src/jalview/ext/archaeopteryx/JalviewToAptxAssociation.java

   1 package jalview.ext.archaeopteryx;
   2
   3 import jalview.analysis.SequenceIdMatcher;
   4 import jalview.datamodel.SequenceI;
   5
   6 import java.util.ArrayList;
   7 import java.util.List;
   8
   9 import org.forester.phylogeny.Phylogeny;
  10 import org.forester.phylogeny.PhylogenyNode;
  11
  12 public class JalviewToAptxAssociation
  13         implements ExternalLoadedTreeAssociationI<Phylogeny>
  14 {
  15   SequenceI[] alignSequences;
  16
  17   Phylogeny tree;
  18
  19   public JalviewToAptxAssociation(SequenceI[] alignmentSequences,
  20           Phylogeny aptxTree)
  21   {
  22     alignSequences = alignmentSequences;
  23     tree = aptxTree;
  24
  25   }
  26
  27
  28
  29   /**
  30    * Tries to match sequences from Jalview with tree nodes in Archaeopteryx and
  31    * fills in the tree node with sequence data if a match is found.
  32    *
  33    * Partially refactored from the old Jalview TreeModel
  34    * associateLeavesToSequences method.
  35    *
  36    * @param seqs
  37    * @param aptxTree
  38    */
  39   @Override
  40   public void associateLeavesToSequences(SequenceI[] seqs,
  41           Phylogeny aptxTree)
  42   {
  43     SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
  44
  45     List<PhylogenyNode> leaves = aptxTree.getExternalNodes();
  46
  47     int namesleft = seqs.length;
  48     SequenceI nodeSequence;
  49     String nodeSequenceName;
  50     List<SequenceI> one2many = new ArrayList<>();
  51     // int countOne2Many = 0;
  52
  53     for (PhylogenyNode treeNode : leaves)
  54     {
  55       nodeSequenceName = treeNode.getName();
  56       nodeSequence = null;
  57
  58       if (namesleft > -1)
  59       {
  60         nodeSequence = algnIds.findIdMatch(nodeSequenceName);
  61       }
  62
  63       if (nodeSequence != null)
  64       {
  65
  66         //treeNode.setElement(nodeSequence);
  67         if (one2many.contains(nodeSequence))
  68         {
  69           // countOne2Many++;
  70           if (jalview.bin.Cache.log.isDebugEnabled())
  71           {
  72             jalview.bin.Cache.log.debug("One 2 many relationship for"
  73              +nodeSequence.getName());
  74           }
  75         }
  76         else
  77         {
  78           one2many.add(nodeSequence);
  79           namesleft--;
  80         }
  81       }
  82       else
  83       {
  84        // treeNode.setElement( new Sequence(nodeSequenceName, "THISISAPLACEHOLDER"));
  85         // treeNode.setPlaceholder(true);
  86       }
  87     }
  88     // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
  89     // jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment
  90     // sequence ids (out of "+one2many.size()+" unique ids) linked to two or
  91     // more leaves.");
  92     // }
  93     // one2many.clear();
  94
  95   }
  96 }
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