1 package jalview.schemes;
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3 import jalview.datamodel.*;
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7 public class PIDColourScheme extends ResidueColourScheme {
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8 public Color[] pidColours;
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9 public float[] thresholds;
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11 SequenceGroup group;
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13 public PIDColourScheme() {
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14 this.pidColours = ResidueProperties.pidColours;
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15 this.thresholds = ResidueProperties.pidThresholds;
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17 public Color getColour(SequenceI seq, int j,Vector aa) {
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18 Color c = Color.white;
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20 String s = seq.getSequence(j,j+1);
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22 if (aa != null && j < aa.size()) {
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23 c = findColour(seq,s,j,aa);
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29 public Color findColour(SequenceI seq,String s, int j,Vector aa) {
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30 Color c = Color.white;
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31 Hashtable hash = null;
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34 hash = (Hashtable)aa.elementAt(j);
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39 String max = (String)hash.get("maxResidue");
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42 if (((Integer)hash.get("maxCount")).intValue() != -1 && hash.contains(s)) {
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43 sc = ((Integer)hash.get(s)).intValue()*100.0/Integer.parseInt((String)hash.get("maxResidue"));
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45 // MC Should be isGap
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46 if ( !s.equals("-") && !s.equals(".") && !s.equals(" ")) {
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47 for (int i=0; i < thresholds.length; i++) {
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48 if (sc > thresholds[i]) {
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