src/jalview/ext/treeviewer/LoadedTreeAssociationI.java

   1 package jalview.ext.treeviewer;
   2
   3 import jalview.datamodel.SequenceI;
   4
   5 import java.util.Map;
   6
   7 /**
   8  * Interface for associating the nodes of a loaded in (instead of calculated)
   9  * tree to the sequences of an alignment in Jalview.
  10  *
  11  * @author kjvanderheide
  12  *
  13  */
  14 public interface LoadedTreeAssociationI
  15 {
  16   /**
  17    * Tries to match the loaded in tree nodes as best as possible with Jalview
  18    * sequences
  19    *
  20    * Partially refactored from the old Jalview TreeModel
  21    * associateLeavesToSequences method.
  22    */
  23   public void associateNodesToSequences();
  24
  25   /**
  26    * See
  27    * {@link jalview.ext.treeviewer.TreeViewerBindingI#getAlignmentWithNodes()}
  28    *
  29    *
  30    */
  31   public Map<SequenceI, TreeNodeI> getAlignmentWithNodes();
  32
  33   /**
  34    * See
  35    * {@link jalview.ext.treeviewer.TreeViewerBindingI#getNodesWithAlignment()}
  36    *
  37    *
  38    */
  39   public Map<TreeNodeI, SequenceI> getNodesWithAlignment();
  40 }