1 package jalview.schemes;
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3 import jalview.datamodel.*;
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4 import jalview.jbgui.*;
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9 public class ScoreColourScheme extends ResidueColourScheme {
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12 public double[] scores;
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14 public ScoreColourScheme( double[] scores,
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20 this.scores = scores;
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25 public Color getColour(SequenceI seq, int j, Vector aa) {
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26 Color c = Color.white;
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27 String s = seq.getSequence(j,j+1);
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31 if (aboveThreshold(aa,seq,j,threshold))
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32 c = findColour(seq,s,j,aa);
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34 else if ( !s.equals("-") && !s.equals(".") && !s.equals(" ") )
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35 c = findColour(seq,s,j,aa);
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42 public Color findColour(SequenceI seq,String s,int j,Vector aa)
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45 float red = (float)(scores[((Integer)ResidueProperties.aaHash.get(s)).intValue()]
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46 - (float)min)/(float)(max - min);
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47 if (red > (float)1.0)
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50 if (red < (float)0.0)
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53 if(s.equals(" ")|| s.equals(".") || s.equals("-"))
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56 // This isn';t great - pool of colours in here?
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57 return makeColour(red);
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59 public Color makeColour(float c) {
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60 return new Color(c,(float)0.0,(float)1.0-c);
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