src/jalview/ext/archaeopteryx/LoadedTreeSequenceAssociation.java

   1 package jalview.ext.archaeopteryx;
   2
   3 import jalview.analysis.SequenceIdMatcher;
   4 import jalview.datamodel.SequenceI;
   5 import jalview.ext.treeviewer.ExternalLoadedTreeAssociationI;
   6 import jalview.ext.treeviewer.ExternalTreeI;
   7 import jalview.ext.treeviewer.ExternalTreeNodeI;
   8 import jalview.util.MappingUtils;
   9
  10 import java.util.HashMap;
  11 import java.util.Iterator;
  12 import java.util.Map;
  13
  14
  15 public class LoadedTreeSequenceAssociation
  16         implements ExternalLoadedTreeAssociationI
  17 {
  18   SequenceI[] alignSequences;
  19
  20   ExternalTreeI tree;
  21
  22   Map<SequenceI, ExternalTreeNodeI> alignmentWithNodes;
  23
  24   Map<ExternalTreeNodeI, SequenceI> nodesWithAlignment;
  25
  26   public LoadedTreeSequenceAssociation(SequenceI[] alignmentSequences,
  27           ExternalTreeI aptxTree)
  28   {
  29     alignSequences = alignmentSequences;
  30     tree = aptxTree;
  31     alignmentWithNodes = new HashMap<>(alignSequences.length);
  32     nodesWithAlignment = new HashMap<>(alignSequences.length);
  33
  34   }
  35
  36
  37
  38   /**
  39    * Tries to match sequences from Jalview with tree nodes in Archaeopteryx and
  40    * fills in the tree node with sequence data if a match is found.
  41    *
  42    * Partially refactored from the old Jalview TreeModel
  43    * associateLeavesToSequences method.
  44    *
  45    * @param seqs
  46    * @param aptxTree
  47    */
  48   @Override
  49   public void associateLeavesToSequences()
  50
  51   {
  52     SequenceIdMatcher algnIds = new SequenceIdMatcher(alignSequences);
  53     SequenceI nodeSequence;
  54     String nodeSequenceName;
  55
  56     if (!tree.isEmpty())
  57     {
  58       for (final Iterator<ExternalTreeNodeI> iter = tree
  59               .iterateInPreOrder(); iter
  60               .hasNext();)
  61       {
  62         ExternalTreeNodeI treeNode = iter.next();
  63         nodeSequenceName = treeNode.getNodeName();
  64
  65         nodeSequence = algnIds.findIdMatch(nodeSequenceName);
  66         if (nodeSequence != null)
  67         {
  68
  69           treeNode.setSequence(nodeSequence);
  70
  71           MappingUtils.putWithDuplicationCheck(alignmentWithNodes,
  72                   nodeSequence, treeNode);
  73           MappingUtils.putWithDuplicationCheck(nodesWithAlignment, treeNode,
  74                   nodeSequence);
  75
  76
  77         }
  78
  79     }
  80
  81     }
  82   }
  83
  84
  85
  86   public Map<SequenceI, ExternalTreeNodeI> getAlignmentWithNodes()
  87   {
  88     return alignmentWithNodes;
  89   }
  90
  91   public Map<ExternalTreeNodeI, SequenceI> getNodesWithAlignment()
  92   {
  93     return nodesWithAlignment;
  94   }
  95
  96
  97 }
  98
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