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.forester.DataConversions;
   6 import jalview.ext.treeviewer.ExternalLoadedTreeAssociationI;
   7 import jalview.util.MappingUtils;
   8
   9 import java.util.HashMap;
  10 import java.util.Map;
  11
  12 import org.forester.phylogeny.Phylogeny;
  13 import org.forester.phylogeny.PhylogenyNode;
  14 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  15
  16 public class LoadedTreeSequenceAssociation
  17         implements ExternalLoadedTreeAssociationI
  18 {
  19   SequenceI[] alignSequences;
  20
  21   Phylogeny tree;
  22
  23   Map<SequenceI, PhylogenyNode> alignmentWithNodes;
  24
  25   Map<PhylogenyNode, SequenceI> nodesWithAlignment;
  26
  27   public LoadedTreeSequenceAssociation(SequenceI[] alignmentSequences,
  28           Phylogeny aptxTree)
  29   {
  30     alignSequences = alignmentSequences;
  31     tree = aptxTree;
  32     alignmentWithNodes = new HashMap<>(alignSequences.length);
  33     nodesWithAlignment = new HashMap<>(alignSequences.length);
  34
  35   }
  36
  37
  38
  39   /**
  40    * Tries to match sequences from Jalview with tree nodes in Archaeopteryx and
  41    * fills in the tree node with sequence data if a match is found.
  42    *
  43    * Partially refactored from the old Jalview TreeModel
  44    * associateLeavesToSequences method.
  45    *
  46    * @param seqs
  47    * @param aptxTree
  48    */
  49   @Override
  50   public void associateLeavesToSequences()
  51
  52   {
  53     SequenceIdMatcher algnIds = new SequenceIdMatcher(alignSequences);
  54     SequenceI nodeSequence;
  55     String nodeSequenceName;
  56
  57     if (!tree.isEmpty())
  58     {
  59       for (final PhylogenyNodeIterator iter = tree.iteratorPreorder(); iter
  60               .hasNext();)
  61       {
  62         PhylogenyNode treeNode = iter.next();
  63         nodeSequenceName = treeNode.getName();
  64
  65         nodeSequence = algnIds.findIdMatch(nodeSequenceName);
  66         if (nodeSequence != null)
  67         {
  68           org.forester.phylogeny.data.Sequence foresterNodeSeq = DataConversions
  69                   .createForesterSequence(nodeSequence, true);
  70           treeNode.getNodeData().setSequence(foresterNodeSeq);
  71
  72           MappingUtils.putWithDuplicationCheck(alignmentWithNodes,
  73                   nodeSequence, treeNode);
  74           MappingUtils.putWithDuplicationCheck(nodesWithAlignment, treeNode,
  75                   nodeSequence);
  76
  77
  78         }
  79
  80     }
  81
  82     }
  83   }
  84
  85
  86
  87   public Map<SequenceI, PhylogenyNode> getAlignmentWithNodes()
  88   {
  89     return alignmentWithNodes;
  90   }
  91
  92   public Map<PhylogenyNode, SequenceI> getNodesWithAlignment()
  93   {
  94     return nodesWithAlignment;
  95   }
  96
  97   // {
  98   // SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
  99   //
 100   // List<PhylogenyNode> leaves = aptxTree.getExternalNodes();
 101   //
 102   // int namesleft = seqs.length;
 103   // SequenceI nodeSequence;
 104   // String nodeSequenceName;
 105   // List<SequenceI> one2many = new ArrayList<>();
 106   // int countOne2Many = 0;
 107   //
 108   // for (PhylogenyNode treeNode : leaves)
 109   // {
 110   // nodeSequenceName = treeNode.getName();
 111   // nodeSequence = null;
 112   //
 113   // if (namesleft > -1)
 114   // {
 115   // nodeSequence = algnIds.findIdMatch(nodeSequenceName);
 116   // }
 117   //
 118   // if (nodeSequence != null)
 119   // {
 120   // org.forester.phylogeny.data.Sequence foresterNodeSeq =
 121   // ForesterDataConversions.createForesterSequence(nodeSequence, true);
 122   //
 123   // treeNode.getNodeData().setSequence(foresterNodeSeq);
 124   // if (one2many.contains(nodeSequence))
 125   // {
 126   // countOne2Many++;
 127   // if (jalview.bin.Cache.log.isDebugEnabled())
 128   // {
 129   // jalview.bin.Cache.log.debug("One 2 many relationship for"
 130   // +nodeSequence.getName());
 131   // }
 132   // }
 133   // else
 134   // {
 135   // one2many.add(nodeSequence);
 136   // namesleft--;
 137   // }
 138   // }
 139   // else
 140   // {
 141   // treeNode.setCollapse(true); // collapse nodes that couldn't be connected
 142   // // to a sequence
 143   //
 144   //
 145   // // treeNode.setElement( new Sequence(nodeSequenceName,
 146   // "THISISAPLACEHOLDER"));
 147   // // treeNode.setPlaceholder(true);
 148   // }
 149   // }
 150   // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many > 0)
 151   // {
 152   // jalview.bin.Cache.log.debug("There were " + countOne2Many
 153   // + "alignment sequence ids (out of" + one2many.size()
 154   // + " unique ids) linked to two or more leaves.");
 155   // }
 156   // one2many.clear();
 157   //
 158   // }
 159
 160 }
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