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package jalview.schemes; |
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import java.awt.Color; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.Enumeration; |
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import java.util.HashMap; |
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import java.util.Hashtable; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.Vector; |
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| 97.2% |
Uncovered Elements: 59 (2,109) |
Complexity: 95 |
Complexity Density: 0.05 |
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public class ResidueProperties |
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{ |
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public static final int[] aaIndex; |
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public static final int[] nucleotideIndex; |
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public static final int[] purinepyrimidineIndex; |
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public static final Map<String, Integer> aa3Hash = new HashMap<>(); |
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public static final Map<String, String> aa2Triplet = new HashMap<>(); |
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public static final Map<String, String> nucleotideName = new HashMap<>(); |
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public static final Map<String, String> modifications = new HashMap<>(); |
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| 100% |
Uncovered Elements: 0 (53) |
Complexity: 2 |
Complexity Density: 0.04 |
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static... |
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{ |
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aaIndex = new int[255]; |
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256 |
for (int i = 0; i < 255; i++) |
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{ |
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aaIndex[i] = 23; |
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} |
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aaIndex['A'] = 0; |
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aaIndex['R'] = 1; |
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aaIndex['N'] = 2; |
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aaIndex['D'] = 3; |
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1 |
aaIndex['C'] = 4; |
64 |
1 |
aaIndex['Q'] = 5; |
65 |
1 |
aaIndex['E'] = 6; |
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1 |
aaIndex['G'] = 7; |
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1 |
aaIndex['H'] = 8; |
68 |
1 |
aaIndex['I'] = 9; |
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1 |
aaIndex['L'] = 10; |
70 |
1 |
aaIndex['K'] = 11; |
71 |
1 |
aaIndex['M'] = 12; |
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1 |
aaIndex['F'] = 13; |
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1 |
aaIndex['P'] = 14; |
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1 |
aaIndex['S'] = 15; |
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1 |
aaIndex['T'] = 16; |
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aaIndex['W'] = 17; |
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1 |
aaIndex['Y'] = 18; |
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1 |
aaIndex['V'] = 19; |
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1 |
aaIndex['B'] = 20; |
80 |
1 |
aaIndex['Z'] = 21; |
81 |
1 |
aaIndex['X'] = 22; |
82 |
1 |
aaIndex['U'] = 22; |
83 |
1 |
aaIndex['a'] = 0; |
84 |
1 |
aaIndex['r'] = 1; |
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aaIndex['n'] = 2; |
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1 |
aaIndex['d'] = 3; |
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aaIndex['c'] = 4; |
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aaIndex['q'] = 5; |
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aaIndex['e'] = 6; |
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aaIndex['g'] = 7; |
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aaIndex['h'] = 8; |
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aaIndex['i'] = 9; |
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aaIndex['l'] = 10; |
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aaIndex['k'] = 11; |
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aaIndex['m'] = 12; |
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1 |
aaIndex['f'] = 13; |
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aaIndex['p'] = 14; |
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aaIndex['s'] = 15; |
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aaIndex['t'] = 16; |
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aaIndex['w'] = 17; |
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aaIndex['y'] = 18; |
102 |
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aaIndex['v'] = 19; |
103 |
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aaIndex['b'] = 20; |
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aaIndex['z'] = 21; |
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aaIndex['x'] = 22; |
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aaIndex['u'] = 22; |
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} |
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public final static int maxProteinIndex = 23; |
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public final static int maxNucleotideIndex = 10; |
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| 100% |
Uncovered Elements: 0 (61) |
Complexity: 2 |
Complexity Density: 0.03 |
|
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static... |
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{ |
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nucleotideIndex = new int[255]; |
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for (int i = 0; i < 255; i++) |
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{ |
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nucleotideIndex[i] = 10; |
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} |
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nucleotideIndex['A'] = 0; |
129 |
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nucleotideIndex['a'] = 0; |
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nucleotideIndex['C'] = 1; |
131 |
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nucleotideIndex['c'] = 1; |
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nucleotideIndex['G'] = 2; |
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nucleotideIndex['g'] = 2; |
134 |
1 |
nucleotideIndex['T'] = 3; |
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nucleotideIndex['t'] = 3; |
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nucleotideIndex['U'] = 4; |
137 |
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nucleotideIndex['u'] = 4; |
138 |
1 |
nucleotideIndex['I'] = 5; |
139 |
1 |
nucleotideIndex['i'] = 5; |
140 |
1 |
nucleotideIndex['X'] = 6; |
141 |
1 |
nucleotideIndex['x'] = 6; |
142 |
1 |
nucleotideIndex['R'] = 7; |
143 |
1 |
nucleotideIndex['r'] = 7; |
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1 |
nucleotideIndex['Y'] = 8; |
145 |
1 |
nucleotideIndex['y'] = 8; |
146 |
1 |
nucleotideIndex['N'] = 9; |
147 |
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nucleotideIndex['n'] = 9; |
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|
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nucleotideName.put("A", "Adenine"); |
150 |
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nucleotideName.put("a", "Adenine"); |
151 |
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nucleotideName.put("G", "Guanine"); |
152 |
1 |
nucleotideName.put("g", "Guanine"); |
153 |
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nucleotideName.put("C", "Cytosine"); |
154 |
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nucleotideName.put("c", "Cytosine"); |
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nucleotideName.put("T", "Thymine"); |
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nucleotideName.put("t", "Thymine"); |
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nucleotideName.put("U", "Uracil"); |
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nucleotideName.put("u", "Uracil"); |
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nucleotideName.put("I", "Inosine"); |
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nucleotideName.put("i", "Inosine"); |
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nucleotideName.put("X", "Xanthine"); |
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nucleotideName.put("x", "Xanthine"); |
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nucleotideName.put("R", "Unknown Purine"); |
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nucleotideName.put("r", "Unknown Purine"); |
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nucleotideName.put("Y", "Unknown Pyrimidine"); |
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nucleotideName.put("y", "Unknown Pyrimidine"); |
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nucleotideName.put("N", "Unknown"); |
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nucleotideName.put("n", "Unknown"); |
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nucleotideName.put("W", "Weak nucleotide (A or T)"); |
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nucleotideName.put("w", "Weak nucleotide (A or T)"); |
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nucleotideName.put("S", "Strong nucleotide (G or C)"); |
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nucleotideName.put("s", "Strong nucleotide (G or C)"); |
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nucleotideName.put("M", "Amino (A or C)"); |
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nucleotideName.put("m", "Amino (A or C)"); |
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nucleotideName.put("K", "Keto (G or T)"); |
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1 |
nucleotideName.put("k", "Keto (G or T)"); |
177 |
1 |
nucleotideName.put("B", "Not A (G or C or T)"); |
178 |
1 |
nucleotideName.put("b", "Not A (G or C or T)"); |
179 |
1 |
nucleotideName.put("H", "Not G (A or C or T)"); |
180 |
1 |
nucleotideName.put("h", "Not G (A or C or T)"); |
181 |
1 |
nucleotideName.put("D", "Not C (A or G or T)"); |
182 |
1 |
nucleotideName.put("d", "Not C (A or G or T)"); |
183 |
1 |
nucleotideName.put("V", "Not T (A or G or C"); |
184 |
1 |
nucleotideName.put("v", "Not T (A or G or C"); |
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} |
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| 100% |
Uncovered Elements: 0 (25) |
Complexity: 2 |
Complexity Density: 0.09 |
|
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1 |
static... |
189 |
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{ |
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purinepyrimidineIndex = new int[255]; |
191 |
256 |
for (int i = 0; i < 255; i++) |
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{ |
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purinepyrimidineIndex[i] = 3; |
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} |
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purinepyrimidineIndex['A'] = 0; |
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purinepyrimidineIndex['a'] = 0; |
199 |
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purinepyrimidineIndex['C'] = 1; |
200 |
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purinepyrimidineIndex['c'] = 1; |
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purinepyrimidineIndex['G'] = 0; |
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purinepyrimidineIndex['g'] = 0; |
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purinepyrimidineIndex['T'] = 1; |
204 |
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purinepyrimidineIndex['t'] = 1; |
205 |
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purinepyrimidineIndex['U'] = 1; |
206 |
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purinepyrimidineIndex['u'] = 1; |
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purinepyrimidineIndex['I'] = 2; |
208 |
1 |
purinepyrimidineIndex['i'] = 2; |
209 |
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purinepyrimidineIndex['X'] = 2; |
210 |
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purinepyrimidineIndex['x'] = 2; |
211 |
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purinepyrimidineIndex['R'] = 0; |
212 |
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purinepyrimidineIndex['r'] = 0; |
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purinepyrimidineIndex['Y'] = 1; |
214 |
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purinepyrimidineIndex['y'] = 1; |
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1 |
purinepyrimidineIndex['N'] = 2; |
216 |
1 |
purinepyrimidineIndex['n'] = 2; |
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} |
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private static final Integer ONE = Integer.valueOf(1); |
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private static final Integer ZERO = Integer.valueOf(0); |
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| 100% |
Uncovered Elements: 0 (29) |
Complexity: 1 |
Complexity Density: 0.03 |
|
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1 |
static... |
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{ |
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aa3Hash.put("ALA", ZERO); |
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aa3Hash.put("ARG", ONE); |
227 |
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aa3Hash.put("ASN", Integer.valueOf(2)); |
228 |
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aa3Hash.put("ASP", Integer.valueOf(3)); |
229 |
1 |
aa3Hash.put("CYS", Integer.valueOf(4)); |
230 |
1 |
aa3Hash.put("GLN", Integer.valueOf(5)); |
231 |
1 |
aa3Hash.put("GLU", Integer.valueOf(6)); |
232 |
1 |
aa3Hash.put("GLY", Integer.valueOf(7)); |
233 |
1 |
aa3Hash.put("HIS", Integer.valueOf(8)); |
234 |
1 |
aa3Hash.put("ILE", Integer.valueOf(9)); |
235 |
1 |
aa3Hash.put("LEU", Integer.valueOf(10)); |
236 |
1 |
aa3Hash.put("LYS", Integer.valueOf(11)); |
237 |
1 |
aa3Hash.put("MET", Integer.valueOf(12)); |
238 |
1 |
aa3Hash.put("PHE", Integer.valueOf(13)); |
239 |
1 |
aa3Hash.put("PRO", Integer.valueOf(14)); |
240 |
1 |
aa3Hash.put("SER", Integer.valueOf(15)); |
241 |
1 |
aa3Hash.put("THR", Integer.valueOf(16)); |
242 |
1 |
aa3Hash.put("TRP", Integer.valueOf(17)); |
243 |
1 |
aa3Hash.put("TYR", Integer.valueOf(18)); |
244 |
1 |
aa3Hash.put("VAL", Integer.valueOf(19)); |
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|
246 |
1 |
aa3Hash.put("ASX", Integer.valueOf(20)); |
247 |
1 |
aa3Hash.put("GLX", Integer.valueOf(21)); |
248 |
1 |
aa3Hash.put("XAA", Integer.valueOf(22)); |
249 |
1 |
aa3Hash.put("-", Integer.valueOf(23)); |
250 |
1 |
aa3Hash.put("*", Integer.valueOf(23)); |
251 |
1 |
aa3Hash.put(".", Integer.valueOf(23)); |
252 |
1 |
aa3Hash.put(" ", Integer.valueOf(23)); |
253 |
1 |
aa3Hash.put("Gap", Integer.valueOf(23)); |
254 |
1 |
aa3Hash.put("UR3", Integer.valueOf(24)); |
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} |
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| 100% |
Uncovered Elements: 0 (40) |
Complexity: 1 |
Complexity Density: 0.03 |
|
257 |
1 |
static... |
258 |
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{ |
259 |
1 |
aa2Triplet.put("A", "ALA"); |
260 |
1 |
aa2Triplet.put("a", "ALA"); |
261 |
1 |
aa2Triplet.put("R", "ARG"); |
262 |
1 |
aa2Triplet.put("r", "ARG"); |
263 |
1 |
aa2Triplet.put("N", "ASN"); |
264 |
1 |
aa2Triplet.put("n", "ASN"); |
265 |
1 |
aa2Triplet.put("D", "ASP"); |
266 |
1 |
aa2Triplet.put("d", "ASP"); |
267 |
1 |
aa2Triplet.put("C", "CYS"); |
268 |
1 |
aa2Triplet.put("c", "CYS"); |
269 |
1 |
aa2Triplet.put("Q", "GLN"); |
270 |
1 |
aa2Triplet.put("q", "GLN"); |
271 |
1 |
aa2Triplet.put("E", "GLU"); |
272 |
1 |
aa2Triplet.put("e", "GLU"); |
273 |
1 |
aa2Triplet.put("G", "GLY"); |
274 |
1 |
aa2Triplet.put("g", "GLY"); |
275 |
1 |
aa2Triplet.put("H", "HIS"); |
276 |
1 |
aa2Triplet.put("h", "HIS"); |
277 |
1 |
aa2Triplet.put("I", "ILE"); |
278 |
1 |
aa2Triplet.put("i", "ILE"); |
279 |
1 |
aa2Triplet.put("L", "LEU"); |
280 |
1 |
aa2Triplet.put("l", "LEU"); |
281 |
1 |
aa2Triplet.put("K", "LYS"); |
282 |
1 |
aa2Triplet.put("k", "LYS"); |
283 |
1 |
aa2Triplet.put("M", "MET"); |
284 |
1 |
aa2Triplet.put("m", "MET"); |
285 |
1 |
aa2Triplet.put("F", "PHE"); |
286 |
1 |
aa2Triplet.put("f", "PHE"); |
287 |
1 |
aa2Triplet.put("P", "PRO"); |
288 |
1 |
aa2Triplet.put("p", "PRO"); |
289 |
1 |
aa2Triplet.put("S", "SER"); |
290 |
1 |
aa2Triplet.put("s", "SER"); |
291 |
1 |
aa2Triplet.put("T", "THR"); |
292 |
1 |
aa2Triplet.put("t", "THR"); |
293 |
1 |
aa2Triplet.put("W", "TRP"); |
294 |
1 |
aa2Triplet.put("w", "TRP"); |
295 |
1 |
aa2Triplet.put("Y", "TYR"); |
296 |
1 |
aa2Triplet.put("y", "TYR"); |
297 |
1 |
aa2Triplet.put("V", "VAL"); |
298 |
1 |
aa2Triplet.put("v", "VAL"); |
299 |
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} |
300 |
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301 |
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public static final String[] aa = { "A", "R", "N", "D", "C", "Q", "E", |
302 |
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"G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", |
303 |
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"Z", "X", "_", "*", ".", " ", "U" }; |
304 |
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305 |
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public static final Color midBlue = new Color(100, 100, 255); |
306 |
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307 |
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308 |
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309 |
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310 |
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312 |
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315 |
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316 |
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317 |
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318 |
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319 |
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320 |
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321 |
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322 |
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323 |
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public static final Color[] taylor = { new Color(204, 255, 0), |
324 |
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325 |
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new Color(0, 0, 255), |
326 |
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new Color(204, 0, 255), |
327 |
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new Color(255, 0, 0), |
328 |
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new Color(255, 255, 0), |
329 |
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new Color(255, 0, 204), |
330 |
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new Color(255, 0, 102), |
331 |
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new Color(255, 153, 0), |
332 |
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new Color(0, 102, 255), |
333 |
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new Color(102, 255, 0), |
334 |
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new Color(51, 255, 0), |
335 |
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new Color(102, 0, 255), |
336 |
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new Color(0, 255, 0), |
337 |
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new Color(0, 255, 102), |
338 |
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new Color(255, 204, 0), |
339 |
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new Color(255, 51, 0), |
340 |
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new Color(255, 102, 0), |
341 |
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new Color(0, 204, 255), |
342 |
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new Color(0, 255, 204), |
343 |
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new Color(153, 255, 0), |
344 |
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Color.white, |
345 |
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Color.white, |
346 |
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Color.white, |
347 |
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Color.white, |
348 |
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Color.white, |
349 |
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Color.white |
350 |
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}; |
351 |
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|
352 |
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public static final Color[] nucleotide = { new Color(100, 247, 63), |
353 |
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new Color(255, 179, 64), |
354 |
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new Color(235, 65, 60), |
355 |
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new Color(60, 136, 238), |
356 |
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new Color(60, 136, 238), |
357 |
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Color.white, |
358 |
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Color.white, |
359 |
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Color.white, |
360 |
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Color.white, |
361 |
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Color.white, |
362 |
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Color.white, |
363 |
|
}; |
364 |
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|
365 |
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366 |
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public static final Color[] purinepyrimidine = { new Color(255, 131, 250), |
367 |
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|
368 |
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|
369 |
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|
370 |
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|
371 |
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new Color(64, 224, 208), |
372 |
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Color.white, |
373 |
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Color.white |
374 |
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}; |
375 |
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|
376 |
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377 |
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public static final Color[] zappo = { Color.pink, |
378 |
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midBlue, |
379 |
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Color.green, |
380 |
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Color.red, |
381 |
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Color.yellow, |
382 |
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Color.green, |
383 |
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Color.red, |
384 |
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Color.magenta, |
385 |
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midBlue, |
386 |
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Color.pink, |
387 |
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Color.pink, |
388 |
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midBlue, |
389 |
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Color.pink, |
390 |
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Color.orange, |
391 |
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Color.magenta, |
392 |
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Color.green, |
393 |
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Color.green, |
394 |
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Color.orange, |
395 |
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Color.orange, |
396 |
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Color.pink, |
397 |
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Color.white, |
398 |
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Color.white, |
399 |
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Color.white, |
400 |
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Color.white, |
401 |
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Color.white, |
402 |
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Color.white, |
403 |
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Color.white |
404 |
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}; |
405 |
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|
406 |
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|
407 |
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public static final double[] hyd2 = { 0.62, |
408 |
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0.29, |
409 |
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-0.90, |
410 |
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-0.74, |
411 |
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1.19, |
412 |
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0.48, |
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-0.40, |
414 |
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1.38, |
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-1.50, |
416 |
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1.06, |
417 |
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0.64, |
418 |
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-0.78, |
419 |
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0.12, |
420 |
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-0.85, |
421 |
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-2.53, |
422 |
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-0.18, |
423 |
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-0.05, |
424 |
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1.08, |
425 |
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0.81, |
426 |
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0.0, |
427 |
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0.26, |
428 |
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0.0, |
429 |
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0.0 |
430 |
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}; |
431 |
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|
432 |
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public static final double[] helix = { 1.42, 0.98, 0.67, 1.01, 0.70, 1.11, |
433 |
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1.51, 0.57, 1.00, 1.08, 1.21, 1.16, 1.45, 1.13, 0.57, 0.77, 0.83, |
434 |
|
1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0 }; |
435 |
|
|
436 |
|
public static final double helixmin = 0.57; |
437 |
|
|
438 |
|
public static final double helixmax = 1.51; |
439 |
|
|
440 |
|
public static final double[] strand = { 0.83, 0.93, 0.89, 0.54, 1.19, |
441 |
|
1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74, 1.05, 1.38, 0.55, 0.75, |
442 |
|
1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0 }; |
443 |
|
|
444 |
|
public static final double strandmin = 0.37; |
445 |
|
|
446 |
|
public static final double strandmax = 1.7; |
447 |
|
|
448 |
|
public static final double[] turn = { 0.66, 0.95, 1.56, 1.46, 1.19, 0.98, |
449 |
|
0.74, 1.56, 0.95, 0.47, 0.59, 1.01, 0.60, 0.60, 1.52, 1.43, 0.96, |
450 |
|
0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0 }; |
451 |
|
|
452 |
|
public static final double turnmin = 0.47; |
453 |
|
|
454 |
|
public static final double turnmax = 1.56; |
455 |
|
|
456 |
|
public static final double[] buried = { 1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3, |
457 |
|
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, |
458 |
|
0.3, 1.358, 0.00 }; |
459 |
|
|
460 |
|
public static final double buriedmin = 0.05; |
461 |
|
|
462 |
|
public static final double buriedmax = 4.6; |
463 |
|
|
464 |
|
|
465 |
|
|
466 |
|
|
467 |
|
public static final double[] hyd = { 1.8, -4.5, -3.5, -3.5, 2.5, -3.5, |
468 |
|
-3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9, 2.8, -1.6, -0.8, -0.7, -0.9, |
469 |
|
-1.3, 4.2, -3.5, -3.5, -0.49, 0.0 }; |
470 |
|
|
471 |
|
public static final double hydmax = 4.5; |
472 |
|
|
473 |
|
public static final double hydmin = -3.9; |
474 |
|
|
475 |
|
|
476 |
|
|
477 |
|
|
478 |
|
|
479 |
|
|
480 |
|
|
481 |
|
|
482 |
|
|
483 |
|
|
484 |
|
|
485 |
|
|
486 |
|
|
487 |
|
|
488 |
|
|
489 |
|
|
490 |
|
|
491 |
|
|
492 |
|
|
493 |
|
|
494 |
|
|
495 |
|
|
496 |
|
|
497 |
|
|
498 |
|
|
499 |
|
public static String STOP = "STOP"; |
500 |
|
|
501 |
|
public static List<String> STOP_CODONS = Arrays.asList("TGA", "TAA", "TAG"); |
502 |
|
|
503 |
|
public static String START = "ATG"; |
504 |
|
|
505 |
|
|
506 |
|
|
507 |
|
|
508 |
|
public static final Map<String, String[]> ambiguityCodes = new Hashtable<>(); |
509 |
|
|
510 |
|
|
511 |
|
|
512 |
|
|
513 |
|
|
514 |
|
public static final Hashtable<String, String> codonHash2 = new Hashtable<>(); |
515 |
|
|
516 |
|
|
517 |
|
|
518 |
|
|
519 |
|
public final static Hashtable<String, List<String>> _ambiguityCodes = new Hashtable<>(); |
520 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (76) |
Complexity: 1 |
Complexity Density: 0.01 |
|
521 |
1 |
static... |
522 |
|
{ |
523 |
|
|
524 |
|
|
525 |
|
|
526 |
1 |
ambiguityCodes.put("R", new String[] { "A", "G" }); |
527 |
1 |
ambiguityCodes.put("Y", new String[] { "T", "C" }); |
528 |
1 |
ambiguityCodes.put("W", new String[] { "A", "T" }); |
529 |
1 |
ambiguityCodes.put("S", new String[] { "G", "C" }); |
530 |
1 |
ambiguityCodes.put("M", new String[] { "A", "C" }); |
531 |
1 |
ambiguityCodes.put("K", new String[] { "G", "T" }); |
532 |
1 |
ambiguityCodes.put("H", new String[] { "A", "T", "C" }); |
533 |
1 |
ambiguityCodes.put("B", new String[] { "G", "T", "C" }); |
534 |
1 |
ambiguityCodes.put("V", new String[] { "G", "A", "C" }); |
535 |
1 |
ambiguityCodes.put("D", new String[] { "G", "A", "T" }); |
536 |
1 |
ambiguityCodes.put("N", new String[] { "G", "A", "T", "C" }); |
537 |
|
|
538 |
|
|
539 |
1 |
codonHash2.put("AAA", "K"); |
540 |
1 |
codonHash2.put("AAG", "K"); |
541 |
1 |
codonHash2.put("AAC", "N"); |
542 |
1 |
codonHash2.put("AAT", "N"); |
543 |
|
|
544 |
1 |
codonHash2.put("CAA", "Q"); |
545 |
1 |
codonHash2.put("CAG", "Q"); |
546 |
1 |
codonHash2.put("CAC", "H"); |
547 |
1 |
codonHash2.put("CAT", "H"); |
548 |
|
|
549 |
1 |
codonHash2.put("GAA", "E"); |
550 |
1 |
codonHash2.put("GAG", "E"); |
551 |
1 |
codonHash2.put("GAC", "D"); |
552 |
1 |
codonHash2.put("GAT", "D"); |
553 |
|
|
554 |
1 |
codonHash2.put("TAC", "Y"); |
555 |
1 |
codonHash2.put("TAT", "Y"); |
556 |
|
|
557 |
1 |
codonHash2.put("ACA", "T"); |
558 |
1 |
codonHash2.put("ACC", "T"); |
559 |
1 |
codonHash2.put("ACT", "T"); |
560 |
1 |
codonHash2.put("ACG", "T"); |
561 |
|
|
562 |
1 |
codonHash2.put("CCA", "P"); |
563 |
1 |
codonHash2.put("CCG", "P"); |
564 |
1 |
codonHash2.put("CCC", "P"); |
565 |
1 |
codonHash2.put("CCT", "P"); |
566 |
|
|
567 |
1 |
codonHash2.put("GCA", "A"); |
568 |
1 |
codonHash2.put("GCG", "A"); |
569 |
1 |
codonHash2.put("GCC", "A"); |
570 |
1 |
codonHash2.put("GCT", "A"); |
571 |
|
|
572 |
1 |
codonHash2.put("TCA", "S"); |
573 |
1 |
codonHash2.put("TCG", "S"); |
574 |
1 |
codonHash2.put("TCC", "S"); |
575 |
1 |
codonHash2.put("TCT", "S"); |
576 |
1 |
codonHash2.put("AGC", "S"); |
577 |
1 |
codonHash2.put("AGT", "S"); |
578 |
|
|
579 |
1 |
codonHash2.put("AGA", "R"); |
580 |
1 |
codonHash2.put("AGG", "R"); |
581 |
1 |
codonHash2.put("CGA", "R"); |
582 |
1 |
codonHash2.put("CGG", "R"); |
583 |
1 |
codonHash2.put("CGC", "R"); |
584 |
1 |
codonHash2.put("CGT", "R"); |
585 |
|
|
586 |
1 |
codonHash2.put("GGA", "G"); |
587 |
1 |
codonHash2.put("GGG", "G"); |
588 |
1 |
codonHash2.put("GGC", "G"); |
589 |
1 |
codonHash2.put("GGT", "G"); |
590 |
|
|
591 |
1 |
codonHash2.put("TGA", "*"); |
592 |
1 |
codonHash2.put("TAA", "*"); |
593 |
1 |
codonHash2.put("TAG", "*"); |
594 |
|
|
595 |
1 |
codonHash2.put("TGG", "W"); |
596 |
|
|
597 |
1 |
codonHash2.put("TGC", "C"); |
598 |
1 |
codonHash2.put("TGT", "C"); |
599 |
|
|
600 |
1 |
codonHash2.put("ATA", "I"); |
601 |
1 |
codonHash2.put("ATC", "I"); |
602 |
1 |
codonHash2.put("ATT", "I"); |
603 |
|
|
604 |
1 |
codonHash2.put("ATG", "M"); |
605 |
|
|
606 |
1 |
codonHash2.put("CTA", "L"); |
607 |
1 |
codonHash2.put("CTG", "L"); |
608 |
1 |
codonHash2.put("CTC", "L"); |
609 |
1 |
codonHash2.put("CTT", "L"); |
610 |
1 |
codonHash2.put("TTA", "L"); |
611 |
1 |
codonHash2.put("TTG", "L"); |
612 |
|
|
613 |
1 |
codonHash2.put("GTA", "V"); |
614 |
1 |
codonHash2.put("GTG", "V"); |
615 |
1 |
codonHash2.put("GTC", "V"); |
616 |
1 |
codonHash2.put("GTT", "V"); |
617 |
|
|
618 |
1 |
codonHash2.put("TTC", "F"); |
619 |
1 |
codonHash2.put("TTT", "F"); |
620 |
|
|
621 |
1 |
buildAmbiguityCodonSet(); |
622 |
|
} |
623 |
|
|
624 |
|
|
625 |
|
|
626 |
|
|
|
|
| 90% |
Uncovered Elements: 9 (90) |
Complexity: 22 |
Complexity Density: 0.38 |
|
627 |
1 |
public static void buildAmbiguityCodonSet()... |
628 |
|
{ |
629 |
1 |
if (_ambiguityCodes.size() > 0) |
630 |
|
{ |
631 |
0 |
System.err |
632 |
|
.println("Ignoring multiple calls to buildAmbiguityCodonSet"); |
633 |
0 |
return; |
634 |
|
} |
635 |
|
|
636 |
1 |
for (Map.Entry<String, String[]> acode : ambiguityCodes.entrySet()) |
637 |
|
{ |
638 |
11 |
for (String r : acode.getValue()) |
639 |
|
{ |
640 |
28 |
List<String> codesfor = _ambiguityCodes.get(r); |
641 |
28 |
if (codesfor == null) |
642 |
|
{ |
643 |
4 |
_ambiguityCodes.put(r, codesfor = new ArrayList<>()); |
644 |
|
} |
645 |
28 |
if (!codesfor.contains(acode.getKey())) |
646 |
|
{ |
647 |
28 |
codesfor.add(acode.getKey()); |
648 |
|
} |
649 |
|
else |
650 |
|
{ |
651 |
0 |
System.err.println( |
652 |
|
"Inconsistency in the IUBMB ambiguity code nomenclature table: collision for " |
653 |
|
+ acode.getKey() + " in residue " + r); |
654 |
|
} |
655 |
|
} |
656 |
|
} |
657 |
|
|
658 |
|
|
659 |
1 |
String[] unambcodons = codonHash2.keySet() |
660 |
|
.toArray(new String[codonHash2.size()]); |
661 |
1 |
for (String codon : unambcodons) |
662 |
|
{ |
663 |
64 |
String residue = codonHash2.get(codon); |
664 |
64 |
String acodon[][] = new String[codon.length()][]; |
665 |
256 |
for (int i = 0, iSize = codon.length(); i < iSize; i++) |
666 |
|
{ |
667 |
192 |
String _ac = "" + codon.charAt(i); |
668 |
192 |
List<String> acodes = _ambiguityCodes.get(_ac); |
669 |
192 |
if (acodes != null) |
670 |
|
{ |
671 |
192 |
acodon[i] = acodes.toArray(new String[acodes.size()]); |
672 |
|
} |
673 |
|
else |
674 |
|
{ |
675 |
0 |
acodon[i] = new String[] {}; |
676 |
|
} |
677 |
|
} |
678 |
|
|
679 |
64 |
int tpos[] = new int[codon.length()], |
680 |
|
cpos[] = new int[codon.length()]; |
681 |
256 |
for (int i = 0; i < tpos.length; i++) |
682 |
|
{ |
683 |
192 |
tpos[i] = -1; |
684 |
|
} |
685 |
64 |
tpos[acodon.length - 1] = 0; |
686 |
64 |
int ipos, j; |
687 |
32768 |
while (tpos[0] < acodon[0].length) |
688 |
|
{ |
689 |
|
|
690 |
32704 |
char allres[][] = new char[tpos.length][]; |
691 |
32704 |
String _acodon = ""; |
692 |
130816 |
for (ipos = 0; ipos < tpos.length; ipos++) |
693 |
|
{ |
694 |
98112 |
if (acodon[ipos].length == 0 || tpos[ipos] < 0) |
695 |
|
{ |
696 |
12096 |
_acodon += codon.charAt(ipos); |
697 |
12096 |
allres[ipos] = new char[] { codon.charAt(ipos) }; |
698 |
|
} |
699 |
|
else |
700 |
|
{ |
701 |
86016 |
_acodon += acodon[ipos][tpos[ipos]]; |
702 |
86016 |
String[] altbase = ambiguityCodes.get(acodon[ipos][tpos[ipos]]); |
703 |
86016 |
allres[ipos] = new char[altbase.length]; |
704 |
86016 |
j = 0; |
705 |
86016 |
for (String ab : altbase) |
706 |
|
{ |
707 |
233472 |
allres[ipos][j++] = ab.charAt(0); |
708 |
|
} |
709 |
|
} |
710 |
|
} |
711 |
|
|
712 |
130816 |
for (ipos = 0; ipos < cpos.length; ipos++) |
713 |
|
{ |
714 |
98112 |
cpos[ipos] = 0; |
715 |
|
} |
716 |
32704 |
boolean valid = true; |
717 |
32704 |
do |
718 |
|
{ |
719 |
44109 |
String _codon = ""; |
720 |
176436 |
for (j = 0; j < cpos.length; j++) |
721 |
|
{ |
722 |
132327 |
_codon += allres[j][cpos[j]]; |
723 |
|
} |
724 |
44109 |
String tr = codonHash2.get(_codon); |
725 |
? |
if (valid = (tr != null && tr.equals(residue))) |
726 |
|
{ |
727 |
|
|
728 |
11682 |
ipos = acodon.length - 1; |
729 |
16879 |
while (++cpos[ipos] >= allres[ipos].length && ipos > 0) |
730 |
|
{ |
731 |
5197 |
cpos[ipos] = 0; |
732 |
5197 |
ipos--; |
733 |
|
} |
734 |
|
} |
735 |
44109 |
} while (valid && cpos[0] < allres[0].length); |
736 |
32704 |
if (valid) |
737 |
|
{ |
738 |
|
|
739 |
|
|
740 |
|
|
741 |
277 |
codonHash2.put(_acodon, residue); |
742 |
|
} |
743 |
|
else |
744 |
|
{ |
745 |
|
|
746 |
|
|
747 |
|
} |
748 |
|
|
749 |
32704 |
ipos = acodon.length - 1; |
750 |
37312 |
while (++tpos[ipos] >= acodon[ipos].length && ipos > 0) |
751 |
|
{ |
752 |
4608 |
tpos[ipos] = -1; |
753 |
4608 |
ipos--; |
754 |
|
} |
755 |
|
} |
756 |
|
} |
757 |
|
} |
758 |
|
|
759 |
|
|
760 |
|
public static Map<String, Map<String, Integer>> propHash = new Hashtable<>(); |
761 |
|
|
762 |
|
public static Map<String, Integer> hydrophobic = new Hashtable<>(); |
763 |
|
|
764 |
|
public static Map<String, Integer> polar = new Hashtable<>(); |
765 |
|
|
766 |
|
public static Map<String, Integer> small = new Hashtable<>(); |
767 |
|
|
768 |
|
public static Map<String, Integer> positive = new Hashtable<>(); |
769 |
|
|
770 |
|
public static Map<String, Integer> negative = new Hashtable<>(); |
771 |
|
|
772 |
|
public static Map<String, Integer> charged = new Hashtable<>(); |
773 |
|
|
774 |
|
public static Map<String, Integer> aromatic = new Hashtable<>(); |
775 |
|
|
776 |
|
public static Map<String, Integer> aliphatic = new Hashtable<>(); |
777 |
|
|
778 |
|
public static Map<String, Integer> tiny = new Hashtable<>(); |
779 |
|
|
780 |
|
public static Map<String, Integer> proline = new Hashtable<>(); |
781 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (23) |
Complexity: 1 |
Complexity Density: 0.04 |
|
782 |
1 |
static... |
783 |
|
{ |
784 |
1 |
hydrophobic.put("I", ONE); |
785 |
1 |
hydrophobic.put("L", ONE); |
786 |
1 |
hydrophobic.put("V", ONE); |
787 |
1 |
hydrophobic.put("C", ONE); |
788 |
1 |
hydrophobic.put("A", ONE); |
789 |
1 |
hydrophobic.put("G", ONE); |
790 |
1 |
hydrophobic.put("M", ONE); |
791 |
1 |
hydrophobic.put("F", ONE); |
792 |
1 |
hydrophobic.put("Y", ONE); |
793 |
1 |
hydrophobic.put("W", ONE); |
794 |
1 |
hydrophobic.put("H", ONE); |
795 |
1 |
hydrophobic.put("K", ONE); |
796 |
1 |
hydrophobic.put("X", ONE); |
797 |
1 |
hydrophobic.put("-", ONE); |
798 |
1 |
hydrophobic.put("*", ONE); |
799 |
1 |
hydrophobic.put("R", ZERO); |
800 |
1 |
hydrophobic.put("E", ZERO); |
801 |
1 |
hydrophobic.put("Q", ZERO); |
802 |
1 |
hydrophobic.put("D", ZERO); |
803 |
1 |
hydrophobic.put("N", ZERO); |
804 |
1 |
hydrophobic.put("S", ZERO); |
805 |
1 |
hydrophobic.put("T", ONE); |
806 |
1 |
hydrophobic.put("P", ZERO); |
807 |
|
} |
808 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (23) |
Complexity: 1 |
Complexity Density: 0.04 |
|
809 |
1 |
static... |
810 |
|
{ |
811 |
1 |
polar.put("Y", ONE); |
812 |
1 |
polar.put("W", ONE); |
813 |
1 |
polar.put("H", ONE); |
814 |
1 |
polar.put("K", ONE); |
815 |
1 |
polar.put("R", ONE); |
816 |
1 |
polar.put("E", ONE); |
817 |
1 |
polar.put("Q", ONE); |
818 |
1 |
polar.put("D", ONE); |
819 |
1 |
polar.put("N", ONE); |
820 |
1 |
polar.put("S", ONE); |
821 |
1 |
polar.put("T", ONE); |
822 |
1 |
polar.put("X", ONE); |
823 |
1 |
polar.put("-", ONE); |
824 |
1 |
polar.put("*", ONE); |
825 |
1 |
polar.put("I", ZERO); |
826 |
1 |
polar.put("L", ZERO); |
827 |
1 |
polar.put("V", ZERO); |
828 |
1 |
polar.put("C", ZERO); |
829 |
1 |
polar.put("A", ZERO); |
830 |
1 |
polar.put("G", ZERO); |
831 |
1 |
polar.put("M", ZERO); |
832 |
1 |
polar.put("F", ZERO); |
833 |
1 |
polar.put("P", ZERO); |
834 |
|
} |
835 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (22) |
Complexity: 1 |
Complexity Density: 0.05 |
|
836 |
1 |
static... |
837 |
|
{ |
838 |
1 |
small.put("I", ZERO); |
839 |
1 |
small.put("L", ZERO); |
840 |
1 |
small.put("V", ONE); |
841 |
1 |
small.put("C", ONE); |
842 |
1 |
small.put("A", ONE); |
843 |
1 |
small.put("G", ONE); |
844 |
1 |
small.put("M", ZERO); |
845 |
1 |
small.put("F", ZERO); |
846 |
1 |
small.put("Y", ZERO); |
847 |
1 |
small.put("W", ZERO); |
848 |
1 |
small.put("H", ZERO); |
849 |
1 |
small.put("K", ZERO); |
850 |
1 |
small.put("R", ZERO); |
851 |
1 |
small.put("E", ZERO); |
852 |
1 |
small.put("Q", ZERO); |
853 |
1 |
small.put("D", ONE); |
854 |
1 |
small.put("N", ONE); |
855 |
1 |
small.put("S", ONE); |
856 |
1 |
small.put("T", ONE); |
857 |
1 |
small.put("P", ONE); |
858 |
1 |
small.put("-", ONE); |
859 |
1 |
small.put("*", ONE); |
860 |
|
} |
861 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (22) |
Complexity: 1 |
Complexity Density: 0.05 |
|
862 |
1 |
static... |
863 |
|
{ |
864 |
1 |
positive.put("I", ZERO); |
865 |
1 |
positive.put("L", ZERO); |
866 |
1 |
positive.put("V", ZERO); |
867 |
1 |
positive.put("C", ZERO); |
868 |
1 |
positive.put("A", ZERO); |
869 |
1 |
positive.put("G", ZERO); |
870 |
1 |
positive.put("M", ZERO); |
871 |
1 |
positive.put("F", ZERO); |
872 |
1 |
positive.put("Y", ZERO); |
873 |
1 |
positive.put("W", ZERO); |
874 |
1 |
positive.put("H", ONE); |
875 |
1 |
positive.put("K", ONE); |
876 |
1 |
positive.put("R", ONE); |
877 |
1 |
positive.put("E", ZERO); |
878 |
1 |
positive.put("Q", ZERO); |
879 |
1 |
positive.put("D", ZERO); |
880 |
1 |
positive.put("N", ZERO); |
881 |
1 |
positive.put("S", ZERO); |
882 |
1 |
positive.put("T", ZERO); |
883 |
1 |
positive.put("P", ZERO); |
884 |
1 |
positive.put("-", ONE); |
885 |
1 |
positive.put("*", ONE); |
886 |
|
} |
887 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (22) |
Complexity: 1 |
Complexity Density: 0.05 |
|
888 |
1 |
static... |
889 |
|
{ |
890 |
1 |
negative.put("I", ZERO); |
891 |
1 |
negative.put("L", ZERO); |
892 |
1 |
negative.put("V", ZERO); |
893 |
1 |
negative.put("C", ZERO); |
894 |
1 |
negative.put("A", ZERO); |
895 |
1 |
negative.put("G", ZERO); |
896 |
1 |
negative.put("M", ZERO); |
897 |
1 |
negative.put("F", ZERO); |
898 |
1 |
negative.put("Y", ZERO); |
899 |
1 |
negative.put("W", ZERO); |
900 |
1 |
negative.put("H", ZERO); |
901 |
1 |
negative.put("K", ZERO); |
902 |
1 |
negative.put("R", ZERO); |
903 |
1 |
negative.put("E", ONE); |
904 |
1 |
negative.put("Q", ZERO); |
905 |
1 |
negative.put("D", ONE); |
906 |
1 |
negative.put("N", ZERO); |
907 |
1 |
negative.put("S", ZERO); |
908 |
1 |
negative.put("T", ZERO); |
909 |
1 |
negative.put("P", ZERO); |
910 |
1 |
negative.put("-", ONE); |
911 |
1 |
negative.put("*", ONE); |
912 |
|
} |
913 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (22) |
Complexity: 1 |
Complexity Density: 0.05 |
|
914 |
1 |
static... |
915 |
|
{ |
916 |
1 |
charged.put("I", ZERO); |
917 |
1 |
charged.put("L", ZERO); |
918 |
1 |
charged.put("V", ZERO); |
919 |
1 |
charged.put("C", ZERO); |
920 |
1 |
charged.put("A", ZERO); |
921 |
1 |
charged.put("G", ZERO); |
922 |
1 |
charged.put("M", ZERO); |
923 |
1 |
charged.put("F", ZERO); |
924 |
1 |
charged.put("Y", ZERO); |
925 |
1 |
charged.put("W", ZERO); |
926 |
1 |
charged.put("H", ONE); |
927 |
1 |
charged.put("K", ONE); |
928 |
1 |
charged.put("R", ONE); |
929 |
1 |
charged.put("E", ONE); |
930 |
1 |
charged.put("Q", ZERO); |
931 |
1 |
charged.put("D", ONE); |
932 |
1 |
charged.put("N", ZERO); |
933 |
|
|
934 |
|
|
935 |
|
|
936 |
1 |
charged.put("S", ZERO); |
937 |
1 |
charged.put("T", ZERO); |
938 |
1 |
charged.put("P", ZERO); |
939 |
1 |
charged.put("-", ONE); |
940 |
1 |
charged.put("*", ONE); |
941 |
|
} |
942 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (22) |
Complexity: 1 |
Complexity Density: 0.05 |
|
943 |
1 |
static... |
944 |
|
{ |
945 |
1 |
aromatic.put("I", ZERO); |
946 |
1 |
aromatic.put("L", ZERO); |
947 |
1 |
aromatic.put("V", ZERO); |
948 |
1 |
aromatic.put("C", ZERO); |
949 |
1 |
aromatic.put("A", ZERO); |
950 |
1 |
aromatic.put("G", ZERO); |
951 |
1 |
aromatic.put("M", ZERO); |
952 |
1 |
aromatic.put("F", ONE); |
953 |
1 |
aromatic.put("Y", ONE); |
954 |
1 |
aromatic.put("W", ONE); |
955 |
1 |
aromatic.put("H", ONE); |
956 |
1 |
aromatic.put("K", ZERO); |
957 |
1 |
aromatic.put("R", ZERO); |
958 |
1 |
aromatic.put("E", ZERO); |
959 |
1 |
aromatic.put("Q", ZERO); |
960 |
1 |
aromatic.put("D", ZERO); |
961 |
1 |
aromatic.put("N", ZERO); |
962 |
1 |
aromatic.put("S", ZERO); |
963 |
1 |
aromatic.put("T", ZERO); |
964 |
1 |
aromatic.put("P", ZERO); |
965 |
1 |
aromatic.put("-", ONE); |
966 |
1 |
aromatic.put("*", ONE); |
967 |
|
} |
968 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (22) |
Complexity: 1 |
Complexity Density: 0.05 |
|
969 |
1 |
static... |
970 |
|
{ |
971 |
1 |
aliphatic.put("I", ONE); |
972 |
1 |
aliphatic.put("L", ONE); |
973 |
1 |
aliphatic.put("V", ONE); |
974 |
1 |
aliphatic.put("C", ZERO); |
975 |
1 |
aliphatic.put("A", ZERO); |
976 |
1 |
aliphatic.put("G", ZERO); |
977 |
1 |
aliphatic.put("M", ZERO); |
978 |
1 |
aliphatic.put("F", ZERO); |
979 |
1 |
aliphatic.put("Y", ZERO); |
980 |
1 |
aliphatic.put("W", ZERO); |
981 |
1 |
aliphatic.put("H", ZERO); |
982 |
1 |
aliphatic.put("K", ZERO); |
983 |
1 |
aliphatic.put("R", ZERO); |
984 |
1 |
aliphatic.put("E", ZERO); |
985 |
1 |
aliphatic.put("Q", ZERO); |
986 |
1 |
aliphatic.put("D", ZERO); |
987 |
1 |
aliphatic.put("N", ZERO); |
988 |
1 |
aliphatic.put("S", ZERO); |
989 |
1 |
aliphatic.put("T", ZERO); |
990 |
1 |
aliphatic.put("P", ZERO); |
991 |
1 |
aliphatic.put("-", ONE); |
992 |
1 |
aliphatic.put("*", ONE); |
993 |
|
} |
994 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (22) |
Complexity: 1 |
Complexity Density: 0.05 |
|
995 |
1 |
static... |
996 |
|
{ |
997 |
1 |
tiny.put("I", ZERO); |
998 |
1 |
tiny.put("L", ZERO); |
999 |
1 |
tiny.put("V", ZERO); |
1000 |
1 |
tiny.put("C", ZERO); |
1001 |
1 |
tiny.put("A", ONE); |
1002 |
1 |
tiny.put("G", ONE); |
1003 |
1 |
tiny.put("M", ZERO); |
1004 |
1 |
tiny.put("F", ZERO); |
1005 |
1 |
tiny.put("Y", ZERO); |
1006 |
1 |
tiny.put("W", ZERO); |
1007 |
1 |
tiny.put("H", ZERO); |
1008 |
1 |
tiny.put("K", ZERO); |
1009 |
1 |
tiny.put("R", ZERO); |
1010 |
1 |
tiny.put("E", ZERO); |
1011 |
1 |
tiny.put("Q", ZERO); |
1012 |
1 |
tiny.put("D", ZERO); |
1013 |
1 |
tiny.put("N", ZERO); |
1014 |
1 |
tiny.put("S", ONE); |
1015 |
1 |
tiny.put("T", ZERO); |
1016 |
1 |
tiny.put("P", ZERO); |
1017 |
1 |
tiny.put("-", ONE); |
1018 |
1 |
tiny.put("*", ONE); |
1019 |
|
} |
1020 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (22) |
Complexity: 1 |
Complexity Density: 0.05 |
|
1021 |
1 |
static... |
1022 |
|
{ |
1023 |
1 |
proline.put("I", ZERO); |
1024 |
1 |
proline.put("L", ZERO); |
1025 |
1 |
proline.put("V", ZERO); |
1026 |
1 |
proline.put("C", ZERO); |
1027 |
1 |
proline.put("A", ZERO); |
1028 |
1 |
proline.put("G", ZERO); |
1029 |
1 |
proline.put("M", ZERO); |
1030 |
1 |
proline.put("F", ZERO); |
1031 |
1 |
proline.put("Y", ZERO); |
1032 |
1 |
proline.put("W", ZERO); |
1033 |
1 |
proline.put("H", ZERO); |
1034 |
1 |
proline.put("K", ZERO); |
1035 |
1 |
proline.put("R", ZERO); |
1036 |
1 |
proline.put("E", ZERO); |
1037 |
1 |
proline.put("Q", ZERO); |
1038 |
1 |
proline.put("D", ZERO); |
1039 |
1 |
proline.put("N", ZERO); |
1040 |
1 |
proline.put("S", ZERO); |
1041 |
1 |
proline.put("T", ZERO); |
1042 |
1 |
proline.put("P", ONE); |
1043 |
1 |
proline.put("-", ONE); |
1044 |
1 |
proline.put("*", ONE); |
1045 |
|
} |
1046 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (10) |
Complexity: 1 |
Complexity Density: 0.1 |
|
1047 |
1 |
static... |
1048 |
|
{ |
1049 |
1 |
propHash.put("hydrophobic", hydrophobic); |
1050 |
1 |
propHash.put("small", small); |
1051 |
1 |
propHash.put("positive", positive); |
1052 |
1 |
propHash.put("negative", negative); |
1053 |
1 |
propHash.put("charged", charged); |
1054 |
1 |
propHash.put("aromatic", aromatic); |
1055 |
1 |
propHash.put("aliphatic", aliphatic); |
1056 |
1 |
propHash.put("tiny", tiny); |
1057 |
1 |
propHash.put("proline", proline); |
1058 |
1 |
propHash.put("polar", polar); |
1059 |
|
} |
|
|
| 93.5% |
Uncovered Elements: 4 (62) |
Complexity: 18 |
Complexity Density: 0.53 |
|
1060 |
1 |
static... |
1061 |
|
{ |
1062 |
1 |
int[][] propMatrixF = new int[maxProteinIndex][maxProteinIndex], |
1063 |
|
propMatrixPos = new int[maxProteinIndex][maxProteinIndex], |
1064 |
|
propMatrixEpos = new int[maxProteinIndex][maxProteinIndex]; |
1065 |
24 |
for (int i = 0; i < maxProteinIndex; i++) |
1066 |
|
{ |
1067 |
23 |
int maxF = 0, maxP = 0, maxEP = 0; |
1068 |
23 |
String ic = ""; |
1069 |
23 |
if (aa.length > i) |
1070 |
|
{ |
1071 |
23 |
ic += aa[i]; |
1072 |
|
} |
1073 |
|
else |
1074 |
|
{ |
1075 |
0 |
ic = "-"; |
1076 |
|
} |
1077 |
276 |
for (int j = i + 1; j < maxProteinIndex; j++) |
1078 |
|
{ |
1079 |
253 |
String jc = ""; |
1080 |
253 |
if (aa.length > j) |
1081 |
|
{ |
1082 |
253 |
jc += aa[j]; |
1083 |
|
} |
1084 |
|
else |
1085 |
|
{ |
1086 |
0 |
jc = "-"; |
1087 |
|
} |
1088 |
253 |
propMatrixF[i][j] = 0; |
1089 |
253 |
propMatrixPos[i][j] = 0; |
1090 |
253 |
propMatrixEpos[i][j] = 0; |
1091 |
253 |
for (String ph : propHash.keySet()) |
1092 |
|
{ |
1093 |
2530 |
Map<String, Integer> pph = propHash.get(ph); |
1094 |
2530 |
if (pph.get(ic) != null && pph.get(jc) != null) |
1095 |
|
{ |
1096 |
1940 |
int icp = pph.get(ic).intValue(), jcp = pph.get(jc).intValue(); |
1097 |
|
|
1098 |
1940 |
propMatrixPos[i][j] += icp == jcp && icp > 0 ? 2 : 0; |
1099 |
1940 |
propMatrixPos[j][i] += icp == jcp && icp > 0 ? 2 : 0; |
1100 |
1940 |
propMatrixF[i][j] += icp == jcp ? 2 : 0; |
1101 |
1940 |
propMatrixF[j][i] += icp == jcp ? 2 : 0; |
1102 |
1940 |
propMatrixEpos[i][j] += icp == jcp ? (1 + icp * 2) : 0; |
1103 |
1940 |
propMatrixEpos[j][i] += icp == jcp ? (1 + icp * 2) : 0; |
1104 |
|
} |
1105 |
|
} |
1106 |
253 |
if (maxF < propMatrixF[i][j]) |
1107 |
|
{ |
1108 |
37 |
maxF = propMatrixF[i][j]; |
1109 |
|
} |
1110 |
253 |
if (maxP < propMatrixPos[i][j]) |
1111 |
|
{ |
1112 |
31 |
maxP = propMatrixPos[i][j]; |
1113 |
|
} |
1114 |
253 |
if (maxEP < propMatrixEpos[i][j]) |
1115 |
|
{ |
1116 |
42 |
maxEP = propMatrixEpos[i][j]; |
1117 |
|
} |
1118 |
|
} |
1119 |
23 |
propMatrixF[i][i] = maxF; |
1120 |
23 |
propMatrixPos[i][i] = maxP; |
1121 |
23 |
propMatrixEpos[i][i] = maxEP; |
1122 |
|
} |
1123 |
|
} |
1124 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1125 |
0 |
private ResidueProperties()... |
1126 |
|
{ |
1127 |
|
} |
1128 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1129 |
0 |
public static double getHydmax()... |
1130 |
|
{ |
1131 |
0 |
return hydmax; |
1132 |
|
} |
1133 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1134 |
0 |
public static double getHydmin()... |
1135 |
|
{ |
1136 |
0 |
return hydmin; |
1137 |
|
} |
1138 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1139 |
0 |
public static double[] getHyd()... |
1140 |
|
{ |
1141 |
0 |
return hyd; |
1142 |
|
} |
1143 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1144 |
22376 |
public static Map<String, Integer> getAA3Hash()... |
1145 |
|
{ |
1146 |
22376 |
return aa3Hash; |
1147 |
|
} |
1148 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
1149 |
2150 |
public static String codonTranslate(String lccodon)... |
1150 |
|
{ |
1151 |
2150 |
String cdn = codonHash2.get(lccodon.toUpperCase()); |
1152 |
2150 |
if ("*".equals(cdn)) |
1153 |
|
{ |
1154 |
75 |
return STOP; |
1155 |
|
} |
1156 |
2075 |
return cdn; |
1157 |
|
} |
1158 |
|
|
1159 |
|
public static Hashtable<String, String> toDssp3State; |
|
|
| 100% |
Uncovered Elements: 0 (10) |
Complexity: 1 |
Complexity Density: 0.1 |
|
1160 |
1 |
static... |
1161 |
|
{ |
1162 |
1 |
toDssp3State = new Hashtable<>(); |
1163 |
1 |
toDssp3State.put("H", "H"); |
1164 |
1 |
toDssp3State.put("E", "E"); |
1165 |
1 |
toDssp3State.put("C", " "); |
1166 |
1 |
toDssp3State.put(" ", " "); |
1167 |
1 |
toDssp3State.put("T", " "); |
1168 |
1 |
toDssp3State.put("B", "E"); |
1169 |
1 |
toDssp3State.put("G", "H"); |
1170 |
1 |
toDssp3State.put("I", "H"); |
1171 |
1 |
toDssp3State.put("X", " "); |
1172 |
|
} |
1173 |
|
|
1174 |
|
|
1175 |
|
|
1176 |
|
|
1177 |
|
@param |
1178 |
|
@return |
1179 |
|
|
|
|
| 86.7% |
Uncovered Elements: 2 (15) |
Complexity: 4 |
Complexity Density: 0.44 |
|
1180 |
16778 |
public static String getDssp3state(String ssstring)... |
1181 |
|
{ |
1182 |
16778 |
if (ssstring == null) |
1183 |
|
{ |
1184 |
0 |
return null; |
1185 |
|
} |
1186 |
16778 |
StringBuffer ss = new StringBuffer(); |
1187 |
33556 |
for (int i = 0; i < ssstring.length(); i++) |
1188 |
|
{ |
1189 |
16778 |
String ssc = ssstring.substring(i, i + 1); |
1190 |
16778 |
if (toDssp3State.containsKey(ssc)) |
1191 |
|
{ |
1192 |
4111 |
ss.append(toDssp3State.get(ssc)); |
1193 |
|
} |
1194 |
|
else |
1195 |
|
{ |
1196 |
12667 |
ss.append(" "); |
1197 |
|
} |
1198 |
|
} |
1199 |
16778 |
return ss.toString(); |
1200 |
|
} |
1201 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1,300) |
Complexity: 1 |
Complexity Density: 0 |
|
1202 |
1 |
static... |
1203 |
|
{ |
1204 |
1 |
modifications.put("MSE", "MET"); |
1205 |
|
|
1206 |
|
|
1207 |
|
|
1208 |
|
|
1209 |
|
|
1210 |
|
|
1211 |
|
|
1212 |
|
|
1213 |
|
|
1214 |
|
|
1215 |
|
|
1216 |
|
|
1217 |
|
|
1218 |
1 |
modifications.put("00C", "CYS"); |
1219 |
1 |
modifications.put("01W", "XAA"); |
1220 |
1 |
modifications.put("02K", "ALA"); |
1221 |
1 |
modifications.put("03Y", "CYS"); |
1222 |
1 |
modifications.put("07O", "CYS"); |
1223 |
1 |
modifications.put("08P", "CYS"); |
1224 |
1 |
modifications.put("0A0", "ASP"); |
1225 |
1 |
modifications.put("0A1", "TYR"); |
1226 |
1 |
modifications.put("0A2", "LYS"); |
1227 |
1 |
modifications.put("0A8", "CYS"); |
1228 |
1 |
modifications.put("0AA", "VAL"); |
1229 |
1 |
modifications.put("0AB", "VAL"); |
1230 |
1 |
modifications.put("0AC", "GLY"); |
1231 |
1 |
modifications.put("0AD", "GLY"); |
1232 |
1 |
modifications.put("0AF", "TRP"); |
1233 |
1 |
modifications.put("0AG", "LEU"); |
1234 |
1 |
modifications.put("0AH", "SER"); |
1235 |
1 |
modifications.put("0AK", "ASP"); |
1236 |
1 |
modifications.put("0AM", "ALA"); |
1237 |
1 |
modifications.put("0AP", "CYS"); |
1238 |
1 |
modifications.put("0AU", "UR3"); |
1239 |
1 |
modifications.put("0AV", "ALA"); |
1240 |
1 |
modifications.put("0AZ", "PRO"); |
1241 |
1 |
modifications.put("0BN", "PHE"); |
1242 |
1 |
modifications.put("0C ", "CYS"); |
1243 |
1 |
modifications.put("0CS", "ALA"); |
1244 |
1 |
modifications.put("0DC", "CYS"); |
1245 |
1 |
modifications.put("0DG", "GLY"); |
1246 |
1 |
modifications.put("0DT", "THR"); |
1247 |
1 |
modifications.put("0FL", "ALA"); |
1248 |
1 |
modifications.put("0G ", "GLY"); |
1249 |
1 |
modifications.put("0NC", "ALA"); |
1250 |
1 |
modifications.put("0SP", "ALA"); |
1251 |
1 |
modifications.put("0U ", "UR3"); |
1252 |
1 |
modifications.put("0YG", "YG"); |
1253 |
1 |
modifications.put("10C", "CYS"); |
1254 |
1 |
modifications.put("125", "UR3"); |
1255 |
1 |
modifications.put("126", "UR3"); |
1256 |
1 |
modifications.put("127", "UR3"); |
1257 |
1 |
modifications.put("128", "ASN"); |
1258 |
1 |
modifications.put("12A", "ALA"); |
1259 |
1 |
modifications.put("143", "CYS"); |
1260 |
1 |
modifications.put("175", "ASG"); |
1261 |
1 |
modifications.put("193", "XAA"); |
1262 |
1 |
modifications.put("1AP", "ALA"); |
1263 |
1 |
modifications.put("1MA", "ALA"); |
1264 |
1 |
modifications.put("1MG", "GLY"); |
1265 |
1 |
modifications.put("1PA", "PHE"); |
1266 |
1 |
modifications.put("1PI", "ALA"); |
1267 |
1 |
modifications.put("1PR", "ASN"); |
1268 |
1 |
modifications.put("1SC", "CYS"); |
1269 |
1 |
modifications.put("1TQ", "TRP"); |
1270 |
1 |
modifications.put("1TY", "TYR"); |
1271 |
1 |
modifications.put("1X6", "SER"); |
1272 |
1 |
modifications.put("200", "PHE"); |
1273 |
1 |
modifications.put("23F", "PHE"); |
1274 |
1 |
modifications.put("23S", "XAA"); |
1275 |
1 |
modifications.put("26B", "THR"); |
1276 |
1 |
modifications.put("2AD", "XAA"); |
1277 |
1 |
modifications.put("2AG", "ALA"); |
1278 |
1 |
modifications.put("2AO", "XAA"); |
1279 |
1 |
modifications.put("2AR", "ALA"); |
1280 |
1 |
modifications.put("2AS", "XAA"); |
1281 |
1 |
modifications.put("2AT", "THR"); |
1282 |
1 |
modifications.put("2AU", "UR3"); |
1283 |
1 |
modifications.put("2BD", "ILE"); |
1284 |
1 |
modifications.put("2BT", "THR"); |
1285 |
1 |
modifications.put("2BU", "ALA"); |
1286 |
1 |
modifications.put("2CO", "CYS"); |
1287 |
1 |
modifications.put("2DA", "ALA"); |
1288 |
1 |
modifications.put("2DF", "ASN"); |
1289 |
1 |
modifications.put("2DM", "ASN"); |
1290 |
1 |
modifications.put("2DO", "XAA"); |
1291 |
1 |
modifications.put("2DT", "THR"); |
1292 |
1 |
modifications.put("2EG", "GLY"); |
1293 |
1 |
modifications.put("2FE", "ASN"); |
1294 |
1 |
modifications.put("2FI", "ASN"); |
1295 |
1 |
modifications.put("2FM", "MET"); |
1296 |
1 |
modifications.put("2GT", "THR"); |
1297 |
1 |
modifications.put("2HF", "HIS"); |
1298 |
1 |
modifications.put("2LU", "LEU"); |
1299 |
1 |
modifications.put("2MA", "ALA"); |
1300 |
1 |
modifications.put("2MG", "GLY"); |
1301 |
1 |
modifications.put("2ML", "LEU"); |
1302 |
1 |
modifications.put("2MR", "ARG"); |
1303 |
1 |
modifications.put("2MT", "PRO"); |
1304 |
1 |
modifications.put("2MU", "UR3"); |
1305 |
1 |
modifications.put("2NT", "THR"); |
1306 |
1 |
modifications.put("2OM", "UR3"); |
1307 |
1 |
modifications.put("2OT", "THR"); |
1308 |
1 |
modifications.put("2PI", "XAA"); |
1309 |
1 |
modifications.put("2PR", "GLY"); |
1310 |
1 |
modifications.put("2SA", "ASN"); |
1311 |
1 |
modifications.put("2SI", "XAA"); |
1312 |
1 |
modifications.put("2ST", "THR"); |
1313 |
1 |
modifications.put("2TL", "THR"); |
1314 |
1 |
modifications.put("2TY", "TYR"); |
1315 |
1 |
modifications.put("2VA", "VAL"); |
1316 |
1 |
modifications.put("2XA", "CYS"); |
1317 |
1 |
modifications.put("32S", "XAA"); |
1318 |
1 |
modifications.put("32T", "XAA"); |
1319 |
1 |
modifications.put("3AH", "HIS"); |
1320 |
1 |
modifications.put("3AR", "XAA"); |
1321 |
1 |
modifications.put("3CF", "PHE"); |
1322 |
1 |
modifications.put("3DA", "ALA"); |
1323 |
1 |
modifications.put("3DR", "ASN"); |
1324 |
1 |
modifications.put("3GA", "ALA"); |
1325 |
1 |
modifications.put("3MD", "ASP"); |
1326 |
1 |
modifications.put("3ME", "UR3"); |
1327 |
1 |
modifications.put("3NF", "TYR"); |
1328 |
1 |
modifications.put("3QN", "LYS"); |
1329 |
1 |
modifications.put("3TY", "XAA"); |
1330 |
1 |
modifications.put("3XH", "GLY"); |
1331 |
1 |
modifications.put("4AC", "ASN"); |
1332 |
1 |
modifications.put("4BF", "TYR"); |
1333 |
1 |
modifications.put("4CF", "PHE"); |
1334 |
1 |
modifications.put("4CY", "MET"); |
1335 |
1 |
modifications.put("4DP", "TRP"); |
1336 |
1 |
modifications.put("4F3", "GYG"); |
1337 |
1 |
modifications.put("4FB", "PRO"); |
1338 |
1 |
modifications.put("4FW", "TRP"); |
1339 |
1 |
modifications.put("4HT", "TRP"); |
1340 |
1 |
modifications.put("4IN", "TRP"); |
1341 |
1 |
modifications.put("4MF", "ASN"); |
1342 |
1 |
modifications.put("4MM", "XAA"); |
1343 |
1 |
modifications.put("4OC", "CYS"); |
1344 |
1 |
modifications.put("4PC", "CYS"); |
1345 |
1 |
modifications.put("4PD", "CYS"); |
1346 |
1 |
modifications.put("4PE", "CYS"); |
1347 |
1 |
modifications.put("4PH", "PHE"); |
1348 |
1 |
modifications.put("4SC", "CYS"); |
1349 |
1 |
modifications.put("4SU", "UR3"); |
1350 |
1 |
modifications.put("4TA", "ASN"); |
1351 |
1 |
modifications.put("4U7", "ALA"); |
1352 |
1 |
modifications.put("56A", "HIS"); |
1353 |
1 |
modifications.put("5AA", "ALA"); |
1354 |
1 |
modifications.put("5AB", "ALA"); |
1355 |
1 |
modifications.put("5AT", "THR"); |
1356 |
1 |
modifications.put("5BU", "UR3"); |
1357 |
1 |
modifications.put("5CG", "GLY"); |
1358 |
1 |
modifications.put("5CM", "CYS"); |
1359 |
1 |
modifications.put("5CS", "CYS"); |
1360 |
1 |
modifications.put("5FA", "ALA"); |
1361 |
1 |
modifications.put("5FC", "CYS"); |
1362 |
1 |
modifications.put("5FU", "UR3"); |
1363 |
1 |
modifications.put("5HP", "GLU"); |
1364 |
1 |
modifications.put("5HT", "THR"); |
1365 |
1 |
modifications.put("5HU", "UR3"); |
1366 |
1 |
modifications.put("5IC", "CYS"); |
1367 |
1 |
modifications.put("5IT", "THR"); |
1368 |
1 |
modifications.put("5IU", "UR3"); |
1369 |
1 |
modifications.put("5MC", "CYS"); |
1370 |
1 |
modifications.put("5MD", "ASN"); |
1371 |
1 |
modifications.put("5MU", "UR3"); |
1372 |
1 |
modifications.put("5NC", "CYS"); |
1373 |
1 |
modifications.put("5PC", "CYS"); |
1374 |
1 |
modifications.put("5PY", "THR"); |
1375 |
1 |
modifications.put("5SE", "UR3"); |
1376 |
1 |
modifications.put("5ZA", "TWG"); |
1377 |
1 |
modifications.put("64T", "THR"); |
1378 |
1 |
modifications.put("6CL", "LYS"); |
1379 |
1 |
modifications.put("6CT", "THR"); |
1380 |
1 |
modifications.put("6CW", "TRP"); |
1381 |
1 |
modifications.put("6HA", "ALA"); |
1382 |
1 |
modifications.put("6HC", "CYS"); |
1383 |
1 |
modifications.put("6HG", "GLY"); |
1384 |
1 |
modifications.put("6HN", "LYS"); |
1385 |
1 |
modifications.put("6HT", "THR"); |
1386 |
1 |
modifications.put("6IA", "ALA"); |
1387 |
1 |
modifications.put("6MA", "ALA"); |
1388 |
1 |
modifications.put("6MC", "ALA"); |
1389 |
1 |
modifications.put("6MI", "ASN"); |
1390 |
1 |
modifications.put("6MT", "ALA"); |
1391 |
1 |
modifications.put("6MZ", "ASN"); |
1392 |
1 |
modifications.put("6OG", "GLY"); |
1393 |
1 |
modifications.put("70U", "UR3"); |
1394 |
1 |
modifications.put("7DA", "ALA"); |
1395 |
1 |
modifications.put("7GU", "GLY"); |
1396 |
1 |
modifications.put("7JA", "ILE"); |
1397 |
1 |
modifications.put("7MG", "GLY"); |
1398 |
1 |
modifications.put("8AN", "ALA"); |
1399 |
1 |
modifications.put("8FG", "GLY"); |
1400 |
1 |
modifications.put("8MG", "GLY"); |
1401 |
1 |
modifications.put("8OG", "GLY"); |
1402 |
1 |
modifications.put("9NE", "GLU"); |
1403 |
1 |
modifications.put("9NF", "PHE"); |
1404 |
1 |
modifications.put("9NR", "ARG"); |
1405 |
1 |
modifications.put("9NV", "VAL"); |
1406 |
1 |
modifications.put("A ", "ALA"); |
1407 |
1 |
modifications.put("A1P", "ASN"); |
1408 |
1 |
modifications.put("A23", "ALA"); |
1409 |
1 |
modifications.put("A2L", "ALA"); |
1410 |
1 |
modifications.put("A2M", "ALA"); |
1411 |
1 |
modifications.put("A34", "ALA"); |
1412 |
1 |
modifications.put("A35", "ALA"); |
1413 |
1 |
modifications.put("A38", "ALA"); |
1414 |
1 |
modifications.put("A39", "ALA"); |
1415 |
1 |
modifications.put("A3A", "ALA"); |
1416 |
1 |
modifications.put("A3P", "ALA"); |
1417 |
1 |
modifications.put("A40", "ALA"); |
1418 |
1 |
modifications.put("A43", "ALA"); |
1419 |
1 |
modifications.put("A44", "ALA"); |
1420 |
1 |
modifications.put("A47", "ALA"); |
1421 |
1 |
modifications.put("A5L", "ALA"); |
1422 |
1 |
modifications.put("A5M", "CYS"); |
1423 |
1 |
modifications.put("A5N", "ASN"); |
1424 |
1 |
modifications.put("A5O", "ALA"); |
1425 |
1 |
modifications.put("A66", "XAA"); |
1426 |
1 |
modifications.put("AA3", "ALA"); |
1427 |
1 |
modifications.put("AA4", "ALA"); |
1428 |
1 |
modifications.put("AAR", "ARG"); |
1429 |
1 |
modifications.put("AB7", "XAA"); |
1430 |
1 |
modifications.put("ABA", "ALA"); |
1431 |
1 |
modifications.put("ABR", "ALA"); |
1432 |
1 |
modifications.put("ABS", "ALA"); |
1433 |
1 |
modifications.put("ABT", "ASN"); |
1434 |
1 |
modifications.put("ACB", "ASP"); |
1435 |
1 |
modifications.put("ACL", "ARG"); |
1436 |
1 |
modifications.put("AD2", "ALA"); |
1437 |
1 |
modifications.put("ADD", "XAA"); |
1438 |
1 |
modifications.put("ADX", "ASN"); |
1439 |
1 |
modifications.put("AEA", "XAA"); |
1440 |
1 |
modifications.put("AEI", "ASP"); |
1441 |
1 |
modifications.put("AET", "ALA"); |
1442 |
1 |
modifications.put("AFA", "ASN"); |
1443 |
1 |
modifications.put("AFF", "ASN"); |
1444 |
1 |
modifications.put("AFG", "GLY"); |
1445 |
1 |
modifications.put("AGM", "ARG"); |
1446 |
1 |
modifications.put("AGT", "CYS"); |
1447 |
1 |
modifications.put("AHB", "ASN"); |
1448 |
1 |
modifications.put("AHH", "XAA"); |
1449 |
1 |
modifications.put("AHO", "ALA"); |
1450 |
1 |
modifications.put("AHP", "ALA"); |
1451 |
1 |
modifications.put("AHS", "XAA"); |
1452 |
1 |
modifications.put("AHT", "XAA"); |
1453 |
1 |
modifications.put("AIB", "ALA"); |
1454 |
1 |
modifications.put("AKL", "ASP"); |
1455 |
1 |
modifications.put("AKZ", "ASP"); |
1456 |
1 |
modifications.put("ALA", "ALA"); |
1457 |
1 |
modifications.put("ALC", "ALA"); |
1458 |
1 |
modifications.put("ALM", "ALA"); |
1459 |
1 |
modifications.put("ALN", "ALA"); |
1460 |
1 |
modifications.put("ALO", "THR"); |
1461 |
1 |
modifications.put("ALQ", "XAA"); |
1462 |
1 |
modifications.put("ALS", "ALA"); |
1463 |
1 |
modifications.put("ALT", "ALA"); |
1464 |
1 |
modifications.put("ALV", "ALA"); |
1465 |
1 |
modifications.put("ALY", "LYS"); |
1466 |
1 |
modifications.put("AN8", "ALA"); |
1467 |
1 |
modifications.put("AP7", "ALA"); |
1468 |
1 |
modifications.put("APE", "XAA"); |
1469 |
1 |
modifications.put("APH", "ALA"); |
1470 |
1 |
modifications.put("API", "LYS"); |
1471 |
1 |
modifications.put("APK", "LYS"); |
1472 |
1 |
modifications.put("APM", "XAA"); |
1473 |
1 |
modifications.put("APP", "XAA"); |
1474 |
1 |
modifications.put("AR2", "ARG"); |
1475 |
1 |
modifications.put("AR4", "GLU"); |
1476 |
1 |
modifications.put("AR7", "ARG"); |
1477 |
1 |
modifications.put("ARG", "ARG"); |
1478 |
1 |
modifications.put("ARM", "ARG"); |
1479 |
1 |
modifications.put("ARO", "ARG"); |
1480 |
1 |
modifications.put("ARV", "XAA"); |
1481 |
1 |
modifications.put("AS ", "ALA"); |
1482 |
1 |
modifications.put("AS2", "ASP"); |
1483 |
1 |
modifications.put("AS9", "XAA"); |
1484 |
1 |
modifications.put("ASA", "ASP"); |
1485 |
1 |
modifications.put("ASB", "ASP"); |
1486 |
1 |
modifications.put("ASI", "ASP"); |
1487 |
1 |
modifications.put("ASK", "ASP"); |
1488 |
1 |
modifications.put("ASL", "ASP"); |
1489 |
1 |
modifications.put("ASM", "XAA"); |
1490 |
1 |
modifications.put("ASN", "ASN"); |
1491 |
1 |
modifications.put("ASP", "ASP"); |
1492 |
1 |
modifications.put("ASQ", "ASP"); |
1493 |
1 |
modifications.put("ASU", "ASN"); |
1494 |
1 |
modifications.put("ASX", "ASX"); |
1495 |
1 |
modifications.put("ATD", "THR"); |
1496 |
1 |
modifications.put("ATL", "THR"); |
1497 |
1 |
modifications.put("ATM", "THR"); |
1498 |
1 |
modifications.put("AVC", "ALA"); |
1499 |
1 |
modifications.put("AVN", "XAA"); |
1500 |
1 |
modifications.put("AYA", "ALA"); |
1501 |
1 |
modifications.put("AYG", "AYG"); |
1502 |
1 |
modifications.put("AZK", "LYS"); |
1503 |
1 |
modifications.put("AZS", "SER"); |
1504 |
1 |
modifications.put("AZY", "TYR"); |
1505 |
1 |
modifications.put("B1F", "PHE"); |
1506 |
1 |
modifications.put("B1P", "ASN"); |
1507 |
1 |
modifications.put("B2A", "ALA"); |
1508 |
1 |
modifications.put("B2F", "PHE"); |
1509 |
1 |
modifications.put("B2I", "ILE"); |
1510 |
1 |
modifications.put("B2V", "VAL"); |
1511 |
1 |
modifications.put("B3A", "ALA"); |
1512 |
1 |
modifications.put("B3D", "ASP"); |
1513 |
1 |
modifications.put("B3E", "GLU"); |
1514 |
1 |
modifications.put("B3K", "LYS"); |
1515 |
1 |
modifications.put("B3L", "XAA"); |
1516 |
1 |
modifications.put("B3M", "XAA"); |
1517 |
1 |
modifications.put("B3Q", "XAA"); |
1518 |
1 |
modifications.put("B3S", "SER"); |
1519 |
1 |
modifications.put("B3T", "XAA"); |
1520 |
1 |
modifications.put("B3U", "HIS"); |
1521 |
1 |
modifications.put("B3X", "ASN"); |
1522 |
1 |
modifications.put("B3Y", "TYR"); |
1523 |
1 |
modifications.put("BB6", "CYS"); |
1524 |
1 |
modifications.put("BB7", "CYS"); |
1525 |
1 |
modifications.put("BB8", "PHE"); |
1526 |
1 |
modifications.put("BB9", "CYS"); |
1527 |
1 |
modifications.put("BBC", "CYS"); |
1528 |
1 |
modifications.put("BCS", "CYS"); |
1529 |
1 |
modifications.put("BE2", "XAA"); |
1530 |
1 |
modifications.put("BFD", "ASP"); |
1531 |
1 |
modifications.put("BG1", "SER"); |
1532 |
1 |
modifications.put("BGM", "GLY"); |
1533 |
1 |
modifications.put("BH2", "ASP"); |
1534 |
1 |
modifications.put("BHD", "ASP"); |
1535 |
1 |
modifications.put("BIF", "PHE"); |
1536 |
1 |
modifications.put("BIL", "XAA"); |
1537 |
1 |
modifications.put("BIU", "ILE"); |
1538 |
1 |
modifications.put("BJH", "XAA"); |
1539 |
1 |
modifications.put("BLE", "LEU"); |
1540 |
1 |
modifications.put("BLY", "LYS"); |
1541 |
1 |
modifications.put("BMP", "ASN"); |
1542 |
1 |
modifications.put("BMT", "THR"); |
1543 |
1 |
modifications.put("BNN", "PHE"); |
1544 |
1 |
modifications.put("BNO", "XAA"); |
1545 |
1 |
modifications.put("BOE", "THR"); |
1546 |
1 |
modifications.put("BOR", "ARG"); |
1547 |
1 |
modifications.put("BPE", "CYS"); |
1548 |
1 |
modifications.put("BRU", "UR3"); |
1549 |
1 |
modifications.put("BSE", "SER"); |
1550 |
1 |
modifications.put("BT5", "ASN"); |
1551 |
1 |
modifications.put("BTA", "LEU"); |
1552 |
1 |
modifications.put("BTC", "CYS"); |
1553 |
1 |
modifications.put("BTR", "TRP"); |
1554 |
1 |
modifications.put("BUC", "CYS"); |
1555 |
1 |
modifications.put("BUG", "VAL"); |
1556 |
1 |
modifications.put("BVP", "UR3"); |
1557 |
1 |
modifications.put("BZG", "ASN"); |
1558 |
1 |
modifications.put("C ", "CYS"); |
1559 |
1 |
modifications.put("C12", "TYG"); |
1560 |
1 |
modifications.put("C1X", "LYS"); |
1561 |
1 |
modifications.put("C25", "CYS"); |
1562 |
1 |
modifications.put("C2L", "CYS"); |
1563 |
1 |
modifications.put("C2S", "CYS"); |
1564 |
1 |
modifications.put("C31", "CYS"); |
1565 |
1 |
modifications.put("C32", "CYS"); |
1566 |
1 |
modifications.put("C34", "CYS"); |
1567 |
1 |
modifications.put("C36", "CYS"); |
1568 |
1 |
modifications.put("C37", "CYS"); |
1569 |
1 |
modifications.put("C38", "CYS"); |
1570 |
1 |
modifications.put("C3Y", "CYS"); |
1571 |
1 |
modifications.put("C42", "CYS"); |
1572 |
1 |
modifications.put("C43", "CYS"); |
1573 |
1 |
modifications.put("C45", "CYS"); |
1574 |
1 |
modifications.put("C46", "CYS"); |
1575 |
1 |
modifications.put("C49", "CYS"); |
1576 |
1 |
modifications.put("C4R", "CYS"); |
1577 |
1 |
modifications.put("C4S", "CYS"); |
1578 |
1 |
modifications.put("C5C", "CYS"); |
1579 |
1 |
modifications.put("C66", "XAA"); |
1580 |
1 |
modifications.put("C6C", "CYS"); |
1581 |
1 |
modifications.put("C99", "TFG"); |
1582 |
1 |
modifications.put("CAF", "CYS"); |
1583 |
1 |
modifications.put("CAL", "XAA"); |
1584 |
1 |
modifications.put("CAR", "CYS"); |
1585 |
1 |
modifications.put("CAS", "CYS"); |
1586 |
1 |
modifications.put("CAV", "XAA"); |
1587 |
1 |
modifications.put("CAY", "CYS"); |
1588 |
1 |
modifications.put("CB2", "CYS"); |
1589 |
1 |
modifications.put("CBR", "CYS"); |
1590 |
1 |
modifications.put("CBV", "CYS"); |
1591 |
1 |
modifications.put("CCC", "CYS"); |
1592 |
1 |
modifications.put("CCL", "LYS"); |
1593 |
1 |
modifications.put("CCS", "CYS"); |
1594 |
1 |
modifications.put("CCY", "CYG"); |
1595 |
1 |
modifications.put("CDE", "XAA"); |
1596 |
1 |
modifications.put("CDV", "XAA"); |
1597 |
1 |
modifications.put("CDW", "CYS"); |
1598 |
1 |
modifications.put("CEA", "CYS"); |
1599 |
1 |
modifications.put("CFL", "CYS"); |
1600 |
1 |
modifications.put("CFY", "FCYG"); |
1601 |
1 |
modifications.put("CG1", "GLY"); |
1602 |
1 |
modifications.put("CGA", "GLU"); |
1603 |
1 |
modifications.put("CGU", "GLU"); |
1604 |
1 |
modifications.put("CH ", "CYS"); |
1605 |
1 |
modifications.put("CH6", "MYG"); |
1606 |
1 |
modifications.put("CH7", "KYG"); |
1607 |
1 |
modifications.put("CHF", "XAA"); |
1608 |
1 |
modifications.put("CHG", "XAA"); |
1609 |
1 |
modifications.put("CHP", "GLY"); |
1610 |
1 |
modifications.put("CHS", "XAA"); |
1611 |
1 |
modifications.put("CIR", "ARG"); |
1612 |
1 |
modifications.put("CJO", "GYG"); |
1613 |
1 |
modifications.put("CLE", "LEU"); |
1614 |
1 |
modifications.put("CLG", "LYS"); |
1615 |
1 |
modifications.put("CLH", "LYS"); |
1616 |
1 |
modifications.put("CLV", "AFG"); |
1617 |
1 |
modifications.put("CM0", "ASN"); |
1618 |
1 |
modifications.put("CME", "CYS"); |
1619 |
1 |
modifications.put("CMH", "CYS"); |
1620 |
1 |
modifications.put("CML", "CYS"); |
1621 |
1 |
modifications.put("CMR", "CYS"); |
1622 |
1 |
modifications.put("CMT", "CYS"); |
1623 |
1 |
modifications.put("CNU", "UR3"); |
1624 |
1 |
modifications.put("CP1", "CYS"); |
1625 |
1 |
modifications.put("CPC", "XAA"); |
1626 |
1 |
modifications.put("CPI", "XAA"); |
1627 |
1 |
modifications.put("CQR", "GYG"); |
1628 |
1 |
modifications.put("CR0", "TLG"); |
1629 |
1 |
modifications.put("CR2", "GYG"); |
1630 |
1 |
modifications.put("CR5", "GLY"); |
1631 |
1 |
modifications.put("CR7", "KYG"); |
1632 |
1 |
modifications.put("CR8", "HYG"); |
1633 |
1 |
modifications.put("CRF", "TWG"); |
1634 |
1 |
modifications.put("CRG", "THG"); |
1635 |
1 |
modifications.put("CRK", "MYG"); |
1636 |
1 |
modifications.put("CRO", "GYG"); |
1637 |
1 |
modifications.put("CRQ", "QYG"); |
1638 |
1 |
modifications.put("CRU", "EYG"); |
1639 |
1 |
modifications.put("CRW", "ASG"); |
1640 |
1 |
modifications.put("CRX", "ASG"); |
1641 |
1 |
modifications.put("CS0", "CYS"); |
1642 |
1 |
modifications.put("CS1", "CYS"); |
1643 |
1 |
modifications.put("CS3", "CYS"); |
1644 |
1 |
modifications.put("CS4", "CYS"); |
1645 |
1 |
modifications.put("CS8", "ASN"); |
1646 |
1 |
modifications.put("CSA", "CYS"); |
1647 |
1 |
modifications.put("CSB", "CYS"); |
1648 |
1 |
modifications.put("CSD", "CYS"); |
1649 |
1 |
modifications.put("CSE", "CYS"); |
1650 |
1 |
modifications.put("CSF", "CYS"); |
1651 |
1 |
modifications.put("CSH", "SHG"); |
1652 |
1 |
modifications.put("CSI", "GLY"); |
1653 |
1 |
modifications.put("CSJ", "CYS"); |
1654 |
1 |
modifications.put("CSL", "CYS"); |
1655 |
1 |
modifications.put("CSO", "CYS"); |
1656 |
1 |
modifications.put("CSP", "CYS"); |
1657 |
1 |
modifications.put("CSR", "CYS"); |
1658 |
1 |
modifications.put("CSS", "CYS"); |
1659 |
1 |
modifications.put("CSU", "CYS"); |
1660 |
1 |
modifications.put("CSW", "CYS"); |
1661 |
1 |
modifications.put("CSX", "CYS"); |
1662 |
1 |
modifications.put("CSY", "SYG"); |
1663 |
1 |
modifications.put("CSZ", "CYS"); |
1664 |
1 |
modifications.put("CTE", "TRP"); |
1665 |
1 |
modifications.put("CTG", "THR"); |
1666 |
1 |
modifications.put("CTH", "THR"); |
1667 |
1 |
modifications.put("CUC", "XAA"); |
1668 |
1 |
modifications.put("CWR", "SER"); |
1669 |
1 |
modifications.put("CXM", "MET"); |
1670 |
1 |
modifications.put("CY0", "CYS"); |
1671 |
1 |
modifications.put("CY1", "CYS"); |
1672 |
1 |
modifications.put("CY3", "CYS"); |
1673 |
1 |
modifications.put("CY4", "CYS"); |
1674 |
1 |
modifications.put("CYA", "CYS"); |
1675 |
1 |
modifications.put("CYD", "CYS"); |
1676 |
1 |
modifications.put("CYF", "CYS"); |
1677 |
1 |
modifications.put("CYG", "CYS"); |
1678 |
1 |
modifications.put("CYJ", "XAA"); |
1679 |
1 |
modifications.put("CYM", "CYS"); |
1680 |
1 |
modifications.put("CYQ", "CYS"); |
1681 |
1 |
modifications.put("CYR", "CYS"); |
1682 |
1 |
modifications.put("CYS", "CYS"); |
1683 |
1 |
modifications.put("CZ2", "CYS"); |
1684 |
1 |
modifications.put("CZO", "GYG"); |
1685 |
1 |
modifications.put("CZZ", "CYS"); |
1686 |
1 |
modifications.put("D11", "THR"); |
1687 |
1 |
modifications.put("D1P", "ASN"); |
1688 |
1 |
modifications.put("D3 ", "ASN"); |
1689 |
1 |
modifications.put("D33", "ASN"); |
1690 |
1 |
modifications.put("D3P", "GLY"); |
1691 |
1 |
modifications.put("D3T", "THR"); |
1692 |
1 |
modifications.put("D4M", "THR"); |
1693 |
1 |
modifications.put("D4P", "XAA"); |
1694 |
1 |
modifications.put("DA ", "ALA"); |
1695 |
1 |
modifications.put("DA2", "XAA"); |
1696 |
1 |
modifications.put("DAB", "ALA"); |
1697 |
1 |
modifications.put("DAH", "PHE"); |
1698 |
1 |
modifications.put("DAL", "ALA"); |
1699 |
1 |
modifications.put("DAR", "ARG"); |
1700 |
1 |
modifications.put("DAS", "ASP"); |
1701 |
1 |
modifications.put("DBB", "THR"); |
1702 |
1 |
modifications.put("DBM", "ASN"); |
1703 |
1 |
modifications.put("DBS", "SER"); |
1704 |
1 |
modifications.put("DBU", "THR"); |
1705 |
1 |
modifications.put("DBY", "TYR"); |
1706 |
1 |
modifications.put("DBZ", "ALA"); |
1707 |
1 |
modifications.put("DC ", "CYS"); |
1708 |
1 |
modifications.put("DC2", "CYS"); |
1709 |
1 |
modifications.put("DCG", "GLY"); |
1710 |
1 |
modifications.put("DCI", "XAA"); |
1711 |
1 |
modifications.put("DCL", "XAA"); |
1712 |
1 |
modifications.put("DCT", "CYS"); |
1713 |
1 |
modifications.put("DCY", "CYS"); |
1714 |
1 |
modifications.put("DDE", "HIS"); |
1715 |
1 |
modifications.put("DDG", "GLY"); |
1716 |
1 |
modifications.put("DDN", "UR3"); |
1717 |
1 |
modifications.put("DDX", "ASN"); |
1718 |
1 |
modifications.put("DFC", "CYS"); |
1719 |
1 |
modifications.put("DFG", "GLY"); |
1720 |
1 |
modifications.put("DFI", "XAA"); |
1721 |
1 |
modifications.put("DFO", "XAA"); |
1722 |
1 |
modifications.put("DFT", "ASN"); |
1723 |
1 |
modifications.put("DG ", "GLY"); |
1724 |
1 |
modifications.put("DGH", "GLY"); |
1725 |
1 |
modifications.put("DGI", "GLY"); |
1726 |
1 |
modifications.put("DGL", "GLU"); |
1727 |
1 |
modifications.put("DGN", "GLN"); |
1728 |
1 |
modifications.put("DHA", "SER"); |
1729 |
1 |
modifications.put("DHI", "HIS"); |
1730 |
1 |
modifications.put("DHL", "XAA"); |
1731 |
1 |
modifications.put("DHN", "VAL"); |
1732 |
1 |
modifications.put("DHP", "XAA"); |
1733 |
1 |
modifications.put("DHU", "UR3"); |
1734 |
1 |
modifications.put("DHV", "VAL"); |
1735 |
1 |
modifications.put("DI ", "ILE"); |
1736 |
1 |
modifications.put("DIL", "ILE"); |
1737 |
1 |
modifications.put("DIR", "ARG"); |
1738 |
1 |
modifications.put("DIV", "VAL"); |
1739 |
1 |
modifications.put("DLE", "LEU"); |
1740 |
1 |
modifications.put("DLS", "LYS"); |
1741 |
1 |
modifications.put("DLY", "LYS"); |
1742 |
1 |
modifications.put("DM0", "LYS"); |
1743 |
1 |
modifications.put("DMH", "ASN"); |
1744 |
1 |
modifications.put("DMK", "ASP"); |
1745 |
1 |
modifications.put("DMT", "XAA"); |
1746 |
1 |
modifications.put("DN ", "ASN"); |
1747 |
1 |
modifications.put("DNE", "LEU"); |
1748 |
1 |
modifications.put("DNG", "LEU"); |
1749 |
1 |
modifications.put("DNL", "LYS"); |
1750 |
1 |
modifications.put("DNM", "LEU"); |
1751 |
1 |
modifications.put("DNP", "ALA"); |
1752 |
1 |
modifications.put("DNR", "CYS"); |
1753 |
1 |
modifications.put("DNS", "LYS"); |
1754 |
1 |
modifications.put("DOA", "XAA"); |
1755 |
1 |
modifications.put("DOC", "CYS"); |
1756 |
1 |
modifications.put("DOH", "ASP"); |
1757 |
1 |
modifications.put("DON", "LEU"); |
1758 |
1 |
modifications.put("DPB", "THR"); |
1759 |
1 |
modifications.put("DPH", "PHE"); |
1760 |
1 |
modifications.put("DPL", "PRO"); |
1761 |
1 |
modifications.put("DPP", "ALA"); |
1762 |
1 |
modifications.put("DPQ", "TYR"); |
1763 |
1 |
modifications.put("DPR", "PRO"); |
1764 |
1 |
modifications.put("DPY", "ASN"); |
1765 |
1 |
modifications.put("DRM", "UR3"); |
1766 |
1 |
modifications.put("DRP", "ASN"); |
1767 |
1 |
modifications.put("DRT", "THR"); |
1768 |
1 |
modifications.put("DRZ", "ASN"); |
1769 |
1 |
modifications.put("DSE", "SER"); |
1770 |
1 |
modifications.put("DSG", "ASN"); |
1771 |
1 |
modifications.put("DSN", "SER"); |
1772 |
1 |
modifications.put("DSP", "ASP"); |
1773 |
1 |
modifications.put("DT ", "THR"); |
1774 |
1 |
modifications.put("DTH", "THR"); |
1775 |
1 |
modifications.put("DTR", "TRP"); |
1776 |
1 |
modifications.put("DTY", "TYR"); |
1777 |
1 |
modifications.put("DU ", "UR3"); |
1778 |
1 |
modifications.put("DVA", "VAL"); |
1779 |
1 |
modifications.put("DXD", "ASN"); |
1780 |
1 |
modifications.put("DXN", "ASN"); |
1781 |
1 |
modifications.put("DYG", "DYG"); |
1782 |
1 |
modifications.put("DYS", "CYS"); |
1783 |
1 |
modifications.put("DZM", "ALA"); |
1784 |
1 |
modifications.put("E ", "ALA"); |
1785 |
1 |
modifications.put("E1X", "ALA"); |
1786 |
1 |
modifications.put("ECC", "GLN"); |
1787 |
1 |
modifications.put("EDA", "ALA"); |
1788 |
1 |
modifications.put("EFC", "CYS"); |
1789 |
1 |
modifications.put("EHP", "PHE"); |
1790 |
1 |
modifications.put("EIT", "THR"); |
1791 |
1 |
modifications.put("ENP", "ASN"); |
1792 |
1 |
modifications.put("ESB", "TYR"); |
1793 |
1 |
modifications.put("ESC", "MET"); |
1794 |
1 |
modifications.put("EXB", "XAA"); |
1795 |
1 |
modifications.put("EXY", "LEU"); |
1796 |
1 |
modifications.put("EY5", "ASN"); |
1797 |
1 |
modifications.put("EYS", "XAA"); |
1798 |
1 |
modifications.put("F2F", "PHE"); |
1799 |
1 |
modifications.put("FA2", "ALA"); |
1800 |
1 |
modifications.put("FA5", "ASN"); |
1801 |
1 |
modifications.put("FAG", "ASN"); |
1802 |
1 |
modifications.put("FAI", "ASN"); |
1803 |
1 |
modifications.put("FB5", "ALA"); |
1804 |
1 |
modifications.put("FB6", "ALA"); |
1805 |
1 |
modifications.put("FCL", "PHE"); |
1806 |
1 |
modifications.put("FFD", "ASN"); |
1807 |
1 |
modifications.put("FGA", "GLU"); |
1808 |
1 |
modifications.put("FGL", "GLY"); |
1809 |
1 |
modifications.put("FGP", "SER"); |
1810 |
1 |
modifications.put("FHL", "XAA"); |
1811 |
1 |
modifications.put("FHO", "LYS"); |
1812 |
1 |
modifications.put("FHU", "UR3"); |
1813 |
1 |
modifications.put("FLA", "ALA"); |
1814 |
1 |
modifications.put("FLE", "LEU"); |
1815 |
1 |
modifications.put("FLT", "TYR"); |
1816 |
1 |
modifications.put("FME", "MET"); |
1817 |
1 |
modifications.put("FMG", "GLY"); |
1818 |
1 |
modifications.put("FMU", "ASN"); |
1819 |
1 |
modifications.put("FOE", "CYS"); |
1820 |
1 |
modifications.put("FOX", "GLY"); |
1821 |
1 |
modifications.put("FP9", "PRO"); |
1822 |
1 |
modifications.put("FPA", "PHE"); |
1823 |
1 |
modifications.put("FRD", "XAA"); |
1824 |
1 |
modifications.put("FT6", "TRP"); |
1825 |
1 |
modifications.put("FTR", "TRP"); |
1826 |
1 |
modifications.put("FTY", "TYR"); |
1827 |
1 |
modifications.put("FVA", "VAL"); |
1828 |
1 |
modifications.put("FZN", "LYS"); |
1829 |
1 |
modifications.put("G ", "GLY"); |
1830 |
1 |
modifications.put("G25", "GLY"); |
1831 |
1 |
modifications.put("G2L", "GLY"); |
1832 |
1 |
modifications.put("G2S", "GLY"); |
1833 |
1 |
modifications.put("G31", "GLY"); |
1834 |
1 |
modifications.put("G32", "GLY"); |
1835 |
1 |
modifications.put("G33", "GLY"); |
1836 |
1 |
modifications.put("G36", "GLY"); |
1837 |
1 |
modifications.put("G38", "GLY"); |
1838 |
1 |
modifications.put("G42", "GLY"); |
1839 |
1 |
modifications.put("G46", "GLY"); |
1840 |
1 |
modifications.put("G47", "GLY"); |
1841 |
1 |
modifications.put("G48", "GLY"); |
1842 |
1 |
modifications.put("G49", "GLY"); |
1843 |
1 |
modifications.put("G4P", "ASN"); |
1844 |
1 |
modifications.put("G7M", "GLY"); |
1845 |
1 |
modifications.put("GAO", "GLY"); |
1846 |
1 |
modifications.put("GAU", "GLU"); |
1847 |
1 |
modifications.put("GCK", "CYS"); |
1848 |
1 |
modifications.put("GCM", "XAA"); |
1849 |
1 |
modifications.put("GDP", "GLY"); |
1850 |
1 |
modifications.put("GDR", "GLY"); |
1851 |
1 |
modifications.put("GFL", "GLY"); |
1852 |
1 |
modifications.put("GGL", "GLU"); |
1853 |
1 |
modifications.put("GH3", "GLY"); |
1854 |
1 |
modifications.put("GHG", "GLN"); |
1855 |
1 |
modifications.put("GHP", "GLY"); |
1856 |
1 |
modifications.put("GL3", "GLY"); |
1857 |
1 |
modifications.put("GLH", "GLN"); |
1858 |
1 |
modifications.put("GLJ", "GLU"); |
1859 |
1 |
modifications.put("GLK", "GLU"); |
1860 |
1 |
modifications.put("GLM", "XAA"); |
1861 |
1 |
modifications.put("GLN", "GLN"); |
1862 |
1 |
modifications.put("GLQ", "GLU"); |
1863 |
1 |
modifications.put("GLU", "GLU"); |
1864 |
1 |
modifications.put("GLX", "GLX"); |
1865 |
1 |
modifications.put("GLY", "GLY"); |
1866 |
1 |
modifications.put("GLZ", "GLY"); |
1867 |
1 |
modifications.put("GMA", "GLU"); |
1868 |
1 |
modifications.put("GMS", "GLY"); |
1869 |
1 |
modifications.put("GMU", "UR3"); |
1870 |
1 |
modifications.put("GN7", "GLY"); |
1871 |
1 |
modifications.put("GND", "XAA"); |
1872 |
1 |
modifications.put("GNE", "ASN"); |
1873 |
1 |
modifications.put("GOM", "GLY"); |
1874 |
1 |
modifications.put("GPL", "LYS"); |
1875 |
1 |
modifications.put("GS ", "GLY"); |
1876 |
1 |
modifications.put("GSC", "GLY"); |
1877 |
1 |
modifications.put("GSR", "GLY"); |
1878 |
1 |
modifications.put("GSS", "GLY"); |
1879 |
1 |
modifications.put("GSU", "GLU"); |
1880 |
1 |
modifications.put("GT9", "CYS"); |
1881 |
1 |
modifications.put("GTP", "GLY"); |
1882 |
1 |
modifications.put("GVL", "XAA"); |
1883 |
1 |
modifications.put("GYC", "CYG"); |
1884 |
1 |
modifications.put("GYS", "SYG"); |
1885 |
1 |
modifications.put("H2U", "UR3"); |
1886 |
1 |
modifications.put("H5M", "PRO"); |
1887 |
1 |
modifications.put("HAC", "ALA"); |
1888 |
1 |
modifications.put("HAR", "ARG"); |
1889 |
1 |
modifications.put("HBN", "HIS"); |
1890 |
1 |
modifications.put("HCS", "XAA"); |
1891 |
1 |
modifications.put("HDP", "UR3"); |
1892 |
1 |
modifications.put("HEU", "UR3"); |
1893 |
1 |
modifications.put("HFA", "XAA"); |
1894 |
1 |
modifications.put("HGL", "XAA"); |
1895 |
1 |
modifications.put("HHI", "HIS"); |
1896 |
1 |
modifications.put("HHK", "AK"); |
1897 |
1 |
modifications.put("HIA", "HIS"); |
1898 |
1 |
modifications.put("HIC", "HIS"); |
1899 |
1 |
modifications.put("HIP", "HIS"); |
1900 |
1 |
modifications.put("HIQ", "HIS"); |
1901 |
1 |
modifications.put("HIS", "HIS"); |
1902 |
1 |
modifications.put("HL2", "LEU"); |
1903 |
1 |
modifications.put("HLU", "LEU"); |
1904 |
1 |
modifications.put("HMR", "ARG"); |
1905 |
1 |
modifications.put("HOL", "ASN"); |
1906 |
1 |
modifications.put("HPC", "PHE"); |
1907 |
1 |
modifications.put("HPE", "PHE"); |
1908 |
1 |
modifications.put("HPH", "PHE"); |
1909 |
1 |
modifications.put("HPQ", "PHE"); |
1910 |
1 |
modifications.put("HQA", "ALA"); |
1911 |
1 |
modifications.put("HRG", "ARG"); |
1912 |
1 |
modifications.put("HRP", "TRP"); |
1913 |
1 |
modifications.put("HS8", "HIS"); |
1914 |
1 |
modifications.put("HS9", "HIS"); |
1915 |
1 |
modifications.put("HSE", "SER"); |
1916 |
1 |
modifications.put("HSL", "SER"); |
1917 |
1 |
modifications.put("HSO", "HIS"); |
1918 |
1 |
modifications.put("HTI", "CYS"); |
1919 |
1 |
modifications.put("HTN", "ASN"); |
1920 |
1 |
modifications.put("HTR", "TRP"); |
1921 |
1 |
modifications.put("HV5", "ALA"); |
1922 |
1 |
modifications.put("HVA", "VAL"); |
1923 |
1 |
modifications.put("HY3", "PRO"); |
1924 |
1 |
modifications.put("HYP", "PRO"); |
1925 |
1 |
modifications.put("HZP", "PRO"); |
1926 |
1 |
modifications.put("I ", "ILE"); |
1927 |
1 |
modifications.put("I2M", "ILE"); |
1928 |
1 |
modifications.put("I58", "LYS"); |
1929 |
1 |
modifications.put("I5C", "CYS"); |
1930 |
1 |
modifications.put("IAM", "ALA"); |
1931 |
1 |
modifications.put("IAR", "ARG"); |
1932 |
1 |
modifications.put("IAS", "ASP"); |
1933 |
1 |
modifications.put("IC ", "CYS"); |
1934 |
1 |
modifications.put("IEL", "LYS"); |
1935 |
1 |
modifications.put("IEY", "HYG"); |
1936 |
1 |
modifications.put("IG ", "GLY"); |
1937 |
1 |
modifications.put("IGL", "GLY"); |
1938 |
1 |
modifications.put("IGU", "GLY"); |
1939 |
1 |
modifications.put("IIC", "SHG"); |
1940 |
1 |
modifications.put("IIL", "ILE"); |
1941 |
1 |
modifications.put("ILE", "ILE"); |
1942 |
1 |
modifications.put("ILG", "GLU"); |
1943 |
1 |
modifications.put("ILX", "ILE"); |
1944 |
1 |
modifications.put("IMC", "CYS"); |
1945 |
1 |
modifications.put("IML", "ILE"); |
1946 |
1 |
modifications.put("IOY", "PHE"); |
1947 |
1 |
modifications.put("IPG", "GLY"); |
1948 |
1 |
modifications.put("IPN", "ASN"); |
1949 |
1 |
modifications.put("IRN", "ASN"); |
1950 |
1 |
modifications.put("IT1", "LYS"); |
1951 |
1 |
modifications.put("IU ", "UR3"); |
1952 |
1 |
modifications.put("IYR", "TYR"); |
1953 |
1 |
modifications.put("IYT", "THR"); |
1954 |
1 |
modifications.put("IZO", "MET"); |
1955 |
1 |
modifications.put("JJJ", "CYS"); |
1956 |
1 |
modifications.put("JJK", "CYS"); |
1957 |
1 |
modifications.put("JJL", "CYS"); |
1958 |
1 |
modifications.put("JW5", "ASN"); |
1959 |
1 |
modifications.put("K1R", "CYS"); |
1960 |
1 |
modifications.put("KAG", "GLY"); |
1961 |
1 |
modifications.put("KCX", "LYS"); |
1962 |
1 |
modifications.put("KGC", "LYS"); |
1963 |
1 |
modifications.put("KNB", "ALA"); |
1964 |
1 |
modifications.put("KOR", "MET"); |
1965 |
1 |
modifications.put("KPI", "LYS"); |
1966 |
1 |
modifications.put("KST", "LYS"); |
1967 |
1 |
modifications.put("KYQ", "LYS"); |
1968 |
1 |
modifications.put("L2A", "XAA"); |
1969 |
1 |
modifications.put("LA2", "LYS"); |
1970 |
1 |
modifications.put("LAA", "ASP"); |
1971 |
1 |
modifications.put("LAL", "ALA"); |
1972 |
1 |
modifications.put("LBY", "LYS"); |
1973 |
1 |
modifications.put("LC ", "CYS"); |
1974 |
1 |
modifications.put("LCA", "ALA"); |
1975 |
1 |
modifications.put("LCC", "ASN"); |
1976 |
1 |
modifications.put("LCG", "GLY"); |
1977 |
1 |
modifications.put("LCH", "ASN"); |
1978 |
1 |
modifications.put("LCK", "LYS"); |
1979 |
1 |
modifications.put("LCX", "LYS"); |
1980 |
1 |
modifications.put("LDH", "LYS"); |
1981 |
1 |
modifications.put("LED", "LEU"); |
1982 |
1 |
modifications.put("LEF", "LEU"); |
1983 |
1 |
modifications.put("LEH", "LEU"); |
1984 |
1 |
modifications.put("LEI", "VAL"); |
1985 |
1 |
modifications.put("LEM", "LEU"); |
1986 |
1 |
modifications.put("LEN", "LEU"); |
1987 |
1 |
modifications.put("LET", "XAA"); |
1988 |
1 |
modifications.put("LEU", "LEU"); |
1989 |
1 |
modifications.put("LEX", "LEU"); |
1990 |
1 |
modifications.put("LG ", "GLY"); |
1991 |
1 |
modifications.put("LGP", "GLY"); |
1992 |
1 |
modifications.put("LHC", "XAA"); |
1993 |
1 |
modifications.put("LHU", "UR3"); |
1994 |
1 |
modifications.put("LKC", "ASN"); |
1995 |
1 |
modifications.put("LLP", "LYS"); |
1996 |
1 |
modifications.put("LLY", "LYS"); |
1997 |
1 |
modifications.put("LME", "GLU"); |
1998 |
1 |
modifications.put("LMF", "LYS"); |
1999 |
1 |
modifications.put("LMQ", "GLN"); |
2000 |
1 |
modifications.put("LMS", "ASN"); |
2001 |
1 |
modifications.put("LP6", "LYS"); |
2002 |
1 |
modifications.put("LPD", "PRO"); |
2003 |
1 |
modifications.put("LPG", "GLY"); |
2004 |
1 |
modifications.put("LPL", "XAA"); |
2005 |
1 |
modifications.put("LPS", "SER"); |
2006 |
1 |
modifications.put("LSO", "XAA"); |
2007 |
1 |
modifications.put("LTA", "XAA"); |
2008 |
1 |
modifications.put("LTR", "TRP"); |
2009 |
1 |
modifications.put("LVG", "GLY"); |
2010 |
1 |
modifications.put("LVN", "VAL"); |
2011 |
1 |
modifications.put("LYF", "LYS"); |
2012 |
1 |
modifications.put("LYK", "LYS"); |
2013 |
1 |
modifications.put("LYM", "LYS"); |
2014 |
1 |
modifications.put("LYN", "LYS"); |
2015 |
1 |
modifications.put("LYR", "LYS"); |
2016 |
1 |
modifications.put("LYS", "LYS"); |
2017 |
1 |
modifications.put("LYX", "LYS"); |
2018 |
1 |
modifications.put("LYZ", "LYS"); |
2019 |
1 |
modifications.put("M0H", "CYS"); |
2020 |
1 |
modifications.put("M1G", "GLY"); |
2021 |
1 |
modifications.put("M2G", "GLY"); |
2022 |
1 |
modifications.put("M2L", "LYS"); |
2023 |
1 |
modifications.put("M2S", "MET"); |
2024 |
1 |
modifications.put("M30", "GLY"); |
2025 |
1 |
modifications.put("M3L", "LYS"); |
2026 |
1 |
modifications.put("M5M", "CYS"); |
2027 |
1 |
modifications.put("MA ", "ALA"); |
2028 |
1 |
modifications.put("MA6", "ALA"); |
2029 |
1 |
modifications.put("MA7", "ALA"); |
2030 |
1 |
modifications.put("MAA", "ALA"); |
2031 |
1 |
modifications.put("MAD", "ALA"); |
2032 |
1 |
modifications.put("MAI", "ARG"); |
2033 |
1 |
modifications.put("MBQ", "TYR"); |
2034 |
1 |
modifications.put("MBZ", "ASN"); |
2035 |
1 |
modifications.put("MC1", "SER"); |
2036 |
1 |
modifications.put("MCG", "XAA"); |
2037 |
1 |
modifications.put("MCL", "LYS"); |
2038 |
1 |
modifications.put("MCS", "CYS"); |
2039 |
1 |
modifications.put("MCY", "CYS"); |
2040 |
1 |
modifications.put("MD3", "CYS"); |
2041 |
1 |
modifications.put("MD6", "GLY"); |
2042 |
1 |
modifications.put("MDH", "XAA"); |
2043 |
1 |
modifications.put("MDO", "ASG"); |
2044 |
1 |
modifications.put("MDR", "ASN"); |
2045 |
1 |
modifications.put("MEA", "PHE"); |
2046 |
1 |
modifications.put("MED", "MET"); |
2047 |
1 |
modifications.put("MEG", "GLU"); |
2048 |
1 |
modifications.put("MEN", "ASN"); |
2049 |
1 |
modifications.put("MEP", "UR3"); |
2050 |
1 |
modifications.put("MEQ", "GLN"); |
2051 |
1 |
modifications.put("MET", "MET"); |
2052 |
1 |
modifications.put("MEU", "GLY"); |
2053 |
1 |
modifications.put("MF3", "XAA"); |
2054 |
1 |
modifications.put("MFC", "GYG"); |
2055 |
1 |
modifications.put("MG1", "GLY"); |
2056 |
1 |
modifications.put("MGG", "ARG"); |
2057 |
1 |
modifications.put("MGN", "GLN"); |
2058 |
1 |
modifications.put("MGQ", "ALA"); |
2059 |
1 |
modifications.put("MGV", "GLY"); |
2060 |
1 |
modifications.put("MGY", "GLY"); |
2061 |
1 |
modifications.put("MHL", "LEU"); |
2062 |
1 |
modifications.put("MHO", "MET"); |
2063 |
1 |
modifications.put("MHS", "HIS"); |
2064 |
1 |
modifications.put("MIA", "ALA"); |
2065 |
1 |
modifications.put("MIS", "SER"); |
2066 |
1 |
modifications.put("MK8", "LEU"); |
2067 |
1 |
modifications.put("ML3", "LYS"); |
2068 |
1 |
modifications.put("MLE", "LEU"); |
2069 |
1 |
modifications.put("MLL", "LEU"); |
2070 |
1 |
modifications.put("MLY", "LYS"); |
2071 |
1 |
modifications.put("MLZ", "LYS"); |
2072 |
1 |
modifications.put("MME", "MET"); |
2073 |
1 |
modifications.put("MMO", "ARG"); |
2074 |
1 |
modifications.put("MMT", "THR"); |
2075 |
1 |
modifications.put("MND", "ASN"); |
2076 |
1 |
modifications.put("MNL", "LEU"); |
2077 |
1 |
modifications.put("MNU", "UR3"); |
2078 |
1 |
modifications.put("MNV", "VAL"); |
2079 |
1 |
modifications.put("MOD", "XAA"); |
2080 |
1 |
modifications.put("MP8", "PRO"); |
2081 |
1 |
modifications.put("MPH", "XAA"); |
2082 |
1 |
modifications.put("MPJ", "XAA"); |
2083 |
1 |
modifications.put("MPQ", "GLY"); |
2084 |
1 |
modifications.put("MRG", "GLY"); |
2085 |
1 |
modifications.put("MSA", "GLY"); |
2086 |
1 |
modifications.put("MSE", "MET"); |
2087 |
1 |
modifications.put("MSL", "MET"); |
2088 |
1 |
modifications.put("MSO", "MET"); |
2089 |
1 |
modifications.put("MSP", "XAA"); |
2090 |
1 |
modifications.put("MT2", "MET"); |
2091 |
1 |
modifications.put("MTR", "THR"); |
2092 |
1 |
modifications.put("MTU", "ALA"); |
2093 |
1 |
modifications.put("MTY", "TYR"); |
2094 |
1 |
modifications.put("MVA", "VAL"); |
2095 |
1 |
modifications.put("N ", "ASN"); |
2096 |
1 |
modifications.put("N10", "SER"); |
2097 |
1 |
modifications.put("N2C", "XAA"); |
2098 |
1 |
modifications.put("N5I", "ASN"); |
2099 |
1 |
modifications.put("N5M", "CYS"); |
2100 |
1 |
modifications.put("N6G", "GLY"); |
2101 |
1 |
modifications.put("N7P", "PRO"); |
2102 |
1 |
modifications.put("NA8", "ALA"); |
2103 |
1 |
modifications.put("NAL", "ALA"); |
2104 |
1 |
modifications.put("NAM", "ALA"); |
2105 |
1 |
modifications.put("NB8", "ASN"); |
2106 |
1 |
modifications.put("NBQ", "TYR"); |
2107 |
1 |
modifications.put("NC1", "SER"); |
2108 |
1 |
modifications.put("NCB", "ALA"); |
2109 |
1 |
modifications.put("NCX", "ASN"); |
2110 |
1 |
modifications.put("NCY", "XAA"); |
2111 |
1 |
modifications.put("NDF", "PHE"); |
2112 |
1 |
modifications.put("NDN", "UR3"); |
2113 |
1 |
modifications.put("NEM", "HIS"); |
2114 |
1 |
modifications.put("NEP", "HIS"); |
2115 |
1 |
modifications.put("NF2", "ASN"); |
2116 |
1 |
modifications.put("NFA", "PHE"); |
2117 |
1 |
modifications.put("NHL", "GLU"); |
2118 |
1 |
modifications.put("NIT", "XAA"); |
2119 |
1 |
modifications.put("NIY", "TYR"); |
2120 |
1 |
modifications.put("NLE", "LEU"); |
2121 |
1 |
modifications.put("NLN", "LEU"); |
2122 |
1 |
modifications.put("NLO", "LEU"); |
2123 |
1 |
modifications.put("NLP", "LEU"); |
2124 |
1 |
modifications.put("NLQ", "GLN"); |
2125 |
1 |
modifications.put("NMC", "GLY"); |
2126 |
1 |
modifications.put("NMM", "ARG"); |
2127 |
1 |
modifications.put("NMS", "THR"); |
2128 |
1 |
modifications.put("NMT", "THR"); |
2129 |
1 |
modifications.put("NNH", "ARG"); |
2130 |
1 |
modifications.put("NP3", "ASN"); |
2131 |
1 |
modifications.put("NPH", "CYS"); |
2132 |
1 |
modifications.put("NPI", "ALA"); |
2133 |
1 |
modifications.put("NRP", "LYG"); |
2134 |
1 |
modifications.put("NRQ", "MYG"); |
2135 |
1 |
modifications.put("NSK", "XAA"); |
2136 |
1 |
modifications.put("NTY", "TYR"); |
2137 |
1 |
modifications.put("NVA", "VAL"); |
2138 |
1 |
modifications.put("NYC", "TWG"); |
2139 |
1 |
modifications.put("NYG", "NYG"); |
2140 |
1 |
modifications.put("NYM", "ASN"); |
2141 |
1 |
modifications.put("NYS", "CYS"); |
2142 |
1 |
modifications.put("NZH", "HIS"); |
2143 |
1 |
modifications.put("O12", "XAA"); |
2144 |
1 |
modifications.put("O2C", "ASN"); |
2145 |
1 |
modifications.put("O2G", "GLY"); |
2146 |
1 |
modifications.put("OAD", "ASN"); |
2147 |
1 |
modifications.put("OAS", "SER"); |
2148 |
1 |
modifications.put("OBF", "XAA"); |
2149 |
1 |
modifications.put("OBS", "XAA"); |
2150 |
1 |
modifications.put("OCS", "CYS"); |
2151 |
1 |
modifications.put("OCY", "CYS"); |
2152 |
1 |
modifications.put("ODP", "ASN"); |
2153 |
1 |
modifications.put("OHI", "HIS"); |
2154 |
1 |
modifications.put("OHS", "ASP"); |
2155 |
1 |
modifications.put("OIC", "XAA"); |
2156 |
1 |
modifications.put("OIP", "ILE"); |
2157 |
1 |
modifications.put("OLE", "XAA"); |
2158 |
1 |
modifications.put("OLT", "THR"); |
2159 |
1 |
modifications.put("OLZ", "SER"); |
2160 |
1 |
modifications.put("OMC", "CYS"); |
2161 |
1 |
modifications.put("OMG", "GLY"); |
2162 |
1 |
modifications.put("OMT", "MET"); |
2163 |
1 |
modifications.put("OMU", "UR3"); |
2164 |
1 |
modifications.put("ONE", "UR3"); |
2165 |
1 |
modifications.put("ONH", "ALA"); |
2166 |
1 |
modifications.put("ONL", "XAA"); |
2167 |
1 |
modifications.put("OPR", "ARG"); |
2168 |
1 |
modifications.put("ORN", "ALA"); |
2169 |
1 |
modifications.put("ORQ", "ARG"); |
2170 |
1 |
modifications.put("OSE", "SER"); |
2171 |
1 |
modifications.put("OTB", "XAA"); |
2172 |
1 |
modifications.put("OTH", "THR"); |
2173 |
1 |
modifications.put("OTY", "TYR"); |
2174 |
1 |
modifications.put("OXX", "ASP"); |
2175 |
1 |
modifications.put("P ", "GLY"); |
2176 |
1 |
modifications.put("P1L", "CYS"); |
2177 |
1 |
modifications.put("P1P", "ASN"); |
2178 |
1 |
modifications.put("P2T", "THR"); |
2179 |
1 |
modifications.put("P2U", "UR3"); |
2180 |
1 |
modifications.put("P2Y", "PRO"); |
2181 |
1 |
modifications.put("P5P", "ALA"); |
2182 |
1 |
modifications.put("PAQ", "TYR"); |
2183 |
1 |
modifications.put("PAS", "ASP"); |
2184 |
1 |
modifications.put("PAT", "TRP"); |
2185 |
1 |
modifications.put("PAU", "ALA"); |
2186 |
1 |
modifications.put("PBB", "CYS"); |
2187 |
1 |
modifications.put("PBF", "PHE"); |
2188 |
1 |
modifications.put("PBT", "ASN"); |
2189 |
1 |
modifications.put("PCA", "GLU"); |
2190 |
1 |
modifications.put("PCC", "PRO"); |
2191 |
1 |
modifications.put("PCE", "XAA"); |
2192 |
1 |
modifications.put("PCS", "PHE"); |
2193 |
1 |
modifications.put("PDL", "XAA"); |
2194 |
1 |
modifications.put("PDU", "UR3"); |
2195 |
1 |
modifications.put("PEC", "CYS"); |
2196 |
1 |
modifications.put("PF5", "PHE"); |
2197 |
1 |
modifications.put("PFF", "PHE"); |
2198 |
1 |
modifications.put("PFX", "XAA"); |
2199 |
1 |
modifications.put("PG1", "SER"); |
2200 |
1 |
modifications.put("PG7", "GLY"); |
2201 |
1 |
modifications.put("PG9", "GLY"); |
2202 |
1 |
modifications.put("PGL", "XAA"); |
2203 |
1 |
modifications.put("PGN", "GLY"); |
2204 |
1 |
modifications.put("PGP", "GLY"); |
2205 |
1 |
modifications.put("PGY", "GLY"); |
2206 |
1 |
modifications.put("PHA", "PHE"); |
2207 |
1 |
modifications.put("PHD", "ASP"); |
2208 |
1 |
modifications.put("PHE", "PHE"); |
2209 |
1 |
modifications.put("PHI", "PHE"); |
2210 |
1 |
modifications.put("PHL", "PHE"); |
2211 |
1 |
modifications.put("PHM", "PHE"); |
2212 |
1 |
modifications.put("PIA", "AYG"); |
2213 |
1 |
modifications.put("PIV", "XAA"); |
2214 |
1 |
modifications.put("PLE", "LEU"); |
2215 |
1 |
modifications.put("PM3", "PHE"); |
2216 |
1 |
modifications.put("PMT", "CYS"); |
2217 |
1 |
modifications.put("POM", "PRO"); |
2218 |
1 |
modifications.put("PPN", "PHE"); |
2219 |
1 |
modifications.put("PPU", "ALA"); |
2220 |
1 |
modifications.put("PPW", "GLY"); |
2221 |
1 |
modifications.put("PQ1", "ASN"); |
2222 |
1 |
modifications.put("PR3", "CYS"); |
2223 |
1 |
modifications.put("PR5", "ALA"); |
2224 |
1 |
modifications.put("PR9", "PRO"); |
2225 |
1 |
modifications.put("PRN", "ALA"); |
2226 |
1 |
modifications.put("PRO", "PRO"); |
2227 |
1 |
modifications.put("PRS", "PRO"); |
2228 |
1 |
modifications.put("PSA", "PHE"); |
2229 |
1 |
modifications.put("PSH", "HIS"); |
2230 |
1 |
modifications.put("PST", "THR"); |
2231 |
1 |
modifications.put("PSU", "UR3"); |
2232 |
1 |
modifications.put("PSW", "CYS"); |
2233 |
1 |
modifications.put("PTA", "XAA"); |
2234 |
1 |
modifications.put("PTH", "TYR"); |
2235 |
1 |
modifications.put("PTM", "TYR"); |
2236 |
1 |
modifications.put("PTR", "TYR"); |
2237 |
1 |
modifications.put("PU ", "ALA"); |
2238 |
1 |
modifications.put("PUY", "ASN"); |
2239 |
1 |
modifications.put("PVH", "HIS"); |
2240 |
1 |
modifications.put("PVL", "XAA"); |
2241 |
1 |
modifications.put("PYA", "ALA"); |
2242 |
1 |
modifications.put("PYO", "UR3"); |
2243 |
1 |
modifications.put("PYX", "CYS"); |
2244 |
1 |
modifications.put("PYY", "ASN"); |
2245 |
1 |
modifications.put("QLG", "QLG"); |
2246 |
1 |
modifications.put("QMM", "GLN"); |
2247 |
1 |
modifications.put("QPA", "CYS"); |
2248 |
1 |
modifications.put("QPH", "PHE"); |
2249 |
1 |
modifications.put("QUO", "GLY"); |
2250 |
1 |
modifications.put("R ", "ALA"); |
2251 |
1 |
modifications.put("R1A", "CYS"); |
2252 |
1 |
modifications.put("R4K", "TRP"); |
2253 |
1 |
modifications.put("RC7", "HYG"); |
2254 |
1 |
modifications.put("RE0", "TRP"); |
2255 |
1 |
modifications.put("RE3", "TRP"); |
2256 |
1 |
modifications.put("RIA", "ALA"); |
2257 |
1 |
modifications.put("RMP", "ALA"); |
2258 |
1 |
modifications.put("RON", "XAA"); |
2259 |
1 |
modifications.put("RT ", "THR"); |
2260 |
1 |
modifications.put("RTP", "ASN"); |
2261 |
1 |
modifications.put("S1H", "SER"); |
2262 |
1 |
modifications.put("S2C", "CYS"); |
2263 |
1 |
modifications.put("S2D", "ALA"); |
2264 |
1 |
modifications.put("S2M", "THR"); |
2265 |
1 |
modifications.put("S2P", "ALA"); |
2266 |
1 |
modifications.put("S4A", "ALA"); |
2267 |
1 |
modifications.put("S4C", "CYS"); |
2268 |
1 |
modifications.put("S4G", "GLY"); |
2269 |
1 |
modifications.put("S4U", "UR3"); |
2270 |
1 |
modifications.put("S6G", "GLY"); |
2271 |
1 |
modifications.put("SAC", "SER"); |
2272 |
1 |
modifications.put("SAH", "CYS"); |
2273 |
1 |
modifications.put("SAR", "GLY"); |
2274 |
1 |
modifications.put("SBL", "SER"); |
2275 |
1 |
modifications.put("SC ", "CYS"); |
2276 |
1 |
modifications.put("SCH", "CYS"); |
2277 |
1 |
modifications.put("SCS", "CYS"); |
2278 |
1 |
modifications.put("SCY", "CYS"); |
2279 |
1 |
modifications.put("SD2", "XAA"); |
2280 |
1 |
modifications.put("SDG", "GLY"); |
2281 |
1 |
modifications.put("SDP", "SER"); |
2282 |
1 |
modifications.put("SEB", "SER"); |
2283 |
1 |
modifications.put("SEC", "ALA"); |
2284 |
1 |
modifications.put("SEG", "ALA"); |
2285 |
1 |
modifications.put("SEL", "SER"); |
2286 |
1 |
modifications.put("SEM", "SER"); |
2287 |
1 |
modifications.put("SEN", "SER"); |
2288 |
1 |
modifications.put("SEP", "SER"); |
2289 |
1 |
modifications.put("SER", "SER"); |
2290 |
1 |
modifications.put("SET", "SER"); |
2291 |
1 |
modifications.put("SGB", "SER"); |
2292 |
1 |
modifications.put("SHC", "CYS"); |
2293 |
1 |
modifications.put("SHP", "GLY"); |
2294 |
1 |
modifications.put("SHR", "LYS"); |
2295 |
1 |
modifications.put("SIB", "CYS"); |
2296 |
1 |
modifications.put("SIC", "DC"); |
2297 |
1 |
modifications.put("SLA", "PRO"); |
2298 |
1 |
modifications.put("SLR", "PRO"); |
2299 |
1 |
modifications.put("SLZ", "LYS"); |
2300 |
1 |
modifications.put("SMC", "CYS"); |
2301 |
1 |
modifications.put("SME", "MET"); |
2302 |
1 |
modifications.put("SMF", "PHE"); |
2303 |
1 |
modifications.put("SMP", "ALA"); |
2304 |
1 |
modifications.put("SMT", "THR"); |
2305 |
1 |
modifications.put("SNC", "CYS"); |
2306 |
1 |
modifications.put("SNN", "ASN"); |
2307 |
1 |
modifications.put("SOC", "CYS"); |
2308 |
1 |
modifications.put("SOS", "ASN"); |
2309 |
1 |
modifications.put("SOY", "SER"); |
2310 |
1 |
modifications.put("SPT", "THR"); |
2311 |
1 |
modifications.put("SRA", "ALA"); |
2312 |
1 |
modifications.put("SSU", "UR3"); |
2313 |
1 |
modifications.put("STY", "TYR"); |
2314 |
1 |
modifications.put("SUB", "XAA"); |
2315 |
1 |
modifications.put("SUI", "DG"); |
2316 |
1 |
modifications.put("SUN", "SER"); |
2317 |
1 |
modifications.put("SUR", "UR3"); |
2318 |
1 |
modifications.put("SVA", "SER"); |
2319 |
1 |
modifications.put("SVV", "SER"); |
2320 |
1 |
modifications.put("SVW", "SER"); |
2321 |
1 |
modifications.put("SVX", "SER"); |
2322 |
1 |
modifications.put("SVY", "SER"); |
2323 |
1 |
modifications.put("SVZ", "XAA"); |
2324 |
1 |
modifications.put("SWG", "SWG"); |
2325 |
1 |
modifications.put("SYS", "CYS"); |
2326 |
1 |
modifications.put("T ", "THR"); |
2327 |
1 |
modifications.put("T11", "PHE"); |
2328 |
1 |
modifications.put("T23", "THR"); |
2329 |
1 |
modifications.put("T2S", "THR"); |
2330 |
1 |
modifications.put("T2T", "ASN"); |
2331 |
1 |
modifications.put("T31", "UR3"); |
2332 |
1 |
modifications.put("T32", "THR"); |
2333 |
1 |
modifications.put("T36", "THR"); |
2334 |
1 |
modifications.put("T37", "THR"); |
2335 |
1 |
modifications.put("T38", "THR"); |
2336 |
1 |
modifications.put("T39", "THR"); |
2337 |
1 |
modifications.put("T3P", "THR"); |
2338 |
1 |
modifications.put("T41", "THR"); |
2339 |
1 |
modifications.put("T48", "THR"); |
2340 |
1 |
modifications.put("T49", "THR"); |
2341 |
1 |
modifications.put("T4S", "THR"); |
2342 |
1 |
modifications.put("T5O", "UR3"); |
2343 |
1 |
modifications.put("T5S", "THR"); |
2344 |
1 |
modifications.put("T66", "XAA"); |
2345 |
1 |
modifications.put("T6A", "ALA"); |
2346 |
1 |
modifications.put("TA3", "THR"); |
2347 |
1 |
modifications.put("TA4", "XAA"); |
2348 |
1 |
modifications.put("TAF", "THR"); |
2349 |
1 |
modifications.put("TAL", "ASN"); |
2350 |
1 |
modifications.put("TAV", "ASP"); |
2351 |
1 |
modifications.put("TBG", "VAL"); |
2352 |
1 |
modifications.put("TBM", "THR"); |
2353 |
1 |
modifications.put("TC1", "CYS"); |
2354 |
1 |
modifications.put("TCP", "THR"); |
2355 |
1 |
modifications.put("TCQ", "TYR"); |
2356 |
1 |
modifications.put("TCR", "TRP"); |
2357 |
1 |
modifications.put("TCY", "ALA"); |
2358 |
1 |
modifications.put("TDD", "LEU"); |
2359 |
1 |
modifications.put("TDY", "THR"); |
2360 |
1 |
modifications.put("TFE", "THR"); |
2361 |
1 |
modifications.put("TFO", "ALA"); |
2362 |
1 |
modifications.put("TFQ", "PHE"); |
2363 |
1 |
modifications.put("TFT", "THR"); |
2364 |
1 |
modifications.put("TGP", "GLY"); |
2365 |
1 |
modifications.put("TH6", "THR"); |
2366 |
1 |
modifications.put("THC", "THR"); |
2367 |
1 |
modifications.put("THO", "XAA"); |
2368 |
1 |
modifications.put("THR", "THR"); |
2369 |
1 |
modifications.put("THX", "ASN"); |
2370 |
1 |
modifications.put("THZ", "ARG"); |
2371 |
1 |
modifications.put("TIH", "ALA"); |
2372 |
1 |
modifications.put("TLB", "ASN"); |
2373 |
1 |
modifications.put("TLC", "THR"); |
2374 |
1 |
modifications.put("TLN", "UR3"); |
2375 |
1 |
modifications.put("TMB", "THR"); |
2376 |
1 |
modifications.put("TMD", "THR"); |
2377 |
1 |
modifications.put("TNB", "CYS"); |
2378 |
1 |
modifications.put("TNR", "SER"); |
2379 |
1 |
modifications.put("TOX", "TRP"); |
2380 |
1 |
modifications.put("TP1", "THR"); |
2381 |
1 |
modifications.put("TPC", "CYS"); |
2382 |
1 |
modifications.put("TPG", "GLY"); |
2383 |
1 |
modifications.put("TPH", "XAA"); |
2384 |
1 |
modifications.put("TPL", "TRP"); |
2385 |
1 |
modifications.put("TPO", "THR"); |
2386 |
1 |
modifications.put("TPQ", "TYR"); |
2387 |
1 |
modifications.put("TQI", "TRP"); |
2388 |
1 |
modifications.put("TQQ", "TRP"); |
2389 |
1 |
modifications.put("TRF", "TRP"); |
2390 |
1 |
modifications.put("TRG", "LYS"); |
2391 |
1 |
modifications.put("TRN", "TRP"); |
2392 |
1 |
modifications.put("TRO", "TRP"); |
2393 |
1 |
modifications.put("TRP", "TRP"); |
2394 |
1 |
modifications.put("TRQ", "TRP"); |
2395 |
1 |
modifications.put("TRW", "TRP"); |
2396 |
1 |
modifications.put("TRX", "TRP"); |
2397 |
1 |
modifications.put("TS ", "ASN"); |
2398 |
1 |
modifications.put("TST", "XAA"); |
2399 |
1 |
modifications.put("TT ", "ASN"); |
2400 |
1 |
modifications.put("TTD", "THR"); |
2401 |
1 |
modifications.put("TTI", "UR3"); |
2402 |
1 |
modifications.put("TTM", "THR"); |
2403 |
1 |
modifications.put("TTQ", "TRP"); |
2404 |
1 |
modifications.put("TTS", "TYR"); |
2405 |
1 |
modifications.put("TY1", "TYR"); |
2406 |
1 |
modifications.put("TY2", "TYR"); |
2407 |
1 |
modifications.put("TY3", "TYR"); |
2408 |
1 |
modifications.put("TY5", "TYR"); |
2409 |
1 |
modifications.put("TYB", "TYR"); |
2410 |
1 |
modifications.put("TYI", "TYR"); |
2411 |
1 |
modifications.put("TYJ", "TYR"); |
2412 |
1 |
modifications.put("TYN", "TYR"); |
2413 |
1 |
modifications.put("TYO", "TYR"); |
2414 |
1 |
modifications.put("TYQ", "TYR"); |
2415 |
1 |
modifications.put("TYR", "TYR"); |
2416 |
1 |
modifications.put("TYS", "TYR"); |
2417 |
1 |
modifications.put("TYT", "TYR"); |
2418 |
1 |
modifications.put("TYU", "ASN"); |
2419 |
1 |
modifications.put("TYW", "TYR"); |
2420 |
1 |
modifications.put("TYX", "XAA"); |
2421 |
1 |
modifications.put("TYY", "TYR"); |
2422 |
1 |
modifications.put("TZB", "XAA"); |
2423 |
1 |
modifications.put("TZO", "XAA"); |
2424 |
1 |
modifications.put("U ", "UR3"); |
2425 |
1 |
modifications.put("U25", "UR3"); |
2426 |
1 |
modifications.put("U2L", "UR3"); |
2427 |
1 |
modifications.put("U2N", "UR3"); |
2428 |
1 |
modifications.put("U2P", "UR3"); |
2429 |
1 |
modifications.put("U31", "UR3"); |
2430 |
1 |
modifications.put("U33", "UR3"); |
2431 |
1 |
modifications.put("U34", "UR3"); |
2432 |
1 |
modifications.put("U36", "UR3"); |
2433 |
1 |
modifications.put("U37", "UR3"); |
2434 |
1 |
modifications.put("U8U", "UR3"); |
2435 |
1 |
modifications.put("UAR", "UR3"); |
2436 |
1 |
modifications.put("UCL", "UR3"); |
2437 |
1 |
modifications.put("UD5", "UR3"); |
2438 |
1 |
modifications.put("UDP", "ASN"); |
2439 |
1 |
modifications.put("UFP", "ASN"); |
2440 |
1 |
modifications.put("UFR", "UR3"); |
2441 |
1 |
modifications.put("UFT", "UR3"); |
2442 |
1 |
modifications.put("UMA", "ALA"); |
2443 |
1 |
modifications.put("UMP", "UR3"); |
2444 |
1 |
modifications.put("UMS", "UR3"); |
2445 |
1 |
modifications.put("UN1", "XAA"); |
2446 |
1 |
modifications.put("UN2", "XAA"); |
2447 |
1 |
modifications.put("UNK", "XAA"); |
2448 |
1 |
modifications.put("UR3", "UR3"); |
2449 |
1 |
modifications.put("URD", "UR3"); |
2450 |
1 |
modifications.put("US1", "UR3"); |
2451 |
1 |
modifications.put("US2", "UR3"); |
2452 |
1 |
modifications.put("US3", "THR"); |
2453 |
1 |
modifications.put("US5", "UR3"); |
2454 |
1 |
modifications.put("USM", "UR3"); |
2455 |
1 |
modifications.put("VAD", "VAL"); |
2456 |
1 |
modifications.put("VAF", "VAL"); |
2457 |
1 |
modifications.put("VAL", "VAL"); |
2458 |
1 |
modifications.put("VB1", "LYS"); |
2459 |
1 |
modifications.put("VDL", "XAA"); |
2460 |
1 |
modifications.put("VLL", "XAA"); |
2461 |
1 |
modifications.put("VLM", "XAA"); |
2462 |
1 |
modifications.put("VMS", "XAA"); |
2463 |
1 |
modifications.put("VOL", "XAA"); |
2464 |
1 |
modifications.put("WCR", "GYG"); |
2465 |
1 |
modifications.put("X ", "GLY"); |
2466 |
1 |
modifications.put("X2W", "GLU"); |
2467 |
1 |
modifications.put("X4A", "ASN"); |
2468 |
1 |
modifications.put("X9Q", "AFG"); |
2469 |
1 |
modifications.put("XAD", "ALA"); |
2470 |
1 |
modifications.put("XAE", "ASN"); |
2471 |
1 |
modifications.put("XAL", "ALA"); |
2472 |
1 |
modifications.put("XAR", "ASN"); |
2473 |
1 |
modifications.put("XCL", "CYS"); |
2474 |
1 |
modifications.put("XCN", "CYS"); |
2475 |
1 |
modifications.put("XCP", "XAA"); |
2476 |
1 |
modifications.put("XCR", "CYS"); |
2477 |
1 |
modifications.put("XCS", "ASN"); |
2478 |
1 |
modifications.put("XCT", "CYS"); |
2479 |
1 |
modifications.put("XCY", "CYS"); |
2480 |
1 |
modifications.put("XGA", "ASN"); |
2481 |
1 |
modifications.put("XGL", "GLY"); |
2482 |
1 |
modifications.put("XGR", "GLY"); |
2483 |
1 |
modifications.put("XGU", "GLY"); |
2484 |
1 |
modifications.put("XPR", "PRO"); |
2485 |
1 |
modifications.put("XSN", "ASN"); |
2486 |
1 |
modifications.put("XTH", "THR"); |
2487 |
1 |
modifications.put("XTL", "THR"); |
2488 |
1 |
modifications.put("XTR", "THR"); |
2489 |
1 |
modifications.put("XTS", "GLY"); |
2490 |
1 |
modifications.put("XTY", "ASN"); |
2491 |
1 |
modifications.put("XUA", "ALA"); |
2492 |
1 |
modifications.put("XUG", "GLY"); |
2493 |
1 |
modifications.put("XX1", "LYS"); |
2494 |
1 |
modifications.put("XXY", "THG"); |
2495 |
1 |
modifications.put("XYG", "DYG"); |
2496 |
1 |
modifications.put("Y ", "ALA"); |
2497 |
1 |
modifications.put("YCM", "CYS"); |
2498 |
1 |
modifications.put("YG ", "GLY"); |
2499 |
1 |
modifications.put("YOF", "TYR"); |
2500 |
1 |
modifications.put("YRR", "ASN"); |
2501 |
1 |
modifications.put("YYG", "GLY"); |
2502 |
1 |
modifications.put("Z ", "CYS"); |
2503 |
1 |
modifications.put("Z01", "ALA"); |
2504 |
1 |
modifications.put("ZAD", "ALA"); |
2505 |
1 |
modifications.put("ZAL", "ALA"); |
2506 |
1 |
modifications.put("ZBC", "CYS"); |
2507 |
1 |
modifications.put("ZBU", "UR3"); |
2508 |
1 |
modifications.put("ZCL", "PHE"); |
2509 |
1 |
modifications.put("ZCY", "CYS"); |
2510 |
1 |
modifications.put("ZDU", "UR3"); |
2511 |
1 |
modifications.put("ZFB", "XAA"); |
2512 |
1 |
modifications.put("ZGU", "GLY"); |
2513 |
1 |
modifications.put("ZHP", "ASN"); |
2514 |
1 |
modifications.put("ZTH", "THR"); |
2515 |
1 |
modifications.put("ZU0", "THR"); |
2516 |
1 |
modifications.put("ZZJ", "ALA"); |
2517 |
|
|
2518 |
|
} |
2519 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
2520 |
4557 |
public static String getCanonicalAminoAcid(String aA)... |
2521 |
|
{ |
2522 |
4557 |
String canonical = modifications.get(aA); |
2523 |
4557 |
return canonical == null ? aA : canonical; |
2524 |
|
} |
2525 |
|
|
2526 |
|
|
2527 |
|
|
|
|
| 0% |
Uncovered Elements: 35 (35) |
Complexity: 7 |
Complexity Density: 0.3 |
|
2528 |
0 |
public static void main(String[] args)... |
2529 |
|
{ |
2530 |
0 |
Hashtable<String, Vector<String>> aaProps = new Hashtable<>(); |
2531 |
0 |
System.out.println("my %aa = {"); |
2532 |
|
|
2533 |
0 |
for (String pname : propHash.keySet()) |
2534 |
|
{ |
2535 |
0 |
Map<String, Integer> phash = propHash.get(pname); |
2536 |
0 |
for (String rname : phash.keySet()) |
2537 |
|
{ |
2538 |
0 |
Vector<String> aprops = aaProps.get(rname); |
2539 |
0 |
if (aprops == null) |
2540 |
|
{ |
2541 |
0 |
aprops = new Vector<>(); |
2542 |
0 |
aaProps.put(rname, aprops); |
2543 |
|
} |
2544 |
0 |
Integer hasprop = phash.get(rname); |
2545 |
0 |
if (hasprop.intValue() == 1) |
2546 |
|
{ |
2547 |
0 |
aprops.addElement(pname); |
2548 |
|
} |
2549 |
|
} |
2550 |
|
} |
2551 |
0 |
Enumeration<String> res = aaProps.keys(); |
2552 |
0 |
while (res.hasMoreElements()) |
2553 |
|
{ |
2554 |
0 |
String rname = res.nextElement(); |
2555 |
|
|
2556 |
0 |
System.out.print("'" + rname + "' => ["); |
2557 |
0 |
Enumeration<String> props = aaProps.get(rname).elements(); |
2558 |
0 |
while (props.hasMoreElements()) |
2559 |
|
{ |
2560 |
0 |
System.out.print("'" + props.nextElement() + "'"); |
2561 |
0 |
if (props.hasMoreElements()) |
2562 |
|
{ |
2563 |
0 |
System.out.println(", "); |
2564 |
|
} |
2565 |
|
} |
2566 |
0 |
System.out.println("]" + (res.hasMoreElements() ? "," : "")); |
2567 |
|
} |
2568 |
0 |
System.out.println("};"); |
2569 |
|
} |
2570 |
|
|
2571 |
|
|
2572 |
|
|
2573 |
|
|
2574 |
|
|
2575 |
|
|
2576 |
|
@param |
2577 |
|
@param |
2578 |
|
@return |
2579 |
|
|
|
|
| 96.3% |
Uncovered Elements: 1 (27) |
Complexity: 10 |
Complexity Density: 0.59 |
|
2580 |
4 |
public static List<String> getResidues(boolean forNucleotide,... |
2581 |
|
boolean includeAmbiguous) |
2582 |
|
{ |
2583 |
4 |
List<String> result = new ArrayList<>(); |
2584 |
4 |
if (forNucleotide) |
2585 |
|
{ |
2586 |
2 |
for (String nuc : nucleotideName.keySet()) |
2587 |
|
{ |
2588 |
72 |
int val = nucleotideIndex[nuc.charAt(0)]; |
2589 |
72 |
if ((!includeAmbiguous && val > 4) || (val >= maxNucleotideIndex)) |
2590 |
|
{ |
2591 |
42 |
continue; |
2592 |
|
} |
2593 |
30 |
nuc = nuc.toUpperCase(); |
2594 |
30 |
if (!result.contains(nuc)) |
2595 |
|
{ |
2596 |
15 |
result.add(nuc); |
2597 |
|
} |
2598 |
|
} |
2599 |
|
} |
2600 |
|
else |
2601 |
|
{ |
2602 |
|
|
2603 |
|
|
2604 |
|
|
2605 |
2 |
for (String res : aa3Hash.keySet()) |
2606 |
|
{ |
2607 |
58 |
int index = aa3Hash.get(res).intValue(); |
2608 |
58 |
if ((!includeAmbiguous && index >= 20) || index >= maxProteinIndex) |
2609 |
|
{ |
2610 |
15 |
continue; |
2611 |
|
} |
2612 |
43 |
res = res.toUpperCase(); |
2613 |
43 |
if (!result.contains(res)) |
2614 |
|
{ |
2615 |
43 |
result.add(res); |
2616 |
|
} |
2617 |
|
} |
2618 |
|
} |
2619 |
|
|
2620 |
4 |
return result; |
2621 |
|
} |
2622 |
|
|
2623 |
|
|
2624 |
|
|
2625 |
|
|
2626 |
|
@param |
2627 |
|
|
2628 |
|
@return |
2629 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (8) |
Complexity: 3 |
Complexity Density: 0.75 |
|
2630 |
8 |
public static char getSingleCharacterCode(String threeLetterCode)... |
2631 |
|
{ |
2632 |
8 |
if (threeLetterCode == null) |
2633 |
|
{ |
2634 |
2 |
return '0'; |
2635 |
|
} |
2636 |
6 |
Integer index = ResidueProperties.aa3Hash |
2637 |
|
.get(threeLetterCode.toUpperCase()); |
2638 |
6 |
return index == null ? '0' : aa[index].charAt(0); |
2639 |
|
} |
2640 |
|
} |