JAL-1953 first pass of adding javadoc, some methods renamed

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

diff --git a/src/jalview/ext/treeviewer/TreeI.java b/src/jalview/ext/treeviewer/TreeI.java
index 702ff61..fbda8f1 100644 (file)
--- a/src/jalview/ext/treeviewer/TreeI.java
+++ b/src/jalview/ext/treeviewer/TreeI.java
@@ -7,42 +7,70 @@ import java.io.IOException;
 import java.util.Iterator;
 import java.util.List;
 
+/**
+ * Interface for a generic phylogenetic tree, this does not necessarily have to
+ * be part of a tree panel.
+ * 
+ * @author kjvanderheide
+ *
+ */
 public interface TreeI
 {
-  public TreeNodeI getRoot();
-
-  public TreeNodeI getNodeWithName(String name);
+  /**
+   * Uses this tree as the basis for a new tree frame.
+   * 
+   * @param instanceTitle
+   *          name of the new tree frame.
+   * @return
+   */
+  TreeFrameI createTreeViewerFromTree(String instanceTitle);
 
-  public TreeNodeI getFurthestNode();
+  public String[] getAllLeafNames();
 
   public TreeNodeI[] getAllNodes();
 
-  public String[] getAllLeafNames();
+  public TreeNodeI getFurthestNode();
+
+  public double getHeight(boolean adjustForCollapsedSubtrees);
 
   public List<SequenceI> getNodeSequences();
 
-  public void setTreeName(String treeTitle);
+  public TreeNodeI getNodeWithName(String name);
 
-  public void setRerootable(boolean b);
+  public TreeNodeI getRoot();
 
-  public void setRooted(boolean b);
+  public String getTreeName();
 
+  /**
+   * Check if the tree actually contains any nodes.
+   * 
+   * @return true if tree has no nodes (or is deleted), false otherwise.
+   */
   public boolean isEmpty();
 
-  public String getTreeName();
-
-  public void setRoot(TreeNodeI rootNode);
+  public Iterator<TreeNodeI> iterateInLevelOrder();
 
-  public double getHeight(boolean adjustForCollapsedSubtrees);
+  public Iterator<TreeNodeI> iterateInPostOrder();
 
   public Iterator<TreeNodeI> iterateInPreOrder();
 
-  public Iterator<TreeNodeI> iterateInLevelOrder();
+  /**
+   * This should write the tree to the richest file format available for
+   * compatibility reasons as this is the method used when Jalview saves a tree
+   * to its project.
+   * 
+   * @param outputFile
+   *          File that tree should be written to
+   * @throws IOException
+   */
+  public void outputAsFile(File outputFile) throws IOException;
 
-  public Iterator<TreeNodeI> iterateInPostOrder();
+  public void setRerootable(boolean b);
 
-  TreeFrameI createTreeViewerFromTree(String instanceTitle);
+  public void setRoot(TreeNodeI rootNode);
 
-  public void writeToXml(File outputFile) throws IOException;
+  public void setRooted(boolean b);
+
+  public void setTreeName(String treeTitle);
 
 }