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.List;
  12 import java.util.Map;
  13
  14 public class HMMERColourScheme extends ResidueColourScheme
  15 {
  16
  17   AnnotatedCollectionI alignment;
  18
  19   HiddenMarkovModel hmm;
  20
  21   boolean peptideSpecific;
  22
  23   boolean nucleotideSpecific;
  24
  25   public HMMERColourScheme(HiddenMarkovModel markov)
  26   {
  27     hmm = markov;
  28   }
  29   public HMMERColourScheme()
  30   {
  31
  32   }
  33
  34   @Override
  35   public Color findColour(char symbol, int position, SequenceI seq,
  36           String consensusResidue, float pid)
  37   {
  38     if (hmm ==null)
  39     {
  40       return Color.white;
  41     }
  42     return findColour(symbol, position);
  43   }
  44
  45   public Color findColour(char symbol, int position)
  46   {
  47
  48     if (Comparison.isGap(symbol))
  49     {
  50       return Color.white;
  51     }
  52     if (Character.isLowerCase(symbol))
  53     {
  54       return new Color(230, 0, 0);
  55     }
  56     Double prob;
  57     prob = hmm.getMatchEmissionProbability(position, symbol);
  58     double freq = 0;
  59     if ("amino".equals(hmm.getAlphabetType()))
  60     {
  61       if (!ResidueProperties.aminoBackgroundFrequencies.containsKey(symbol))
  62       {
  63         return Color.white;
  64       }
  65       freq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
  66     }
  67     else if ("DNA".equals(hmm.getAlphabetType()))
  68     {
  69       if (!ResidueProperties.dnaBackgroundFrequencies.containsKey(symbol))
  70       {
  71         return Color.white;
  72       }
  73       freq = ResidueProperties.dnaBackgroundFrequencies.get(symbol);
  74     }
  75     else if ("RNA".equals(hmm.getAlphabetType()))
  76     {
  77       if (!ResidueProperties.rnaBackgroundFrequencies.containsKey(symbol))
  78       {
  79         return Color.white;
  80       }
  81       freq = ResidueProperties.rnaBackgroundFrequencies.get(symbol);
  82     }
  83     if (prob == 0)
  84     {
  85       return new Color(230, 0, 0);
  86     }
  87     Double value = Math.log(prob / freq);
  88     Color colour = null;
  89     if (value > 0)
  90     {
  91
  92       colour = ColorUtils.getGraduatedColour(value.floatValue(), 0,
  93               Color.WHITE, 4.52f, Color.blue);
  94     }
  95     else if (value < 0)
  96     {
  97       return Color.ORANGE;
  98
  99     }
 100     return colour;
 101
 102   }
 103
 104
 105
 106
 107
 108
 109   @Override
 110   public void alignmentChanged(AnnotatedCollectionI collection,
 111           Map<SequenceI, SequenceCollectionI> hiddenReps)
 112   {
 113           List<SequenceI> seqs = collection.getSequences();
 114             for (SequenceI seq : seqs)
 115             {
 116               if (seq.getHMM() != null)
 117               {
 118                 hmm = seq.getHMM();
 119                 break;
 120               }
 121             }
 122
 123   }
 124
 125
 126
 127   @Override
 128   public ColourSchemeI getInstance(AnnotatedCollectionI sg,
 129           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
 130   {
 131           HiddenMarkovModel markov = null;
 132             List<SequenceI> seqs = sg.getSequences();
 133             for (SequenceI seq : seqs)
 134             {
 135               if (seq.getHMM() != null)
 136               {
 137                 markov = seq.getHMM();
 138                 break;
 139               }
 140             }
 141             HMMERColourScheme colour = new HMMERColourScheme(markov);
 142             return colour;
 143
 144   }
 145
 146   @Override
 147   public boolean isApplicableTo(AnnotatedCollectionI ac)
 148   {
 149       return true;
 150
 151   }
 152
 153   @Override
 154   public String getSchemeName()
 155   {
 156
 157     return JalviewColourScheme.HMMER.name();
 158   }
 159
 160   @Override
 161   public boolean isSimple()
 162   {
 163     // TODO Auto-generated method stub
 164     return false;
 165   }
 166
 167 }