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.SequenceCollectionI;
   9 import jalview.datamodel.SequenceI;
  10 import jalview.io.TCoffeeScoreFile;
  11
  12 import java.awt.Color;
  13 import java.util.ArrayList;
  14 import java.util.IdentityHashMap;
  15 import java.util.Map;
  16 import java.util.TreeMap;
  17
  18 /**
  19  * Defines the color score for T-Coffee MSA
  20  * <p>
  21  * See http://tcoffee.org
  22  *
  23  *
  24  * @author Paolo Di Tommaso
  25  *
  26  */
  27 public class TCoffeeColourScheme extends ResidueColourScheme {
  28
  29         static final Color[] colors = {
  30                 new Color( 102, 102, 255 ),     // #6666FF
  31                 new Color( 0, 255, 0),          // #00FF00
  32                 new Color( 102, 255, 0),        // #66FF00
  33                 new Color( 204, 255, 0),        // #CCFF00
  34                 new Color( 255, 255, 0),        // #FFFF00
  35                 new Color( 255, 204, 0),        // #FFCC00
  36                 new Color( 255, 153, 0),        // #FF9900
  37                 new Color( 255, 102, 0),        // #FF6600
  38                 new Color( 255, 51, 0),         // #FF3300
  39                 new Color( 255, 34, 0)          // #FF2000
  40         };
  41
  42
  43         IdentityHashMap<SequenceI, Color[]> seqMap;
  44         /**
  45          * the color scheme needs to look at the alignment to get and cache T-COFFEE scores
  46          *
  47          * @param alignment - annotated sequences to be searched
  48          */
  49         public TCoffeeColourScheme(AnnotatedCollectionI alignment) {
  50           alignmentChanged(alignment, null);
  51         }
  52         @Override
  53         public void alignmentChanged(AnnotatedCollectionI alignment, Map<SequenceI, SequenceCollectionI> hiddenReps)
  54         {
  55           // TODO: if sequences have been represented and they have scores, could compute an average sequence score for the representative
  56
  57           // assume only one set of TCOFFEE scores - but could have more than one potentially.
  58           ArrayList<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
  59           // Search alignment to get all tcoffee annotation and pick one set of annotation to use to colour seqs.
  60           seqMap = new IdentityHashMap<SequenceI, Color[]>();
  61           int w=0;
  62           for (AlignmentAnnotation al:alignment.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
  63           {
  64             if (al.sequenceRef!=null && !al.belowAlignment)
  65             {
  66               annots.add(al);
  67               if (w<al.annotations.length)
  68               {
  69                 w=al.annotations.length;
  70               }
  71               Color[] scores=new Color[al.annotations.length];
  72               int i=0;
  73               for (Annotation an:al.annotations)
  74               {
  75                 scores[i++]=(an!=null) ? an.colour : Color.white;
  76               }
  77               seqMap.put(al.sequenceRef, scores);
  78             }
  79           }
  80     // TODO: compute average colour for each symbol type in each column - gives
  81     // a second order colourscheme for colouring a sequence logo derived from
  82     // the alignment (colour reflects quality of alignment for each residue
  83     // class)
  84         }
  85         @Override
  86         public Color findColour(char c, int j, SequenceI seq) {
  87           Color[] cols;
  88
  89           if( seqMap==null || (cols=seqMap.get(seq))==null) {
  90 //      see above TODO about computing a colour for each residue in each column:            cc = _rcols[i][indexFor[c]];
  91             return Color.white;
  92           }
  93
  94           if( j < 0 || j>= cols.length ) {
  95             return Color.white;
  96           }
  97           return cols[j];
  98         }
  99 }