JAL-1953 2.11.2 with Archeopteryx!

[jalview.git] / src / jalview / ext / treeviewer / LoadedTreeAssociationI.java

diff --git a/src/jalview/ext/treeviewer/LoadedTreeAssociationI.java b/src/jalview/ext/treeviewer/LoadedTreeAssociationI.java
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+++ b/src/jalview/ext/treeviewer/LoadedTreeAssociationI.java
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+package jalview.ext.treeviewer;
+
+import jalview.datamodel.SequenceI;
+
+import java.util.Map;
+
+/**
+ * Interface for associating the nodes of a loaded in (instead of calculated)
+ * tree to the sequences of an alignment in Jalview.
+ * 
+ * @author kjvanderheide
+ *
+ */
+public interface LoadedTreeAssociationI
+{
+  /**
+   * Tries to match the loaded in tree nodes as best as possible with Jalview
+   * sequences
+   * 
+   * Partially refactored from the old Jalview TreeModel
+   * associateLeavesToSequences method.
+   */
+  public void associateNodesToSequences();
+
+  /**
+   * @see jalview.ext.treeviewer.TreeViewerBindingI#getAlignmentWithNodes()
+   * 
+   * 
+   */
+  public Map<SequenceI, TreeNodeI> getAlignmentWithNodes();
+
+  /**
+   * @see jalview.ext.treeviewer.TreeViewerBindingI#getNodesWithAlignment()
+   * 
+   * 
+   * 
+   */
+  public Map<TreeNodeI, SequenceI> getNodesWithAlignment();
+}