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.List;
  11 import java.util.Map;
  12
  13 import org.forester.phylogeny.Phylogeny;
  14 import org.forester.phylogeny.PhylogenyNode;
  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
  55     List<PhylogenyNode> leaves = tree.getExternalNodes();
  56     SequenceI nodeSequence;
  57     String nodeSequenceName;
  58
  59     for (PhylogenyNode treeNode : leaves)
  60     {
  61       nodeSequenceName = treeNode.getName();
  62
  63       nodeSequence = algnIds.findIdMatch(nodeSequenceName);
  64       if (nodeSequence != null)
  65       {
  66         org.forester.phylogeny.data.Sequence foresterNodeSeq = DataConversions
  67                 .createForesterSequence(nodeSequence, true);
  68         treeNode.getNodeData().setSequence(foresterNodeSeq);
  69
  70         MappingUtils.putWithDuplicationCheck(alignmentWithNodes,
  71                 nodeSequence, treeNode);
  72         MappingUtils.putWithDuplicationCheck(nodesWithAlignment,
  73                 treeNode, nodeSequence);
  74
  75
  76       }
  77
  78     }
  79
  80   }
  81
  82
  83
  84   public Map<SequenceI, PhylogenyNode> getAlignmentWithNodes()
  85   {
  86     return alignmentWithNodes;
  87   }
  88
  89   public Map<PhylogenyNode, SequenceI> getNodesWithAlignment()
  90   {
  91     return nodesWithAlignment;
  92   }
  93
  94   // {
  95   // SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
  96   //
  97   // List<PhylogenyNode> leaves = aptxTree.getExternalNodes();
  98   //
  99   // int namesleft = seqs.length;
 100   // SequenceI nodeSequence;
 101   // String nodeSequenceName;
 102   // List<SequenceI> one2many = new ArrayList<>();
 103   // int countOne2Many = 0;
 104   //
 105   // for (PhylogenyNode treeNode : leaves)
 106   // {
 107   // nodeSequenceName = treeNode.getName();
 108   // nodeSequence = null;
 109   //
 110   // if (namesleft > -1)
 111   // {
 112   // nodeSequence = algnIds.findIdMatch(nodeSequenceName);
 113   // }
 114   //
 115   // if (nodeSequence != null)
 116   // {
 117   // org.forester.phylogeny.data.Sequence foresterNodeSeq =
 118   // ForesterDataConversions.createForesterSequence(nodeSequence, true);
 119   //
 120   // treeNode.getNodeData().setSequence(foresterNodeSeq);
 121   // if (one2many.contains(nodeSequence))
 122   // {
 123   // countOne2Many++;
 124   // if (jalview.bin.Cache.log.isDebugEnabled())
 125   // {
 126   // jalview.bin.Cache.log.debug("One 2 many relationship for"
 127   // +nodeSequence.getName());
 128   // }
 129   // }
 130   // else
 131   // {
 132   // one2many.add(nodeSequence);
 133   // namesleft--;
 134   // }
 135   // }
 136   // else
 137   // {
 138   // treeNode.setCollapse(true); // collapse nodes that couldn't be connected
 139   // // to a sequence
 140   //
 141   //
 142   // // treeNode.setElement( new Sequence(nodeSequenceName,
 143   // "THISISAPLACEHOLDER"));
 144   // // treeNode.setPlaceholder(true);
 145   // }
 146   // }
 147   // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many > 0)
 148   // {
 149   // jalview.bin.Cache.log.debug("There were " + countOne2Many
 150   // + "alignment sequence ids (out of" + one2many.size()
 151   // + " unique ids) linked to two or more leaves.");
 152   // }
 153   // one2many.clear();
 154   //
 155   // }
 156
 157 }
 158
 159
 160
 161
 162
 163