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 LoadedTreeAssociationI
  13 {
  14   SequenceI[] alignSequences;
  15
  16   TreeI tree;
  17
  18   Map<SequenceI, TreeNodeI> alignmentWithNodes;
  19
  20   Map<TreeNodeI, SequenceI> nodesWithAlignment;
  21
  22   public LoadedTreeSequenceAssociation(SequenceI[] alignmentSequences,
  23           TreeI 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<TreeNodeI> iter = tree
  53               .iterateInPreOrder(); iter
  54               .hasNext();)
  55       {
  56         TreeNodeI treeNode = iter.next();
  57         nodeSequenceName = treeNode.getNodeName();
  58
  59         nodeSequence = algnIds.findIdMatch(nodeSequenceName);
  60         if (nodeSequence != null)
  61         {
  62           // is there already a sequence present for the node?
  63           // If so, does it actually match Jalview's sequence?
  64           if (treeNode.getSequence() != null)
  65           {
  66             if (!(treeNode.getSequence().getSequenceAsString()
  67                     .equals(nodeSequence.getSequenceAsString())))
  68             {
  69               System.err.println(
  70                       "Sequence detected in tree node that does not match corresponding Jalview sequence:"
  71                               + nodeSequenceName);
  72               // which sequence gets precedence?
  73
  74             }
  75
  76           }
  77           else
  78           {
  79           treeNode.setSequence(nodeSequence);
  80           }
  81           MappingUtils.putWithDuplicationCheck(alignmentWithNodes,
  82                   nodeSequence, treeNode);
  83           MappingUtils.putWithDuplicationCheck(nodesWithAlignment, treeNode,
  84                   nodeSequence);
  85
  86
  87         }
  88
  89     }
  90
  91     }
  92   }
  93
  94
  95
  96   @Override
  97   public Map<SequenceI, TreeNodeI> getAlignmentWithNodes()
  98   {
  99     return alignmentWithNodes;
 100   }
 101
 102   @Override
 103   public Map<TreeNodeI, SequenceI> getNodesWithAlignment()
 104   {
 105     return nodesWithAlignment;
 106   }
 107
 108
 109 }
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