResidueProperties.proline.put ("E", new Integer (0));
\r
939 jalview.schemes.ResidueProperties.proline.put ("Q", new Integer (0));
\r
940 jalview.schemes.ResidueProperties.proline.put ("D", new Integer (0));
\r
941 jalview.schemes.ResidueProperties.proline.put ("N", new Integer (0));
\r
942 jalview.schemes.ResidueProperties.proline.put ("S", new Integer (0));
\r
943 jalview.schemes.ResidueProperties.proline.put ("T", new Integer (0));
\r
944 jalview.schemes.ResidueProperties.proline.put ("P", new Integer (1));
\r
945 jalview.schemes.ResidueProperties.proline.put ("-", new Integer (1));
\r
946 jalview.schemes.ResidueProperties.proline.put ("*", new Integer (1));
\r
948 jalview.schemes.ResidueProperties.propHash.put ("hydrophobic", jalview.schemes.ResidueProperties.hydrophobic);
\r
949 jalview.schemes.ResidueProperties.propHash.put ("small", jalview.schemes.ResidueProperties.small);
\r
950 jalview.schemes.ResidueProperties.propHash.put ("positive", jalview.schemes.ResidueProperties.positive);
\r
951 jalview.schemes.ResidueProperties.propHash.put ("negative", jalview.schemes.ResidueProperties.negative);
\r
952 jalview.schemes.ResidueProperties.propHash.put ("charged", jalview.schemes.ResidueProperties.charged);
\r
953 jalview.schemes.ResidueProperties.propHash.put ("aromatic", jalview.schemes.ResidueProperties.aromatic);
\r
954 jalview.schemes.ResidueProperties.propHash.put ("aliphatic", jalview.schemes.ResidueProperties.aliphatic);
\r
955 jalview.schemes.ResidueProperties.propHash.put ("tiny", jalview.schemes.ResidueProperties.tiny);
\r
956 jalview.schemes.ResidueProperties.propHash.put ("proline", jalview.schemes.ResidueProperties.proline);
\r
957 jalview.schemes.ResidueProperties.propHash.put ("polar", jalview.schemes.ResidueProperties.polar);
\r
959 var propMatrixF = Clazz.newIntArray (23, 23, 0);
\r
960 var propMatrixPos = Clazz.newIntArray (23, 23, 0);
\r
961 var propMatrixEpos = Clazz.newIntArray (23, 23, 0);
\r
962 for (var i = 0; i < 23; i++) {
\r
967 if (jalview.schemes.ResidueProperties.aa.length > i) {
\r
968 ic += jalview.schemes.ResidueProperties.aa[i];
\r
971 }for (var j = i + 1; j < 23; j++) {
\r
973 if (jalview.schemes.ResidueProperties.aa.length > j) {
\r
974 jc += jalview.schemes.ResidueProperties.aa[j];
\r
977 }propMatrixF[i][j] = 0;
\r
978 propMatrixPos[i][j] = 0;
\r
979 propMatrixEpos[i][j] = 0;
\r
980 for (var en = jalview.schemes.ResidueProperties.propHash.keys (); en.hasMoreElements (); ) {
\r
981 var ph = en.nextElement ();
\r
982 var pph = jalview.schemes.ResidueProperties.propHash.get (ph);
\r
983 if (pph.get (ic) != null && pph.get (jc) != null) {
\r
984 var icp = pph.get (ic).intValue ();
\r
985 var jcp = pph.get (jc).intValue ();
\r
986 propMatrixPos[i][j] += icp == jcp && icp > 0 ? 2 : 0;
\r
987 propMatrixPos[j][i] += icp == jcp && icp > 0 ? 2 : 0;
\r
988 propMatrixF[i][j] += icp == jcp ? 2 : 0;
\r
989 propMatrixF[j][i] += icp == jcp ? 2 : 0;
\r
990 propMatrixEpos[i][j] += icp == jcp ? (1 + icp * 2) : 0;
\r
991 propMatrixEpos[j][i] += icp == jcp ? (1 + icp * 2) : 0;
\r
993 if (maxF < propMatrixF[i][j]) {
\r
994 maxF = propMatrixF[i][j];
\r
995 }if (maxP < propMatrixPos[i][j]) {
\r
996 maxP = propMatrixPos[i][j];
\r
997 }if (maxEP < propMatrixEpos[i][j]) {
\r
998 maxEP = propMatrixEpos[i][j];
\r
1000 propMatrixF[i][i] = maxF;
\r
1001 propMatrixPos[i][i] = maxP;
\r
1002 propMatrixEpos[i][i] = maxEP;
\r
1004 jalview.schemes.ResidueProperties.scoreMatrices.put ("PID", new jalview.analysis.scoremodels.PIDScoreModel ());
\r
1005 jalview.schemes.ResidueProperties.scoreMatrices.put ("Displayed Features", new jalview.analysis.scoremodels.FeatureScoreModel ());
\r
1006 }Clazz.defineStatics (c$,
\r
1007 "toDssp3State", null);
\r
1009 jalview.schemes.ResidueProperties.toDssp3State = new java.util.Hashtable ();
\r
1010 jalview.schemes.ResidueProperties.toDssp3State.put ("H", "H");
\r
1011 jalview.schemes.ResidueProperties.toDssp3State.put ("E", "E");
\r
1012 jalview.schemes.ResidueProperties.toDssp3State.put ("C", " ");
\r
1013 jalview.schemes.ResidueProperties.toDssp3State.put (" ", " ");
\r
1014 jalview.schemes.ResidueProperties.toDssp3State.put ("T", " ");
\r
1015 jalview.schemes.ResidueProperties.toDssp3State.put ("B", "E");
\r
1016 jalview.schemes.ResidueProperties.toDssp3State.put ("G", "H");
\r
1017 jalview.schemes.ResidueProperties.toDssp3State.put ("I", "H");
\r
1018 jalview.schemes.ResidueProperties.toDssp3State.put ("X", " ");
\r
1019 }Clazz.defineStatics (c$,
\r
1020 "toRNAssState", null,
\r
1021 "RNAcloseParen", Clazz.newBooleanArray (255, false));
\r
1023 jalview.schemes.ResidueProperties.toRNAssState = new java.util.Hashtable ();
\r
1024 jalview.schemes.ResidueProperties.toRNAssState.put (")", "(");
\r
1025 jalview.schemes.ResidueProperties.toRNAssState.put ("(", "(");
\r
1026 jalview.schemes.ResidueProperties.toRNAssState.put ("]", "[");
\r
1027 jalview.schemes.ResidueProperties.toRNAssState.put ("[", "[");
\r
1028 jalview.schemes.ResidueProperties.toRNAssState.put ("{", "{");
\r
1029 jalview.schemes.ResidueProperties.toRNAssState.put ("}", "{");
\r
1030 jalview.schemes.ResidueProperties.toRNAssState.put (">", ">");
\r
1031 jalview.schemes.ResidueProperties.toRNAssState.put ("<", ">");
\r
1032 jalview.schemes.ResidueProperties.toRNAssState.put ("A", "A");
\r
1033 jalview.schemes.ResidueProperties.toRNAssState.put ("a", "A");
\r
1034 jalview.schemes.ResidueProperties.toRNAssState.put ("B", "B");
\r
1035 jalview.schemes.ResidueProperties.toRNAssState.put ("b", "B");
\r
1036 jalview.schemes.ResidueProperties.toRNAssState.put ("C", "C");
\r
1037 jalview.schemes.ResidueProperties.toRNAssState.put ("c", "C");
\r
1038 jalview.schemes.ResidueProperties.toRNAssState.put ("D", "D");
\r
1039 jalview.schemes.ResidueProperties.toRNAssState.put ("d", "D");
\r
1040 jalview.schemes.ResidueProperties.toRNAssState.put ("E", "E");
\r
1041 jalview.schemes.ResidueProperties.toRNAssState.put ("e", "E");
\r
1042 jalview.schemes.ResidueProperties.toRNAssState.put ("F", "F");
\r
1043 jalview.schemes.ResidueProperties.toRNAssState.put ("f", "F");
\r
1044 jalview.schemes.ResidueProperties.toRNAssState.put ("G", "G");
\r
1045 jalview.schemes.ResidueProperties.toRNAssState.put ("g", "G");
\r
1046 jalview.schemes.ResidueProperties.toRNAssState.put ("H", "H");
\r
1047 jalview.schemes.ResidueProperties.toRNAssState.put ("h", "H");
\r
1048 jalview.schemes.ResidueProperties.toRNAssState.put ("I", "I");
\r
1049 jalview.schemes.ResidueProperties.toRNAssState.put ("i", "I");
\r
1050 jalview.schemes.ResidueProperties.toRNAssState.put ("J", "J");
\r
1051 jalview.schemes.ResidueProperties.toRNAssState.put ("j", "J");
\r
1052 jalview.schemes.ResidueProperties.toRNAssState.put ("K", "K");
\r
1053 jalview.schemes.ResidueProperties.toRNAssState.put ("k", "K");
\r
1054 jalview.schemes.ResidueProperties.toRNAssState.put ("L", "L");
\r
1055 jalview.schemes.ResidueProperties.toRNAssState.put ("l", "L");
\r
1056 jalview.schemes.ResidueProperties.toRNAssState.put ("M", "M");
\r
1057 jalview.schemes.ResidueProperties.toRNAssState.put ("m", "M");
\r
1058 jalview.schemes.ResidueProperties.toRNAssState.put ("N", "N");
\r
1059 jalview.schemes.ResidueProperties.toRNAssState.put ("n", "N");
\r
1060 jalview.schemes.ResidueProperties.toRNAssState.put ("O", "O");
\r
1061 jalview.schemes.ResidueProperties.toRNAssState.put ("o", "O");
\r
1062 jalview.schemes.ResidueProperties.toRNAssState.put ("P", "P");
\r
1063 jalview.schemes.ResidueProperties.toRNAssState.put ("p", "P");
\r
1064 jalview.schemes.ResidueProperties.toRNAssState.put ("Q", "Q");
\r
1065 jalview.schemes.ResidueProperties.toRNAssState.put ("q", "Q");
\r
1066 jalview.schemes.ResidueProperties.toRNAssState.put ("R", "R");
\r
1067 jalview.schemes.ResidueProperties.toRNAssState.put ("r", "R");
\r
1068 jalview.schemes.ResidueProperties.toRNAssState.put ("S", "S");
\r
1069 jalview.schemes.ResidueProperties.toRNAssState.put ("s", "S");
\r
1070 jalview.schemes.ResidueProperties.toRNAssState.put ("T", "T");
\r
1071 jalview.schemes.ResidueProperties.toRNAssState.put ("t", "T");
\r
1072 jalview.schemes.ResidueProperties.toRNAssState.put ("U", "U");
\r
1073 jalview.schemes.ResidueProperties.toRNAssState.put ("u", "U");
\r
1074 jalview.schemes.ResidueProperties.toRNAssState.put ("V", "V");
\r
1075 jalview.schemes.ResidueProperties.toRNAssState.put ("v", "V");
\r
1076 jalview.schemes.ResidueProperties.toRNAssState.put ("W", "W");
\r
1077 jalview.schemes.ResidueProperties.toRNAssState.put ("w", "W");
\r
1078 jalview.schemes.ResidueProperties.toRNAssState.put ("X", "X");
\r
1079 jalview.schemes.ResidueProperties.toRNAssState.put ("x", "X");
\r
1080 jalview.schemes.ResidueProperties.toRNAssState.put ("Y", "Y");
\r
1081 jalview.schemes.ResidueProperties.toRNAssState.put ("y", "Y");
\r
1082 jalview.schemes.ResidueProperties.toRNAssState.put ("Z", "Z");
\r
1083 jalview.schemes.ResidueProperties.toRNAssState.put ("z", "Z");
\r
1084 for (var p = 0; p < jalview.schemes.ResidueProperties.RNAcloseParen.length; p++) {
\r
1085 jalview.schemes.ResidueProperties.RNAcloseParen[p] = false;
\r
1087 for (var k, $k = jalview.schemes.ResidueProperties.toRNAssState.keySet ().iterator (); $k.hasNext () && ((k = $k.next ()) || true);) {
\r
1088 jalview.schemes.ResidueProperties.RNAcloseParen[k.charCodeAt (0)] = k.charAt (0) != jalview.schemes.ResidueProperties.toRNAssState.get (k).charAt (0);
\r
git://source.jalview.org / jalviewjs.git / blob