src/jalview/schemes/TCoffeeColourScheme.java

   1 package jalview.schemes;
   2
   3 import jalview.io.TCoffeeScoreFile;
   4
   5 import java.awt.Color;
   6
   7 /**
   8  * Defines the color score for T-Coffee MSA
   9  * <p>
  10  * See http://tcoffee.org
  11  *
  12  *
  13  * @author Paolo Di Tommaso
  14  *
  15  */
  16 public class TCoffeeColourScheme extends ResidueColourScheme {
  17
  18         static final Color[] colors = {
  19                 new Color( 102, 102, 255 ),     // #6666FF
  20                 new Color( 0, 255, 0),          // #00FF00
  21                 new Color( 102, 255, 0),        // #66FF00
  22                 new Color( 204, 255, 0),        // #CCFF00
  23                 new Color( 255, 255, 0),        // #FFFF00
  24                 new Color( 255, 204, 0),        // #FFCC00
  25                 new Color( 255, 153, 0),        // #FF9900
  26                 new Color( 255, 102, 0),        // #FF6600
  27                 new Color( 255, 51, 0),         // #FF3300
  28                 new Color( 255, 34, 0)          // #FF2000
  29         };
  30
  31
  32         byte[][] scoreMatrix = null;
  33
  34         /**
  35          * Initialize the color sheme based on the content of the T-Coffee score file
  36          *
  37          * @param scoreFile
  38          */
  39         public TCoffeeColourScheme(TCoffeeScoreFile scoreFile) {
  40
  41                 scoreMatrix = scoreFile != null ? scoreFile.getScoresArray() : null;
  42
  43         }
  44
  45         @Override
  46         public Color findColour(char c, int j, int sequenceIndex) {
  47
  48                 if( scoreMatrix == null ) {
  49                         return Color.white;
  50                 }
  51
  52                 if( sequenceIndex<0  || sequenceIndex >= scoreMatrix.length ) {
  53                         System.out.printf("Sequence index out of range for the T-Coffee color scheme. Index:  %s\n", sequenceIndex);
  54                         return Color.white;
  55                 }
  56
  57                 byte[] seqScores = scoreMatrix[sequenceIndex];
  58                 if( j < 0 || j>= seqScores.length ) {
  59                         System.out.printf("Residue index out of range for the T-Coffee color scheme. Sequence %s - residue: %s\n", sequenceIndex, j);
  60                         return Color.white;
  61                 }
  62
  63                 byte val = seqScores[j];
  64                 return val >= 0 && val < colors.length ? colors[val] : Color.white;
  65         }
  66 }