src/jalview/ext/treeviewer/LoadedTreeSequenceAssociation.java

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