2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.schemes;
25 public class ResidueProperties
27 public static Hashtable scoreMatrices=new Hashtable();
28 //Stores residue codes/names and colours and other things
29 public static final int [] aaIndex; // aaHash version 2.1.1 and below
30 public static final int [] nucleotideIndex;
31 public static final Hashtable aa3Hash = new Hashtable();
32 public static final Hashtable aa2Triplet = new Hashtable();
33 public static final Hashtable nucleotideName = new Hashtable();
38 aaIndex = new int[255];
39 for(int i=0; i<255; i++)
94 nucleotideIndex = new int[255];
95 for (int i = 0; i < 255; i++)
96 nucleotideIndex[i] = -1;
98 nucleotideIndex['A'] = 0;
99 nucleotideIndex['a'] = 0;
100 nucleotideIndex['C'] = 1;
101 nucleotideIndex['c'] = 1;
102 nucleotideIndex['G'] = 2;
103 nucleotideIndex['g'] = 2;
104 nucleotideIndex['T'] = 3;
105 nucleotideIndex['t'] = 3;
106 nucleotideIndex['U'] = 4;
107 nucleotideIndex['u'] = 4;
108 nucleotideIndex['I'] = 5;
109 nucleotideIndex['i'] = 5;
110 nucleotideIndex['X'] = 6;
111 nucleotideIndex['x'] = 6;
112 nucleotideIndex['R'] = 7;
113 nucleotideIndex['r'] = 7;
114 nucleotideIndex['Y'] = 8;
115 nucleotideIndex['y'] = 8;
116 nucleotideIndex['N'] = 9;
117 nucleotideIndex['n'] = 9;
120 nucleotideName.put("A", "Adenine");
121 nucleotideName.put("a", "Adenine");
122 nucleotideName.put("G", "Guanine");
123 nucleotideName.put("g", "Guanine");
124 nucleotideName.put("C", "Cytosine");
125 nucleotideName.put("c", "Cytosine");
126 nucleotideName.put("T", "Thymine");
127 nucleotideName.put("t", "Thymine");
128 nucleotideName.put("U", "Uracil");
129 nucleotideName.put("u", "Uracil");
130 nucleotideName.put("I", "Inosine");
131 nucleotideName.put("i", "Inosine");
132 nucleotideName.put("X", "Xanthine");
133 nucleotideName.put("x", "Xanthine");
134 nucleotideName.put("R", "Unknown Purine");
135 nucleotideName.put("r", "Unknown Purine");
136 nucleotideName.put("Y", "Unknown Pyrimidine");
137 nucleotideName.put("y", "Unknown Pyrimidine");
138 nucleotideName.put("N", "Unknown");
139 nucleotideName.put("n", "Unknown");
145 aa3Hash.put("ALA", new Integer(0));
146 aa3Hash.put("ARG", new Integer(1));
147 aa3Hash.put("ASN", new Integer(2));
148 aa3Hash.put("ASP", new Integer(3)); //D
149 aa3Hash.put("CYS", new Integer(4));
150 aa3Hash.put("GLN", new Integer(5)); //Q
151 aa3Hash.put("GLU", new Integer(6)); // E
152 aa3Hash.put("GLY", new Integer(7));
153 aa3Hash.put("HIS", new Integer(8));
154 aa3Hash.put("ILE", new Integer(9));
155 aa3Hash.put("LEU", new Integer(10));
156 aa3Hash.put("LYS", new Integer(11));
157 aa3Hash.put("MET", new Integer(12));
158 aa3Hash.put("PHE", new Integer(13));
159 aa3Hash.put("PRO", new Integer(14));
160 aa3Hash.put("SER", new Integer(15));
161 aa3Hash.put("THR", new Integer(16));
162 aa3Hash.put("TRP", new Integer(17));
163 aa3Hash.put("TYR", new Integer(18));
164 aa3Hash.put("VAL", new Integer(19));
165 // IUB Nomenclature for ambiguous peptides
166 aa3Hash.put("ASX", new Integer(20)); // "B";
167 aa3Hash.put("GLX", new Integer(21)); // X
168 aa3Hash.put("XAA", new Integer(22));// X unknown
169 aa3Hash.put("-", new Integer(23));
170 aa3Hash.put("*", new Integer(23));
171 aa3Hash.put(".", new Integer(23));
172 aa3Hash.put(" ", new Integer(23));
173 aa3Hash.put("Gap", new Integer(23));
178 aa2Triplet.put("A", "ALA");
179 aa2Triplet.put("a", "ALA");
180 aa2Triplet.put("R", "ARG");
181 aa2Triplet.put("r", "ARG");
182 aa2Triplet.put("N", "ASN");
183 aa2Triplet.put("n", "ASN");
184 aa2Triplet.put("D", "ASP");
185 aa2Triplet.put("d", "ASP");
186 aa2Triplet.put("C", "CYS");
187 aa2Triplet.put("c", "CYS");
188 aa2Triplet.put("Q", "GLN");
189 aa2Triplet.put("q", "GLN");
190 aa2Triplet.put("E", "GLU");
191 aa2Triplet.put("e", "GLU");
192 aa2Triplet.put("G", "GLY");
193 aa2Triplet.put("g", "GLY");
194 aa2Triplet.put("H", "HIS");
195 aa2Triplet.put("h", "HIS");
196 aa2Triplet.put("I", "ILE");
197 aa2Triplet.put("i", "ILE");
198 aa2Triplet.put("L", "LEU");
199 aa2Triplet.put("l", "LEU");
200 aa2Triplet.put("K", "LYS");
201 aa2Triplet.put("k", "LYS");
202 aa2Triplet.put("M", "MET");
203 aa2Triplet.put("m", "MET");
204 aa2Triplet.put("F", "PHE");
205 aa2Triplet.put("f", "PHE");
206 aa2Triplet.put("P", "PRO");
207 aa2Triplet.put("p", "PRO");
208 aa2Triplet.put("S", "SER");
209 aa2Triplet.put("s", "SER");
210 aa2Triplet.put("T", "THR");
211 aa2Triplet.put("t", "THR");
212 aa2Triplet.put("W", "TRP");
213 aa2Triplet.put("w", "TRP");
214 aa2Triplet.put("Y", "TYR");
215 aa2Triplet.put("y", "TYR");
216 aa2Triplet.put("V", "VAL");
217 aa2Triplet.put("v", "VAL");
220 public static final String[] aa =
222 "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",
223 "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " "
225 public static final Color midBlue = new Color(100, 100, 255);
226 public static final Vector scaleColours = new Vector();
230 scaleColours.addElement(new Color(114, 0, 147));
231 scaleColours.addElement(new Color(156, 0, 98));
232 scaleColours.addElement(new Color(190, 0, 0));
233 scaleColours.addElement(Color.red);
234 scaleColours.addElement(new Color(255, 125, 0));
235 scaleColours.addElement(Color.orange);
236 scaleColours.addElement(new Color(255, 194, 85));
237 scaleColours.addElement(Color.yellow);
238 scaleColours.addElement(new Color(255, 255, 181));
239 scaleColours.addElement(Color.white);
242 public static final Color[] taylor =
244 new Color(204, 255, 0), // A Greenish-yellowy-yellow
245 new Color(0, 0, 255), // R Blueish-bluey-blue
246 new Color(204, 0, 255), // N Blueish-reddy-blue
247 new Color(255, 0, 0), // D Reddish-reddy-red
248 new Color(255, 255, 0), // C Yellowish-yellowy-yellow
249 new Color(255, 0, 204), // Q Reddish-bluey-red
250 new Color(255, 0, 102), // E Blueish-reddy-red
251 new Color(255, 153, 0), // G Yellowy-reddy-yellow
252 new Color(0, 102, 255), // H Greenish-bluey-blue
253 new Color(102, 255, 0), // I Greenish-yellowy-green
254 new Color(51, 255, 0), // L Yellowish-greeny-green
255 new Color(102, 0, 255), // K Reddish-bluey-blue
256 new Color(0, 255, 0), // M Greenish-greeny-green
257 new Color(0, 255, 102), // F Blueish-greeny-green
258 new Color(255, 204, 0), // P Reddish-yellowy-yellow
259 new Color(255, 51, 0), // S Yellowish-reddy-red
260 new Color(255, 102, 0), // T Reddish-yellowy-red
261 new Color(0, 204, 255), // W Blueish-greeny-green
262 new Color(0, 255, 204), // Y Greenish-bluey-green
263 new Color(153, 255, 0), // V Yellowish-greeny-yellow
271 public static final Color[] nucleotide =
273 new Color(100, 247, 63), // A
274 new Color(255, 179, 64), // C
275 new Color(235, 65, 60), // G
276 new Color(60, 136, 238), // T
277 new Color(60, 136, 238) // U
279 public static final Color[] color =
310 // Dunno where I got these numbers from
311 public static final double[] hyd2 =
337 public static final double[] helix =
339 1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16,
340 1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0
342 public static final double helixmin = 0.57;
343 public static final double helixmax = 1.51;
344 public static final double[] strand =
346 0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74,
347 1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0
349 public static final double strandmin = 0.37;
350 public static final double strandmax = 1.7;
351 public static final double[] turn =
353 0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01,
354 0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0
356 public static final double turnmin = 0.47;
357 public static final double turnmax = 1.56;
358 public static final double[] buried =
360 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,
361 0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4, 0.3, 1.358, 0.00
363 public static final double buriedmin = 0.05;
364 public static final double buriedmax = 4.6;
366 // This is hydropathy index
367 // Kyte, J., and Doolittle, R.F., J. Mol. Biol.
368 // 1157, 105-132, 1982
369 public static final double[] hyd =
371 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,
372 2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0
374 public static final double hydmax = 4.5;
375 public static final double hydmin = -3.9;
377 //public static final double hydmax = 1.38;
378 //public static final double hydmin = -2.53;
379 private static final int[][] BLOSUM62 =
382 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3,
386 -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2,
390 -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3,
394 -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4,
398 0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2,
399 -2, -1, -3, -3, -2, -4
402 -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1,
406 -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2,
410 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2,
411 -3, -3, -1, -2, -1, -4
414 -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2,
418 -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3,
419 -1, 3, -3, -3, -1, -4
422 -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2,
423 -1, 1, -4, -3, -1, -4
426 -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2,
430 -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1,
431 -1, 1, -3, -1, -1, -4
434 -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3,
438 -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1,
439 -4, -3, -2, -2, -1, -2, -4
442 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2,
446 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2,
450 -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2,
451 11, 2, -3, -4, -3, -2, -4
454 -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2,
455 7, -1, -3, -2, -1, -4
458 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3,
459 -1, 4, -3, -2, -1, -4
462 -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3,
466 -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2,
470 0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2,
471 -1, -1, -1, -1, -1, -4
474 -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,
475 -4, -4, -4, -4, -4, -4, 1
478 static final int[][] PAM250 =
481 2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3, 0,
485 -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4,
489 0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2,
493 0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4, -2,
497 -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2,
498 -8, 0, -2, -4, -5, -3, -8
501 0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4,
505 0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4, -2,
509 1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5,
513 -1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0,
517 -1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5,
518 -1, 4, -2, -2, -1, -8
521 -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2,
522 -1, 2, -3, -3, -1, -8
525 -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4, -2,
529 -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4, -2,
533 -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0, 7,
537 1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5,
541 1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3, -1,
545 1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3, 0,
549 -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5, 17,
550 0, -6, -5, -6, -4, -8
553 -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0,
554 10, -2, -3, -4, -2, -8
557 0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6,
558 -2, 4, -2, -2, -1, -8
561 0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3, -2,
565 0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4, -2,
569 0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4,
570 -2, -1, -1, -1, -1, -8
573 -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,
574 -8, -8, -8, -8, -8, -8, 1
577 public static final Hashtable ssHash = new Hashtable(); // stores the number value of the aa
581 ssHash.put("H", Color.magenta);
582 ssHash.put("E", Color.yellow);
583 ssHash.put("-", Color.white);
584 ssHash.put(".", Color.white);
585 ssHash.put("S", Color.cyan);
586 ssHash.put("T", Color.blue);
587 ssHash.put("G", Color.pink);
588 ssHash.put("I", Color.pink);
589 ssHash.put("B", Color.yellow);
592 static final int[][] DNA =
595 5, -4, -4, -4, 1}, // C
597 -4, 5, -4, -4, 1}, // T
599 -4, -4, 5, -4, 1}, // A
601 -4, -4, -4, 5, 1}, // G
606 * register matrices in list
609 scoreMatrices.put("BLOSUM62", new ScoreMatrix("BLOSUM62",BLOSUM62, 0));
610 scoreMatrices.put("PAM250", new ScoreMatrix("PAM250",PAM250, 0));
611 scoreMatrices.put("DNA", new ScoreMatrix("DNA", DNA, 1));
613 public static final Color[] pidColours =
615 midBlue, new Color(153, 153, 255),
617 new Color(204, 204, 255),
619 public static final float[] pidThresholds =
622 public static Hashtable codonHash = new Hashtable();
623 public static Vector Lys = new Vector();
624 public static Vector Asn = new Vector();
625 public static Vector Gln = new Vector();
626 public static Vector His = new Vector();
627 public static Vector Glu = new Vector();
628 public static Vector Asp = new Vector();
629 public static Vector Tyr = new Vector();
630 public static Vector Thr = new Vector();
631 public static Vector Pro = new Vector();
632 public static Vector Ala = new Vector();
633 public static Vector Ser = new Vector();
634 public static Vector Arg = new Vector();
635 public static Vector Gly = new Vector();
636 public static Vector Trp = new Vector();
637 public static Vector Cys = new Vector();
638 public static Vector Ile = new Vector();
639 public static Vector Met = new Vector();
640 public static Vector Leu = new Vector();
641 public static Vector Val = new Vector();
642 public static Vector Phe = new Vector();
643 public static Vector STOP = new Vector();
647 codonHash.put("K", Lys);
648 codonHash.put("N", Asn);
649 codonHash.put("Q", Gln);
650 codonHash.put("H", His);
651 codonHash.put("E", Glu);
652 codonHash.put("D", Asp);
653 codonHash.put("Y", Tyr);
654 codonHash.put("T", Thr);
655 codonHash.put("P", Pro);
656 codonHash.put("A", Ala);
657 codonHash.put("S", Ser);
658 codonHash.put("R", Arg);
659 codonHash.put("G", Gly);
660 codonHash.put("W", Trp);
661 codonHash.put("C", Cys);
662 codonHash.put("I", Ile);
663 codonHash.put("M", Met);
664 codonHash.put("L", Leu);
665 codonHash.put("V", Val);
666 codonHash.put("F", Phe);
667 codonHash.put("STOP", STOP);
670 public static Hashtable codonHash2 = new Hashtable();
674 codonHash2.put("AAA", "K");
675 codonHash2.put("AAG", "K");
676 codonHash2.put("AAC", "N");
677 codonHash2.put("AAT", "N");
679 codonHash2.put("CAA", "E");
680 codonHash2.put("CAG", "E");
681 codonHash2.put("CAC", "H");
682 codonHash2.put("CAT", "H");
684 codonHash2.put("GAA", "Q");
685 codonHash2.put("GAG", "Q");
686 codonHash2.put("GAC", "D");
687 codonHash2.put("GAT", "D");
689 codonHash2.put("TAC", "Y");
690 codonHash2.put("TAT", "Y");
692 codonHash2.put("ACA", "T");
693 codonHash2.put("AAG", "T");
694 codonHash2.put("ACC", "T");
695 codonHash2.put("ACT", "T");
697 codonHash2.put("CCA", "P");
698 codonHash2.put("CCG", "P");
699 codonHash2.put("CCC", "P");
700 codonHash2.put("CCT", "P");
702 codonHash2.put("GCA", "A");
703 codonHash2.put("GCG", "A");
704 codonHash2.put("GCC", "A");
705 codonHash2.put("GCT", "A");
707 codonHash2.put("TCA", "S");
708 codonHash2.put("TCG", "S");
709 codonHash2.put("TCC", "S");
710 codonHash2.put("TCT", "S");
711 codonHash2.put("AGC", "S");
712 codonHash2.put("AGT", "S");
714 codonHash2.put("AGA", "R");
715 codonHash2.put("AGG", "R");
716 codonHash2.put("CGA", "R");
717 codonHash2.put("CGG", "R");
718 codonHash2.put("CGC", "R");
719 codonHash2.put("CGT", "R");
721 codonHash2.put("GGA", "G");
722 codonHash2.put("GGG", "G");
723 codonHash2.put("GGC", "G");
724 codonHash2.put("GGT", "G");
726 codonHash2.put("TGA", "*");
727 codonHash2.put("TAA", "*");
728 codonHash2.put("TAG", "*");
730 codonHash2.put("TGG", "W");
732 codonHash2.put("TGC", "C");
733 codonHash2.put("TGT", "C");
735 codonHash2.put("ATA", "I");
736 codonHash2.put("ATC", "I");
737 codonHash2.put("ATT", "I");
739 codonHash2.put("ATG", "M");
741 codonHash2.put("CTA", "L");
742 codonHash2.put("CTG", "L");
743 codonHash2.put("CTC", "L");
744 codonHash2.put("CTT", "L");
745 codonHash2.put("TTA", "L");
746 codonHash2.put("TTG", "L");
748 codonHash2.put("GTA", "V");
749 codonHash2.put("GTG", "V");
750 codonHash2.put("GTC", "V");
751 codonHash2.put("GTT", "V");
753 codonHash2.put("TTC", "F");
754 codonHash2.put("TTT", "F");
759 Lys.addElement("AAA");
760 Lys.addElement("AAG");
761 Asn.addElement("AAC");
762 Asn.addElement("AAT");
764 Gln.addElement("CAA");
765 Gln.addElement("CAG");
766 His.addElement("CAC");
767 His.addElement("CAT");
769 Glu.addElement("GAA");
770 Glu.addElement("GAG");
771 Asp.addElement("GAC");
772 Asp.addElement("GAT");
774 Tyr.addElement("TAC");
775 Tyr.addElement("TAT");
777 Thr.addElement("ACA");
778 Thr.addElement("ACG");
779 Thr.addElement("ACC");
780 Thr.addElement("ACT");
782 Pro.addElement("CCA");
783 Pro.addElement("CCG");
784 Pro.addElement("CCC");
785 Pro.addElement("CCT");
787 Ala.addElement("GCA");
788 Ala.addElement("GCG");
789 Ala.addElement("GCC");
790 Ala.addElement("GCT");
792 Ser.addElement("TCA");
793 Ser.addElement("TCG");
794 Ser.addElement("TCC");
795 Ser.addElement("TCT");
796 Ser.addElement("AGC");
797 Ser.addElement("AGT");
799 Arg.addElement("AGA");
800 Arg.addElement("AGG");
801 Arg.addElement("CGA");
802 Arg.addElement("CGG");
803 Arg.addElement("CGC");
804 Arg.addElement("CGT");
806 Gly.addElement("GGA");
807 Gly.addElement("GGG");
808 Gly.addElement("GGC");
809 Gly.addElement("GGT");
811 STOP.addElement("TGA");
812 STOP.addElement("TAA");
813 STOP.addElement("TAG");
815 Trp.addElement("TGG");
817 Cys.addElement("TGC");
818 Cys.addElement("TGT");
820 Ile.addElement("ATA");
821 Ile.addElement("ATC");
822 Ile.addElement("ATT");
824 Met.addElement("ATG");
826 Leu.addElement("CTA");
827 Leu.addElement("CTG");
828 Leu.addElement("CTC");
829 Leu.addElement("CTT");
830 Leu.addElement("TTA");
831 Leu.addElement("TTG");
833 Val.addElement("GTA");
834 Val.addElement("GTG");
835 Val.addElement("GTC");
836 Val.addElement("GTT");
838 Phe.addElement("TTC");
839 Phe.addElement("TTT");
843 //Stores residue codes/names and colours and other things
844 public static Hashtable propHash = new Hashtable();
845 public static Hashtable hydrophobic = new Hashtable();
846 public static Hashtable polar = new Hashtable();
847 public static Hashtable small = new Hashtable();
848 public static Hashtable positive = new Hashtable();
849 public static Hashtable negative = new Hashtable();
850 public static Hashtable charged = new Hashtable();
851 public static Hashtable aromatic = new Hashtable();
852 public static Hashtable aliphatic = new Hashtable();
853 public static Hashtable tiny = new Hashtable();
854 public static Hashtable proline = new Hashtable();
858 hydrophobic.put("I", new Integer(1));
859 hydrophobic.put("L", new Integer(1));
860 hydrophobic.put("V", new Integer(1));
861 hydrophobic.put("C", new Integer(1));
862 hydrophobic.put("A", new Integer(1));
863 hydrophobic.put("G", new Integer(1));
864 hydrophobic.put("M", new Integer(1));
865 hydrophobic.put("F", new Integer(1));
866 hydrophobic.put("Y", new Integer(1));
867 hydrophobic.put("W", new Integer(1));
868 hydrophobic.put("H", new Integer(1));
869 hydrophobic.put("K", new Integer(1));
870 hydrophobic.put("X", new Integer(1));
871 hydrophobic.put("-", new Integer(1));
872 hydrophobic.put("*", new Integer(1));
873 hydrophobic.put("R", new Integer(0));
874 hydrophobic.put("E", new Integer(0));
875 hydrophobic.put("Q", new Integer(0));
876 hydrophobic.put("D", new Integer(0));
877 hydrophobic.put("N", new Integer(0));
878 hydrophobic.put("S", new Integer(0));
879 hydrophobic.put("T", new Integer(0));
880 hydrophobic.put("P", new Integer(0));
885 polar.put("Y", new Integer(1));
886 polar.put("W", new Integer(1));
887 polar.put("H", new Integer(1));
888 polar.put("K", new Integer(1));
889 polar.put("R", new Integer(1));
890 polar.put("E", new Integer(1));
891 polar.put("Q", new Integer(1));
892 polar.put("D", new Integer(1));
893 polar.put("N", new Integer(1));
894 polar.put("S", new Integer(1));
895 polar.put("T", new Integer(1));
896 polar.put("X", new Integer(1));
897 polar.put("-", new Integer(1));
898 polar.put("*", new Integer(1));
899 polar.put("I", new Integer(0));
900 polar.put("L", new Integer(0));
901 polar.put("V", new Integer(0));
902 polar.put("C", new Integer(0));
903 polar.put("A", new Integer(0));
904 polar.put("G", new Integer(0));
905 polar.put("M", new Integer(0));
906 polar.put("F", new Integer(0));
907 polar.put("P", new Integer(0));
912 small.put("I", new Integer(0));
913 small.put("L", new Integer(0));
914 small.put("V", new Integer(1));
915 small.put("C", new Integer(1));
916 small.put("A", new Integer(1));
917 small.put("G", new Integer(1));
918 small.put("M", new Integer(0));
919 small.put("F", new Integer(0));
920 small.put("Y", new Integer(0));
921 small.put("W", new Integer(0));
922 small.put("H", new Integer(0));
923 small.put("K", new Integer(0));
924 small.put("R", new Integer(0));
925 small.put("E", new Integer(0));
926 small.put("Q", new Integer(0));
927 small.put("D", new Integer(1));
928 small.put("N", new Integer(1));
929 small.put("S", new Integer(1));
930 small.put("T", new Integer(1));
931 small.put("P", new Integer(1));
932 small.put("-", new Integer(1));
933 small.put("*", new Integer(1));
938 positive.put("I", new Integer(0));
939 positive.put("L", new Integer(0));
940 positive.put("V", new Integer(0));
941 positive.put("C", new Integer(0));
942 positive.put("A", new Integer(0));
943 positive.put("G", new Integer(0));
944 positive.put("M", new Integer(0));
945 positive.put("F", new Integer(0));
946 positive.put("Y", new Integer(0));
947 positive.put("W", new Integer(0));
948 positive.put("H", new Integer(1));
949 positive.put("K", new Integer(1));
950 positive.put("R", new Integer(1));
951 positive.put("E", new Integer(0));
952 positive.put("Q", new Integer(0));
953 positive.put("D", new Integer(0));
954 positive.put("N", new Integer(0));
955 positive.put("S", new Integer(0));
956 positive.put("T", new Integer(0));
957 positive.put("P", new Integer(0));
958 positive.put("-", new Integer(1));
959 positive.put("*", new Integer(1));
964 negative.put("I", new Integer(0));
965 negative.put("L", new Integer(0));
966 negative.put("V", new Integer(0));
967 negative.put("C", new Integer(0));
968 negative.put("A", new Integer(0));
969 negative.put("G", new Integer(0));
970 negative.put("M", new Integer(0));
971 negative.put("F", new Integer(0));
972 negative.put("Y", new Integer(0));
973 negative.put("W", new Integer(0));
974 negative.put("H", new Integer(0));
975 negative.put("K", new Integer(0));
976 negative.put("R", new Integer(0));
977 negative.put("E", new Integer(1));
978 negative.put("Q", new Integer(0));
979 negative.put("D", new Integer(1));
980 negative.put("N", new Integer(0));
981 negative.put("S", new Integer(0));
982 negative.put("T", new Integer(0));
983 negative.put("P", new Integer(0));
984 negative.put("-", new Integer(1));
985 negative.put("*", new Integer(1));
990 charged.put("I", new Integer(0));
991 charged.put("L", new Integer(0));
992 charged.put("V", new Integer(0));
993 charged.put("C", new Integer(0));
994 charged.put("A", new Integer(0));
995 charged.put("G", new Integer(0));
996 charged.put("M", new Integer(0));
997 charged.put("F", new Integer(0));
998 charged.put("Y", new Integer(0));
999 charged.put("W", new Integer(0));
1000 charged.put("H", new Integer(1));
1001 charged.put("K", new Integer(1));
1002 charged.put("R", new Integer(1));
1003 charged.put("E", new Integer(1));
1004 charged.put("Q", new Integer(0));
1005 charged.put("D", new Integer(1));
1006 charged.put("N", new Integer(1));
1007 charged.put("S", new Integer(0));
1008 charged.put("T", new Integer(0));
1009 charged.put("P", new Integer(0));
1010 charged.put("-", new Integer(1));
1011 charged.put("*", new Integer(1));
1016 aromatic.put("I", new Integer(0));
1017 aromatic.put("L", new Integer(0));
1018 aromatic.put("V", new Integer(0));
1019 aromatic.put("C", new Integer(0));
1020 aromatic.put("A", new Integer(0));
1021 aromatic.put("G", new Integer(0));
1022 aromatic.put("M", new Integer(0));
1023 aromatic.put("F", new Integer(1));
1024 aromatic.put("Y", new Integer(1));
1025 aromatic.put("W", new Integer(1));
1026 aromatic.put("H", new Integer(1));
1027 aromatic.put("K", new Integer(0));
1028 aromatic.put("R", new Integer(0));
1029 aromatic.put("E", new Integer(0));
1030 aromatic.put("Q", new Integer(0));
1031 aromatic.put("D", new Integer(0));
1032 aromatic.put("N", new Integer(0));
1033 aromatic.put("S", new Integer(0));
1034 aromatic.put("T", new Integer(0));
1035 aromatic.put("P", new Integer(0));
1036 aromatic.put("-", new Integer(1));
1037 aromatic.put("*", new Integer(1));
1042 aliphatic.put("I", new Integer(1));
1043 aliphatic.put("L", new Integer(1));
1044 aliphatic.put("V", new Integer(1));
1045 aliphatic.put("C", new Integer(0));
1046 aliphatic.put("A", new Integer(0));
1047 aliphatic.put("G", new Integer(0));
1048 aliphatic.put("M", new Integer(0));
1049 aliphatic.put("F", new Integer(0));
1050 aliphatic.put("Y", new Integer(0));
1051 aliphatic.put("W", new Integer(0));
1052 aliphatic.put("H", new Integer(0));
1053 aliphatic.put("K", new Integer(0));
1054 aliphatic.put("R", new Integer(0));
1055 aliphatic.put("E", new Integer(0));
1056 aliphatic.put("Q", new Integer(0));
1057 aliphatic.put("D", new Integer(0));
1058 aliphatic.put("N", new Integer(0));
1059 aliphatic.put("S", new Integer(0));
1060 aliphatic.put("T", new Integer(0));
1061 aliphatic.put("P", new Integer(0));
1062 aliphatic.put("-", new Integer(1));
1063 aliphatic.put("*", new Integer(1));
1068 tiny.put("I", new Integer(0));
1069 tiny.put("L", new Integer(0));
1070 tiny.put("V", new Integer(0));
1071 tiny.put("C", new Integer(0));
1072 tiny.put("A", new Integer(1));
1073 tiny.put("G", new Integer(1));
1074 tiny.put("M", new Integer(0));
1075 tiny.put("F", new Integer(0));
1076 tiny.put("Y", new Integer(0));
1077 tiny.put("W", new Integer(0));
1078 tiny.put("H", new Integer(0));
1079 tiny.put("K", new Integer(0));
1080 tiny.put("R", new Integer(0));
1081 tiny.put("E", new Integer(0));
1082 tiny.put("Q", new Integer(0));
1083 tiny.put("D", new Integer(0));
1084 tiny.put("N", new Integer(0));
1085 tiny.put("S", new Integer(1));
1086 tiny.put("T", new Integer(0));
1087 tiny.put("P", new Integer(0));
1088 tiny.put("-", new Integer(1));
1089 tiny.put("*", new Integer(1));
1094 proline.put("I", new Integer(0));
1095 proline.put("L", new Integer(0));
1096 proline.put("V", new Integer(0));
1097 proline.put("C", new Integer(0));
1098 proline.put("A", new Integer(0));
1099 proline.put("G", new Integer(0));
1100 proline.put("M", new Integer(0));
1101 proline.put("F", new Integer(0));
1102 proline.put("Y", new Integer(0));
1103 proline.put("W", new Integer(0));
1104 proline.put("H", new Integer(0));
1105 proline.put("K", new Integer(0));
1106 proline.put("R", new Integer(0));
1107 proline.put("E", new Integer(0));
1108 proline.put("Q", new Integer(0));
1109 proline.put("D", new Integer(0));
1110 proline.put("N", new Integer(0));
1111 proline.put("S", new Integer(0));
1112 proline.put("T", new Integer(0));
1113 proline.put("P", new Integer(1));
1114 proline.put("-", new Integer(1));
1115 proline.put("*", new Integer(1));
1120 propHash.put("hydrophobic", hydrophobic);
1121 propHash.put("small", small);
1122 propHash.put("positive", positive);
1123 propHash.put("negative", negative);
1124 propHash.put("charged", charged);
1125 propHash.put("aromatic", aromatic);
1126 propHash.put("aliphatic", aliphatic);
1127 propHash.put("tiny", tiny);
1128 propHash.put("proline", proline);
1129 propHash.put("polar", polar);
1132 private ResidueProperties()
1136 public static double getHydmax()
1141 public static double getHydmin()
1146 public static double[] getHyd()
1151 public static Hashtable getAA3Hash()
1156 public static int[][] getDNA()
1158 return ResidueProperties.DNA;
1161 public static int[][] getBLOSUM62()
1163 return ResidueProperties.BLOSUM62;
1166 public static int getPAM250(String A1, String A2)
1168 int a = aaIndex[A1.charAt(0)];
1169 int b = aaIndex[A2.charAt(0)];
1171 int pog = ResidueProperties.PAM250[a][b];
1176 public static int getBLOSUM62(char c1, char c2)
1182 int a = aaIndex[c1];
1183 int b = aaIndex[c2];
1185 pog = ResidueProperties.BLOSUM62[a][b];
1189 //System.out.println("Unknown residue in " + A1 + " " + A2);
1195 public static Vector getCodons(String res)
1197 if (codonHash.containsKey(res))
1199 return (Vector) codonHash.get(res);
1205 public static String codonTranslate(String codon)
1207 Enumeration e = codonHash.keys();
1209 while (e.hasMoreElements())
1211 String key = (String) e.nextElement();
1212 Vector tmp = (Vector) codonHash.get(key);
1214 if (tmp.contains(codon.toUpperCase()))
1223 public static int[][] getDefaultPeptideMatrix() {
1224 return ResidueProperties.getBLOSUM62();
1226 public static int[][] getDefaultDnaMatrix() {
1227 return ResidueProperties.getDNA();
1231 * get a ScoreMatrix based on its string name
1233 * @return matrix in scoreMatrices with key pwtype or null
1235 public static ScoreMatrix getScoreMatrix(String pwtype) {
1236 Object val=scoreMatrices.get(pwtype);
1238 return (ScoreMatrix) val;