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 /**
  12  * Generic implementation of {@link LoadedTreeAssociationI } that tries to
  13  * associate tree nodes based on comparing Jalview's sequence IDs to tree node
  14  * names.
  15  *
  16  * @author kjvanderheide
  17  *
  18  */
  19 public class LoadedTreeSequenceAssociation
  20         implements LoadedTreeAssociationI
  21 {
  22   SequenceI[] alignSequences;
  23
  24   TreeI tree;
  25
  26   Map<SequenceI, TreeNodeI> alignmentWithNodes;
  27
  28   Map<TreeNodeI, SequenceI> nodesWithAlignment;
  29
  30   public LoadedTreeSequenceAssociation(SequenceI[] alignmentSequences,
  31           TreeI extTree)
  32   {
  33     alignSequences = alignmentSequences;
  34     tree = extTree;
  35     alignmentWithNodes = new HashMap<>(alignSequences.length);
  36     nodesWithAlignment = new HashMap<>(alignSequences.length);
  37
  38   }
  39
  40   @Override
  41   public void associateNodesToSequences()
  42
  43   {
  44     SequenceIdMatcher algnIds = new SequenceIdMatcher(alignSequences);
  45     SequenceI nodeSequence;
  46     String nodeSequenceName;
  47
  48     if (!tree.isEmpty())
  49     {
  50       for (final Iterator<TreeNodeI> iter = tree
  51               .iterateInPreOrder(); iter
  52               .hasNext();)
  53       {
  54         TreeNodeI treeNode = iter.next();
  55         nodeSequenceName = treeNode.getNodeName();
  56
  57         nodeSequence = algnIds.findIdMatch(nodeSequenceName);
  58         if (nodeSequence != null)
  59         {
  60           // is there already a sequence present for the node?
  61           // If so, does it actually match Jalview's sequence?
  62           if (treeNode.getSequence() != null)
  63           {
  64             if (!(treeNode.getSequence().getSequenceAsString()
  65                     .equals(nodeSequence.getSequenceAsString())))
  66             {
  67               System.err.println(
  68                       "Sequence detected in tree node that does not match corresponding Jalview sequence:"
  69                               + nodeSequenceName);
  70               // which sequence gets precedence?
  71
  72             }
  73
  74           }
  75           else
  76           {
  77           treeNode.setSequence(nodeSequence);
  78           }
  79           MappingUtils.putWithDuplicationCheck(alignmentWithNodes,
  80                   nodeSequence, treeNode);
  81           MappingUtils.putWithDuplicationCheck(nodesWithAlignment, treeNode,
  82                   nodeSequence);
  83
  84
  85         }
  86
  87     }
  88
  89     }
  90   }
  91
  92
  93
  94   @Override
  95   public Map<SequenceI, TreeNodeI> getAlignmentWithNodes()
  96   {
  97     return alignmentWithNodes;
  98   }
  99
 100   @Override
 101   public Map<TreeNodeI, SequenceI> getNodesWithAlignment()
 102   {
 103     return nodesWithAlignment;
 104   }
 105
 106
 107 }
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