src/jalview/ext/archaeopteryx/MatrixConverter.java

   1 package jalview.ext.archaeopteryx;
   2
   3 import jalview.datamodel.SequenceI;
   4 import jalview.ext.forester.ForesterMatrix;
   5 import jalview.math.MatrixI;
   6
   7 import org.forester.evoinference.matrix.distance.DistanceMatrix;
   8
   9 public final class MatrixConverter
  10 {
  11   /**
  12    * Shouldn't get instantiated
  13    */
  14   private MatrixConverter()
  15   {
  16
  17   }
  18
  19
  20   public static DistanceMatrix convertJalviewToForester(
  21           final MatrixI jalviewInputMatrix,
  22           final SequenceI[] matrixSequences)
  23   {
  24     if (jalviewInputMatrix.width() != jalviewInputMatrix.height())
  25     {
  26       // some kind of warning?
  27     }
  28        DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
  29             matrixSequences);
  30     return foresterMatrix;
  31
  32
  33   }
  34
  35   public static DistanceMatrix convertJalviewToForester(
  36           final MatrixI jalviewInputMatrix,
  37           final String[] matrixIdentifiers)
  38   {
  39     if (jalviewInputMatrix.width() != jalviewInputMatrix.height())
  40     {
  41       // some kind of warning?
  42     }
  43
  44     DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
  45             matrixIdentifiers);
  46     return foresterMatrix;
  47
  48
  49   }
  50
  51
  52
  53
  54 }