src/jalview/schemes/TCoffeeColourScheme.java

   1 package jalview.schemes;
   2
   3 import jalview.analysis.SequenceIdMatcher;
   4 import jalview.datamodel.AlignmentAnnotation;
   5 import jalview.datamodel.AlignmentI;
   6 import jalview.datamodel.AnnotatedCollectionI;
   7 import jalview.datamodel.Annotation;
   8 import jalview.datamodel.SequenceI;
   9 import jalview.io.TCoffeeScoreFile;
  10
  11 import java.awt.Color;
  12 import java.util.ArrayList;
  13 import java.util.IdentityHashMap;
  14 import java.util.TreeMap;
  15
  16 /**
  17  * Defines the color score for T-Coffee MSA
  18  * <p>
  19  * See http://tcoffee.org
  20  *
  21  *
  22  * @author Paolo Di Tommaso
  23  *
  24  */
  25 public class TCoffeeColourScheme extends ResidueColourScheme {
  26
  27         static final Color[] colors = {
  28                 new Color( 102, 102, 255 ),     // #6666FF
  29                 new Color( 0, 255, 0),          // #00FF00
  30                 new Color( 102, 255, 0),        // #66FF00
  31                 new Color( 204, 255, 0),        // #CCFF00
  32                 new Color( 255, 255, 0),        // #FFFF00
  33                 new Color( 255, 204, 0),        // #FFCC00
  34                 new Color( 255, 153, 0),        // #FF9900
  35                 new Color( 255, 102, 0),        // #FF6600
  36                 new Color( 255, 51, 0),         // #FF3300
  37                 new Color( 255, 34, 0)          // #FF2000
  38         };
  39
  40
  41         IdentityHashMap<SequenceI, Color[]> seqMap;
  42         /**
  43          * the color scheme needs to look at the alignment to get and cache T-COFFEE scores
  44          *
  45          * @param alignment - annotated sequences to be searched
  46          */
  47         public TCoffeeColourScheme(AnnotatedCollectionI alignment) {
  48           alignmentChanged(alignment);
  49         }
  50         @Override public void alignmentChanged(AnnotatedCollectionI alignment)
  51         {
  52           // assume only one set of TCOFFEE scores - but could have more than one potentially.
  53           ArrayList<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
  54           // Search alignment to get all tcoffee annotation and pick one set of annotation to use to colour seqs.
  55           seqMap = new IdentityHashMap<SequenceI, Color[]>();
  56           int w=0;
  57           for (AlignmentAnnotation al:alignment.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
  58           {
  59             if (al.sequenceRef!=null && !al.belowAlignment)
  60             {
  61               annots.add(al);
  62               if (w<al.annotations.length)
  63               {
  64                 w=al.annotations.length;
  65               }
  66               Color[] scores=new Color[al.annotations.length];
  67               int i=0;
  68               for (Annotation an:al.annotations)
  69               {
  70                 scores[i++]=(an!=null) ? an.colour : Color.white;
  71               }
  72               seqMap.put(al.sequenceRef, scores);
  73             }
  74           }
  75     // TODO: compute average colour for each symbol type in each column - gives
  76     // a second order colourscheme for colouring a sequence logo derived from
  77     // the alignment (colour reflects quality of alignment for each residue
  78     // class)
  79         }
  80         @Override
  81         public Color findColour(char c, int j, SequenceI seq) {
  82           Color[] cols;
  83
  84           if( seqMap==null || (cols=seqMap.get(seq))==null) {
  85 //      see above TODO about computing a colour for each residue in each column:            cc = _rcols[i][indexFor[c]];
  86             return Color.white;
  87           }
  88
  89           if( j < 0 || j>= cols.length ) {
  90             return Color.white;
  91           }
  92           return cols[j];
  93         }
  94 }