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package jalview.schemes; |
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import java.awt.Color; |
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import java.util.HashMap; |
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import java.util.List; |
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import java.util.Map; |
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import jalview.api.AlignViewportI; |
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import jalview.datamodel.AnnotatedCollectionI; |
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import jalview.datamodel.SequenceCollectionI; |
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import jalview.datamodel.SequenceI; |
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import jalview.util.ColorUtils; |
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import jalview.util.Comparison; |
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| 76.3% |
Uncovered Elements: 56 (236) |
Complexity: 30 |
Complexity Density: 0.15 |
|
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public class ClustalxColourScheme extends ResidueColourScheme |
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{ |
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private static final int EIGHTY_FIVE = 85; |
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private static final int FIFTY = 50; |
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private static final int EIGHTY = 80; |
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private static final int SIXTY = 60; |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 1 |
|
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enum ClustalColour |
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{ |
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RED(0.9f, 0.2f, 0.1f), BLUE(0.5f, 0.7f, 0.9f), GREEN(0.1f, 0.8f, 0.1f), |
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ORANGE(0.9f, 0.6f, 0.3f), CYAN(0.1f, 0.7f, 0.7f), |
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PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f), |
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YELLOW(0.8f, 0.8f, 0.0f); |
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|
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final Color colour; |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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8 |
ClustalColour(float r, float g, float b)... |
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{ |
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colour = new Color(r, g, b); |
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} |
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} |
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|
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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private class ConsensusColour |
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{ |
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Consensus[] cons; |
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|
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Color c; |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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public ConsensusColour(ClustalColour col, Consensus[] conses)... |
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{ |
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this.cons = conses; |
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this.c = col.colour; |
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} |
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} |
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private int[][] cons2; |
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private ConsensusColour[] colours; |
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private ConsensusColour[] residueColour; |
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private int size; |
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private Consensus[] conses = new Consensus[32]; |
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private boolean includeGaps = true; |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
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public ClustalxColourScheme()... |
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{ |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public ClustalxColourScheme(AnnotatedCollectionI alignment,... |
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Map<SequenceI, SequenceCollectionI> hiddenReps) |
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{ |
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alignmentChanged(alignment, hiddenReps); |
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} |
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| 89.5% |
Uncovered Elements: 2 (19) |
Complexity: 3 |
Complexity Density: 0.2 |
|
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17 |
@Override... |
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public synchronized void alignmentChanged(AnnotatedCollectionI alignment, |
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Map<SequenceI, SequenceCollectionI> hiddenReps) |
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{ |
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int maxWidth = alignment.getWidth(); |
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List<SequenceI> seqs = alignment.getSequences(hiddenReps); |
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cons2 = new int[maxWidth][24]; |
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includeGaps = isIncludeGaps(); |
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int res = 0; |
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for (SequenceI sq : seqs) |
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{ |
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int end_j = sq.getLength() - 1; |
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int length = sq.getLength(); |
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|
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10905 |
for (int i = 0; i <= end_j; i++) |
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{ |
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10815 |
if (length - 1 < i) |
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{ |
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0 |
res = 23; |
121 |
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} |
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else |
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{ |
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10815 |
res = ResidueProperties.aaIndex[sq.getCharAt(i)]; |
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} |
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10815 |
cons2[i][res]++; |
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} |
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} |
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|
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this.size = seqs.size(); |
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17 |
makeColours(); |
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} |
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| 100% |
Uncovered Elements: 0 (120) |
Complexity: 1 |
Complexity Density: 0.01 |
|
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17 |
void makeColours()... |
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{ |
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conses[0] = new Consensus("WLVIMAFCYHP", SIXTY); |
137 |
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conses[1] = new Consensus("WLVIMAFCYHP", EIGHTY); |
138 |
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conses[2] = new Consensus("ED", FIFTY); |
139 |
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conses[3] = new Consensus("KR", SIXTY); |
140 |
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conses[4] = new Consensus("G", FIFTY); |
141 |
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conses[5] = new Consensus("N", FIFTY); |
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conses[6] = new Consensus("QE", FIFTY); |
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conses[7] = new Consensus("P", FIFTY); |
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conses[8] = new Consensus("TS", FIFTY); |
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|
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conses[26] = new Consensus("A", EIGHTY_FIVE); |
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conses[27] = new Consensus("C", EIGHTY_FIVE); |
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conses[10] = new Consensus("E", EIGHTY_FIVE); |
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conses[11] = new Consensus("F", EIGHTY_FIVE); |
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conses[12] = new Consensus("G", EIGHTY_FIVE); |
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conses[13] = new Consensus("H", EIGHTY_FIVE); |
152 |
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conses[14] = new Consensus("I", EIGHTY_FIVE); |
153 |
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conses[15] = new Consensus("L", EIGHTY_FIVE); |
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conses[16] = new Consensus("M", EIGHTY_FIVE); |
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conses[17] = new Consensus("N", EIGHTY_FIVE); |
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conses[18] = new Consensus("P", EIGHTY_FIVE); |
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conses[19] = new Consensus("Q", EIGHTY_FIVE); |
158 |
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conses[20] = new Consensus("R", EIGHTY_FIVE); |
159 |
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conses[21] = new Consensus("S", EIGHTY_FIVE); |
160 |
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conses[22] = new Consensus("T", EIGHTY_FIVE); |
161 |
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conses[23] = new Consensus("V", EIGHTY_FIVE); |
162 |
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conses[24] = new Consensus("W", EIGHTY_FIVE); |
163 |
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conses[25] = new Consensus("Y", EIGHTY_FIVE); |
164 |
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conses[28] = new Consensus("K", EIGHTY_FIVE); |
165 |
17 |
conses[29] = new Consensus("D", EIGHTY_FIVE); |
166 |
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|
167 |
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conses[30] = new Consensus("G", 0); |
168 |
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conses[31] = new Consensus("P", 0); |
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170 |
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171 |
17 |
colours = new ConsensusColour[11]; |
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|
173 |
17 |
Consensus[] tmp8 = new Consensus[1]; |
174 |
17 |
tmp8[0] = conses[30]; |
175 |
17 |
colours[7] = new ConsensusColour(ClustalColour.ORANGE, tmp8); |
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|
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17 |
Consensus[] tmp9 = new Consensus[1]; |
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tmp9[0] = conses[31]; |
179 |
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colours[8] = new ConsensusColour(ClustalColour.YELLOW, tmp9); |
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|
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Consensus[] tmp10 = new Consensus[1]; |
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tmp10[0] = conses[27]; |
183 |
17 |
colours[9] = new ConsensusColour(ClustalColour.PINK, tmp8); |
184 |
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185 |
17 |
Consensus[] tmp1 = new Consensus[14]; |
186 |
17 |
tmp1[0] = conses[0]; |
187 |
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tmp1[1] = conses[1]; |
188 |
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tmp1[2] = conses[26]; |
189 |
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tmp1[3] = conses[27]; |
190 |
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tmp1[4] = conses[11]; |
191 |
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tmp1[5] = conses[13]; |
192 |
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tmp1[6] = conses[14]; |
193 |
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tmp1[7] = conses[15]; |
194 |
17 |
tmp1[8] = conses[16]; |
195 |
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tmp1[9] = conses[23]; |
196 |
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tmp1[10] = conses[24]; |
197 |
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tmp1[11] = conses[25]; |
198 |
17 |
tmp1[12] = conses[18]; |
199 |
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tmp1[13] = conses[19]; |
200 |
17 |
colours[0] = new ConsensusColour(ClustalColour.BLUE, tmp1); |
201 |
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202 |
17 |
colours[10] = new ConsensusColour(ClustalColour.CYAN, tmp1); |
203 |
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204 |
17 |
Consensus[] tmp2 = new Consensus[5]; |
205 |
17 |
tmp2[0] = conses[8]; |
206 |
17 |
tmp2[1] = conses[21]; |
207 |
17 |
tmp2[2] = conses[22]; |
208 |
17 |
tmp2[3] = conses[0]; |
209 |
17 |
tmp2[4] = conses[1]; |
210 |
17 |
colours[1] = new ConsensusColour(ClustalColour.GREEN, tmp2); |
211 |
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212 |
17 |
Consensus[] tmp3 = new Consensus[3]; |
213 |
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214 |
17 |
tmp3[0] = conses[17]; |
215 |
17 |
tmp3[1] = conses[29]; |
216 |
17 |
tmp3[2] = conses[5]; |
217 |
17 |
colours[2] = new ConsensusColour(ClustalColour.GREEN, tmp3); |
218 |
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|
219 |
17 |
Consensus[] tmp4 = new Consensus[6]; |
220 |
17 |
tmp4[0] = conses[6]; |
221 |
17 |
tmp4[1] = conses[19]; |
222 |
17 |
tmp4[2] = conses[22]; |
223 |
17 |
tmp4[3] = conses[3]; |
224 |
17 |
tmp4[4] = conses[28]; |
225 |
17 |
tmp4[5] = conses[20]; |
226 |
17 |
colours[3] = new ConsensusColour(ClustalColour.GREEN, tmp4); |
227 |
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|
228 |
17 |
Consensus[] tmp5 = new Consensus[4]; |
229 |
17 |
tmp5[0] = conses[3]; |
230 |
17 |
tmp5[1] = conses[28]; |
231 |
17 |
tmp5[2] = conses[20]; |
232 |
17 |
tmp5[3] = conses[19]; |
233 |
17 |
colours[4] = new ConsensusColour(ClustalColour.RED, tmp5); |
234 |
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|
235 |
17 |
Consensus[] tmp6 = new Consensus[6]; |
236 |
17 |
tmp6[0] = conses[3]; |
237 |
17 |
tmp6[1] = conses[29]; |
238 |
17 |
tmp6[2] = conses[10]; |
239 |
17 |
tmp6[3] = conses[6]; |
240 |
17 |
tmp6[4] = conses[19]; |
241 |
17 |
tmp6[5] = conses[2]; |
242 |
17 |
colours[5] = new ConsensusColour(ClustalColour.MAGENTA, tmp6); |
243 |
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|
244 |
17 |
Consensus[] tmp7 = new Consensus[5]; |
245 |
17 |
tmp7[0] = conses[3]; |
246 |
17 |
tmp7[1] = conses[29]; |
247 |
17 |
tmp7[2] = conses[10]; |
248 |
17 |
tmp7[3] = conses[17]; |
249 |
17 |
tmp7[4] = conses[2]; |
250 |
17 |
colours[6] = new ConsensusColour(ClustalColour.MAGENTA, tmp7); |
251 |
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|
252 |
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|
253 |
17 |
residueColour = new ConsensusColour[20]; |
254 |
17 |
residueColour[0] = colours[0]; |
255 |
17 |
residueColour[1] = colours[4]; |
256 |
17 |
residueColour[2] = colours[2]; |
257 |
17 |
residueColour[3] = colours[6]; |
258 |
17 |
residueColour[4] = colours[0]; |
259 |
17 |
residueColour[5] = colours[3]; |
260 |
17 |
residueColour[6] = colours[5]; |
261 |
17 |
residueColour[7] = colours[7]; |
262 |
17 |
residueColour[8] = colours[10]; |
263 |
17 |
residueColour[9] = colours[0]; |
264 |
17 |
residueColour[10] = colours[0]; |
265 |
17 |
residueColour[11] = colours[4]; |
266 |
17 |
residueColour[12] = colours[0]; |
267 |
17 |
residueColour[13] = colours[0]; |
268 |
17 |
residueColour[14] = colours[8]; |
269 |
17 |
residueColour[15] = colours[1]; |
270 |
17 |
residueColour[16] = colours[1]; |
271 |
17 |
residueColour[17] = colours[0]; |
272 |
17 |
residueColour[18] = colours[10]; |
273 |
17 |
residueColour[19] = colours[0]; |
274 |
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} |
275 |
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|
|
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
276 |
0 |
@Override... |
277 |
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public Color findColour(char c) |
278 |
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{ |
279 |
0 |
return Color.pink; |
280 |
|
} |
281 |
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|
|
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| 84% |
Uncovered Elements: 4 (25) |
Complexity: 8 |
Complexity Density: 0.62 |
|
282 |
19 |
@Override... |
283 |
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protected synchronized Color findColour(char c, int j, SequenceI seq) |
284 |
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{ |
285 |
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|
286 |
19 |
if (cons2.length <= j || Comparison.isGap(c) |
287 |
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) |
288 |
|
{ |
289 |
0 |
return Color.white; |
290 |
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} |
291 |
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|
292 |
19 |
int i = ResidueProperties.aaIndex[c]; |
293 |
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|
294 |
19 |
Color colour = Color.white; |
295 |
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|
296 |
19 |
if (i > 19) |
297 |
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{ |
298 |
0 |
return colour; |
299 |
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} |
300 |
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|
301 |
170 |
for (int k = 0; k < residueColour[i].cons.length; k++) |
302 |
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{ |
303 |
151 |
if (residueColour[i].cons[k].isConserved(cons2, j, size, includeGaps)) |
304 |
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{ |
305 |
22 |
colour = residueColour[i].c; |
306 |
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} |
307 |
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} |
308 |
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|
309 |
19 |
if (i == 4) |
310 |
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{ |
311 |
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|
312 |
|
|
313 |
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|
314 |
3 |
if (conses[27].isConserved(cons2, j, size, includeGaps)) |
315 |
|
{ |
316 |
1 |
colour = ClustalColour.PINK.colour; |
317 |
|
} |
318 |
|
} |
319 |
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|
320 |
19 |
return colour; |
321 |
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} |
322 |
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|
323 |
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|
324 |
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@return |
325 |
|
|
|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
326 |
17 |
protected boolean isIncludeGaps()... |
327 |
|
{ |
328 |
17 |
return includeGaps; |
329 |
|
} |
330 |
|
|
331 |
|
|
332 |
|
@param |
333 |
|
|
334 |
|
|
|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
335 |
2 |
protected void setIncludeGaps(boolean includeGaps)... |
336 |
|
{ |
337 |
2 |
this.includeGaps = includeGaps; |
338 |
|
} |
339 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
340 |
7 |
@Override... |
341 |
|
public ColourSchemeI getInstance(AlignViewportI view, |
342 |
|
AnnotatedCollectionI sg) |
343 |
|
{ |
344 |
7 |
ClustalxColourScheme css = new ClustalxColourScheme(sg, |
345 |
7 |
view == null ? null : view.getHiddenRepSequences()); |
346 |
7 |
css.includeGaps = includeGaps; |
347 |
7 |
return css; |
348 |
|
} |
349 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
350 |
844 |
@Override... |
351 |
|
public boolean isPeptideSpecific() |
352 |
|
{ |
353 |
844 |
return true; |
354 |
|
} |
355 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
356 |
566 |
@Override... |
357 |
|
public String getSchemeName() |
358 |
|
{ |
359 |
566 |
return JalviewColourScheme.Clustal.toString(); |
360 |
|
} |
361 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
362 |
47 |
@Override... |
363 |
|
public boolean isSimple() |
364 |
|
{ |
365 |
47 |
return false; |
366 |
|
} |
367 |
|
|
|
|
| 0% |
Uncovered Elements: 47 (47) |
Complexity: 8 |
Complexity Density: 0.22 |
|
368 |
0 |
public String toRuleRep()... |
369 |
|
{ |
370 |
0 |
makeColours(); |
371 |
0 |
HashMap<String, String> cols = new HashMap(); |
372 |
0 |
for (String res : ResidueProperties.aa) |
373 |
|
{ |
374 |
0 |
StringBuilder sb = new StringBuilder(); |
375 |
|
|
376 |
0 |
int rnum = ResidueProperties.aaIndex[res.charAt(0)]; |
377 |
0 |
if (rnum < 0 || rnum >= residueColour.length) |
378 |
|
{ |
379 |
0 |
continue; |
380 |
|
} |
381 |
|
|
382 |
0 |
ConsensusColour cc = residueColour[rnum]; |
383 |
0 |
if (cc == null) |
384 |
|
{ |
385 |
0 |
continue; |
386 |
|
} |
387 |
|
|
388 |
|
|
389 |
0 |
sb.append(cc.c.toString()); |
390 |
0 |
double f = 0; |
391 |
0 |
sb.append("\t"); |
392 |
0 |
for (Consensus cons : cc.cons) |
393 |
|
{ |
394 |
0 |
if (cons.threshold == 0 || f != cons.threshold) |
395 |
|
{ |
396 |
0 |
if (f != 0) |
397 |
|
{ |
398 |
|
|
399 |
0 |
sb.append("}, {"); |
400 |
|
} |
401 |
|
else |
402 |
|
{ |
403 |
0 |
sb.append("{"); |
404 |
|
} |
405 |
0 |
sb.append(cons.threshold); |
406 |
0 |
sb.append(","); |
407 |
0 |
f = cons.threshold; |
408 |
|
} |
409 |
|
else |
410 |
|
{ |
411 |
0 |
sb.append(","); |
412 |
|
} |
413 |
0 |
sb.append(cons.maskstr); |
414 |
|
} |
415 |
0 |
sb.append("}"); |
416 |
0 |
String clxrep = sb.toString(); |
417 |
0 |
String xres = cols.get(clxrep); |
418 |
0 |
if (xres == null) |
419 |
|
{ |
420 |
0 |
xres = ""; |
421 |
|
} |
422 |
0 |
xres += res; |
423 |
0 |
cols.put(clxrep, xres); |
424 |
|
} |
425 |
0 |
StringBuilder sb = new StringBuilder(); |
426 |
0 |
for (String clxrep : cols.keySet()) |
427 |
|
{ |
428 |
0 |
sb.append(cols.get(clxrep)); |
429 |
0 |
sb.append("\t"); |
430 |
0 |
sb.append(clxrep); |
431 |
0 |
sb.append("\n"); |
432 |
|
|
433 |
|
} |
434 |
0 |
return sb.toString(); |
435 |
|
} |
436 |
|
} |