src/jalview/ext/archaeopteryx/AptxNodeAssociation.java

   1 package jalview.ext.archaeopteryx;
   2
   3 import jalview.analysis.SequenceIdMatcher;
   4 import jalview.datamodel.SequenceI;
   5 import jalview.ext.forester.ForesterDataConversions;
   6
   7 import java.util.ArrayList;
   8 import java.util.List;
   9
  10 import org.forester.phylogeny.Phylogeny;
  11 import org.forester.phylogeny.PhylogenyNode;
  12
  13 public class AptxNodeAssociation
  14         implements ExternalLoadedTreeAssociationI<Phylogeny>
  15 {
  16   SequenceI[] alignSequences;
  17
  18   Phylogeny tree;
  19
  20   public AptxNodeAssociation(SequenceI[] alignmentSequences,
  21           Phylogeny aptxTree)
  22   {
  23     alignSequences = alignmentSequences;
  24     tree = aptxTree;
  25
  26   }
  27
  28
  29
  30   /**
  31    * Tries to match sequences from Jalview with tree nodes in Archaeopteryx and
  32    * fills in the tree node with sequence data if a match is found.
  33    *
  34    * Partially refactored from the old Jalview TreeModel
  35    * associateLeavesToSequences method.
  36    *
  37    * @param seqs
  38    * @param aptxTree
  39    */
  40   @Override
  41   public void associateLeavesToSequences(SequenceI[] seqs,
  42           Phylogeny aptxTree)
  43   {
  44     SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
  45
  46     List<PhylogenyNode> leaves = aptxTree.getExternalNodes();
  47
  48     int namesleft = seqs.length;
  49     SequenceI nodeSequence;
  50     String nodeSequenceName;
  51     List<SequenceI> one2many = new ArrayList<>();
  52     int countOne2Many = 0;
  53
  54     for (PhylogenyNode treeNode : leaves)
  55     {
  56       nodeSequenceName = treeNode.getName();
  57       nodeSequence = null;
  58
  59       if (namesleft > -1)
  60       {
  61         nodeSequence = algnIds.findIdMatch(nodeSequenceName);
  62       }
  63
  64       if (nodeSequence != null)
  65       {
  66         org.forester.phylogeny.data.Sequence foresterNodeSeq = ForesterDataConversions.createForesterSequence(nodeSequence, true);
  67
  68         treeNode.getNodeData().setSequence(foresterNodeSeq);
  69         if (one2many.contains(nodeSequence))
  70         {
  71           countOne2Many++;
  72           if (jalview.bin.Cache.log.isDebugEnabled())
  73           {
  74             jalview.bin.Cache.log.debug("One 2 many relationship for"
  75              +nodeSequence.getName());
  76           }
  77         }
  78         else
  79         {
  80           one2many.add(nodeSequence);
  81           namesleft--;
  82         }
  83       }
  84       else
  85       {
  86        // treeNode.setElement( new Sequence(nodeSequenceName, "THISISAPLACEHOLDER"));
  87         // treeNode.setPlaceholder(true);
  88       }
  89     }
  90     if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many > 0)
  91     {
  92       jalview.bin.Cache.log.debug("There were " + countOne2Many
  93               + "alignment sequence ids (out of" + one2many.size()
  94               + " unique ids) linked to two or more leaves.");
  95     }
  96     one2many.clear();
  97
  98   }
  99 }
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