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package jalview.schemes; |
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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.Comparison; |
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import java.awt.Color; |
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import java.util.List; |
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import java.util.Map; |
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| 95.7% |
Uncovered Elements: 8 (186) |
Complexity: 21 |
Complexity Density: 0.13 |
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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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final Color colour; |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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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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| 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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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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12 |
@Override... |
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public 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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7271 |
for (int i = 0; i <= end_j; i++) |
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{ |
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7204 |
if (length - 1 < i) |
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{ |
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res = 23; |
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} |
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else |
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{ |
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7204 |
res = ResidueProperties.aaIndex[sq.getCharAt(i)]; |
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} |
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cons2[i][res]++; |
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} |
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} |
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this.size = seqs.size(); |
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makeColours(); |
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} |
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| 100% |
Uncovered Elements: 0 (120) |
Complexity: 1 |
Complexity Density: 0.01 |
|
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12 |
void makeColours()... |
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{ |
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conses[0] = new Consensus("WLVIMAFCYHP", SIXTY); |
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conses[1] = new Consensus("WLVIMAFCYHP", EIGHTY); |
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conses[2] = new Consensus("ED", FIFTY); |
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conses[3] = new Consensus("KR", SIXTY); |
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conses[4] = new Consensus("G", FIFTY); |
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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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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); |
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conses[14] = new Consensus("I", EIGHTY_FIVE); |
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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); |
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conses[20] = new Consensus("R", EIGHTY_FIVE); |
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conses[21] = new Consensus("S", EIGHTY_FIVE); |
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conses[22] = new Consensus("T", EIGHTY_FIVE); |
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conses[23] = new Consensus("V", EIGHTY_FIVE); |
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conses[24] = new Consensus("W", EIGHTY_FIVE); |
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conses[25] = new Consensus("Y", EIGHTY_FIVE); |
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conses[28] = new Consensus("K", EIGHTY_FIVE); |
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conses[29] = new Consensus("D", EIGHTY_FIVE); |
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conses[30] = new Consensus("G", 0); |
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conses[31] = new Consensus("P", 0); |
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colours = new ConsensusColour[11]; |
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Consensus[] tmp8 = new Consensus[1]; |
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tmp8[0] = conses[30]; |
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colours[7] = new ConsensusColour(ClustalColour.ORANGE, tmp8); |
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Consensus[] tmp9 = new Consensus[1]; |
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tmp9[0] = conses[31]; |
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colours[8] = new ConsensusColour(ClustalColour.YELLOW, tmp9); |
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Consensus[] tmp10 = new Consensus[1]; |
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tmp10[0] = conses[27]; |
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colours[9] = new ConsensusColour(ClustalColour.PINK, tmp8); |
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Consensus[] tmp1 = new Consensus[14]; |
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tmp1[0] = conses[0]; |
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tmp1[1] = conses[1]; |
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tmp1[2] = conses[26]; |
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tmp1[3] = conses[27]; |
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tmp1[4] = conses[11]; |
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tmp1[5] = conses[13]; |
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tmp1[6] = conses[14]; |
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tmp1[7] = conses[15]; |
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tmp1[8] = conses[16]; |
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tmp1[9] = conses[23]; |
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tmp1[10] = conses[24]; |
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tmp1[11] = conses[25]; |
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tmp1[12] = conses[18]; |
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tmp1[13] = conses[19]; |
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colours[0] = new ConsensusColour(ClustalColour.BLUE, tmp1); |
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colours[10] = new ConsensusColour(ClustalColour.CYAN, tmp1); |
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Consensus[] tmp2 = new Consensus[5]; |
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tmp2[0] = conses[8]; |
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tmp2[1] = conses[21]; |
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tmp2[2] = conses[22]; |
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tmp2[3] = conses[0]; |
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tmp2[4] = conses[1]; |
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colours[1] = new ConsensusColour(ClustalColour.GREEN, tmp2); |
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Consensus[] tmp3 = new Consensus[3]; |
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tmp3[0] = conses[17]; |
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tmp3[1] = conses[29]; |
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tmp3[2] = conses[5]; |
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colours[2] = new ConsensusColour(ClustalColour.GREEN, tmp3); |
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12 |
Consensus[] tmp4 = new Consensus[6]; |
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12 |
tmp4[0] = conses[6]; |
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12 |
tmp4[1] = conses[19]; |
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12 |
tmp4[2] = conses[22]; |
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tmp4[3] = conses[3]; |
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12 |
tmp4[4] = conses[28]; |
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tmp4[5] = conses[20]; |
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12 |
colours[3] = new ConsensusColour(ClustalColour.GREEN, tmp4); |
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12 |
Consensus[] tmp5 = new Consensus[4]; |
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tmp5[0] = conses[3]; |
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tmp5[1] = conses[28]; |
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tmp5[2] = conses[20]; |
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12 |
tmp5[3] = conses[19]; |
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colours[4] = new ConsensusColour(ClustalColour.RED, tmp5); |
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12 |
Consensus[] tmp6 = new Consensus[6]; |
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tmp6[0] = conses[3]; |
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tmp6[1] = conses[29]; |
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tmp6[2] = conses[10]; |
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12 |
tmp6[3] = conses[6]; |
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tmp6[4] = conses[19]; |
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tmp6[5] = conses[2]; |
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12 |
colours[5] = new ConsensusColour(ClustalColour.MAGENTA, tmp6); |
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12 |
Consensus[] tmp7 = new Consensus[5]; |
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12 |
tmp7[0] = conses[3]; |
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12 |
tmp7[1] = conses[29]; |
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12 |
tmp7[2] = conses[10]; |
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12 |
tmp7[3] = conses[17]; |
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tmp7[4] = conses[2]; |
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12 |
colours[6] = new ConsensusColour(ClustalColour.MAGENTA, tmp7); |
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|
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12 |
residueColour = new ConsensusColour[20]; |
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residueColour[0] = colours[0]; |
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residueColour[1] = colours[4]; |
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12 |
residueColour[2] = colours[2]; |
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residueColour[3] = colours[6]; |
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12 |
residueColour[4] = colours[0]; |
256 |
12 |
residueColour[5] = colours[3]; |
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12 |
residueColour[6] = colours[5]; |
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12 |
residueColour[7] = colours[7]; |
259 |
12 |
residueColour[8] = colours[10]; |
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12 |
residueColour[9] = colours[0]; |
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residueColour[10] = colours[0]; |
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residueColour[11] = colours[4]; |
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residueColour[12] = colours[0]; |
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residueColour[13] = colours[0]; |
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12 |
residueColour[14] = colours[8]; |
266 |
12 |
residueColour[15] = colours[1]; |
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residueColour[16] = colours[1]; |
268 |
12 |
residueColour[17] = colours[0]; |
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12 |
residueColour[18] = colours[10]; |
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12 |
residueColour[19] = colours[0]; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
273 |
0 |
@Override... |
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public Color findColour(char c) |
275 |
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{ |
276 |
0 |
return Color.pink; |
277 |
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} |
278 |
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| 84% |
Uncovered Elements: 4 (25) |
Complexity: 8 |
Complexity Density: 0.62 |
|
279 |
19 |
@Override... |
280 |
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protected Color findColour(char c, int j, SequenceI seq) |
281 |
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{ |
282 |
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|
283 |
19 |
if (cons2.length <= j || Comparison.isGap(c) |
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) |
285 |
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{ |
286 |
0 |
return Color.white; |
287 |
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} |
288 |
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19 |
int i = ResidueProperties.aaIndex[c]; |
290 |
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291 |
19 |
Color colour = Color.white; |
292 |
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293 |
19 |
if (i > 19) |
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{ |
295 |
0 |
return colour; |
296 |
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} |
297 |
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|
298 |
170 |
for (int k = 0; k < residueColour[i].cons.length; k++) |
299 |
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{ |
300 |
151 |
if (residueColour[i].cons[k].isConserved(cons2, j, size, includeGaps)) |
301 |
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{ |
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22 |
colour = residueColour[i].c; |
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} |
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} |
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19 |
if (i == 4) |
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{ |
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310 |
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3 |
if (conses[27].isConserved(cons2, j, size, includeGaps)) |
312 |
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{ |
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1 |
colour = ClustalColour.PINK.colour; |
314 |
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} |
315 |
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} |
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19 |
return colour; |
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} |
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320 |
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321 |
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@return |
322 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
323 |
12 |
protected boolean isIncludeGaps()... |
324 |
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{ |
325 |
12 |
return includeGaps; |
326 |
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} |
327 |
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|
328 |
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|
329 |
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@param |
330 |
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|
331 |
|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
332 |
2 |
protected void setIncludeGaps(boolean includeGaps)... |
333 |
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{ |
334 |
2 |
this.includeGaps = includeGaps; |
335 |
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} |
336 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
337 |
5 |
@Override... |
338 |
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public ColourSchemeI getInstance(AnnotatedCollectionI sg, |
339 |
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Map<SequenceI, SequenceCollectionI> hiddenRepSequences) |
340 |
|
{ |
341 |
5 |
ClustalxColourScheme css = new ClustalxColourScheme(sg, |
342 |
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hiddenRepSequences); |
343 |
5 |
css.includeGaps = includeGaps; |
344 |
5 |
return css; |
345 |
|
} |
346 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
347 |
390 |
@Override... |
348 |
|
public boolean isPeptideSpecific() |
349 |
|
{ |
350 |
390 |
return true; |
351 |
|
} |
352 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
353 |
202 |
@Override... |
354 |
|
public String getSchemeName() |
355 |
|
{ |
356 |
202 |
return JalviewColourScheme.Clustal.toString(); |
357 |
|
} |
358 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
359 |
10 |
@Override... |
360 |
|
public boolean isSimple() |
361 |
|
{ |
362 |
10 |
return false; |
363 |
|
} |
364 |
|
} |