src/jalview/schemes/HMMERColourScheme.java

   1 package jalview.schemes;
   2
   3 import jalview.datamodel.AnnotatedCollectionI;
   4 import jalview.datamodel.HiddenMarkovModel;
   5 import jalview.datamodel.SequenceCollectionI;
   6 import jalview.datamodel.SequenceI;
   7 import jalview.util.ColorUtils;
   8 import jalview.util.Comparison;
   9
  10 import java.awt.Color;
  11 import java.util.Map;
  12
  13 public class HMMERColourScheme extends ResidueColourScheme
  14 {
  15
  16   AnnotatedCollectionI alignment;
  17
  18   HiddenMarkovModel hmm;
  19
  20   boolean peptideSpecific;
  21
  22   boolean nucleotideSpecific;
  23
  24   public HMMERColourScheme(HiddenMarkovModel markov)
  25   {
  26     hmm = markov;
  27   }
  28   public HMMERColourScheme()
  29   {
  30
  31   }
  32
  33   @Override
  34   public Color findColour(char symbol, int position, SequenceI seq,
  35           String consensusResidue, float pid)
  36   {
  37     if (hmm ==null)
  38     {
  39       return Color.white;
  40     }
  41     return findColour(symbol, position);
  42   }
  43
  44   public Color findColour(char symbol, int position)
  45   {
  46
  47     if (Comparison.isGap(symbol))
  48     {
  49       return Color.white;
  50     }
  51     Double prob;
  52     prob = hmm.getMatchEmissionProbability(position, symbol);
  53     double freq = 0;
  54     if ("amino".equals(hmm.getAlphabetType()))
  55     {
  56       if (!ResidueProperties.aminoBackgroundFrequencies.containsKey(symbol))
  57       {
  58         return Color.white;
  59       }
  60       freq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
  61     }
  62     else if ("DNA".equals(hmm.getAlphabetType()))
  63     {
  64       if (!ResidueProperties.dnaBackgroundFrequencies.containsKey(symbol))
  65       {
  66         return Color.white;
  67       }
  68       freq = ResidueProperties.dnaBackgroundFrequencies.get(symbol);
  69     }
  70     else if ("RNA".equals(hmm.getAlphabetType()))
  71     {
  72       if (!ResidueProperties.rnaBackgroundFrequencies.containsKey(symbol))
  73       {
  74         return Color.white;
  75       }
  76       freq = ResidueProperties.rnaBackgroundFrequencies.get(symbol);
  77     }
  78     if (prob == 0)
  79     {
  80       return Color.red;
  81     }
  82     Double value = Math.log(prob / freq);
  83     Color colour = null;
  84     if (value > 0)
  85     {
  86
  87       colour = ColorUtils.getGraduatedColour(value.floatValue(), 0,
  88               Color.WHITE, 3f, Color.blue);
  89     }
  90     else if (value < 0)
  91     {
  92       return Color.ORANGE;
  93
  94     }
  95     return colour;
  96
  97   }
  98
  99
 100
 101
 102
 103
 104   @Override
 105   public void alignmentChanged(AnnotatedCollectionI collection,
 106           Map<SequenceI, SequenceCollectionI> hiddenReps)
 107   {
 108     SequenceI seq = collection.getSequences().get(0);
 109     hmm = seq.getHMM();
 110   }
 111
 112
 113
 114   @Override
 115   public ColourSchemeI getInstance(AnnotatedCollectionI sg,
 116           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
 117   {
 118     HiddenMarkovModel markov = null;
 119     SequenceI seq = sg.getSequences().get(0);
 120     markov = seq.getHMM();
 121     HMMERColourScheme colour = new HMMERColourScheme(markov);
 122     return colour;
 123
 124   }
 125
 126   @Override
 127   public boolean isApplicableTo(AnnotatedCollectionI ac)
 128   {
 129       return true;
 130
 131   }
 132
 133   @Override
 134   public String getSchemeName()
 135   {
 136
 137     return JalviewColourScheme.HMMER.name();
 138   }
 139
 140   @Override
 141   public boolean isSimple()
 142   {
 143     // TODO Auto-generated method stub
 144     return false;
 145   }
 146
 147 }