package jalview.ext.treeviewer;

import jalview.datamodel.SequenceI;

import java.io.File;
import java.io.IOException;
import java.util.Iterator;
import java.util.List;

/**
 * Interface for implementing a phylogenetic tree.
 * 
 * @author kjvanderheide
 *
 */
public interface TreeI
{
  /**
   * 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 String[] getAllLeafNames();

  public TreeNodeI[] getAllNodes();

  /**
   * Gets the node that has the maximum branch length from the root (or top
   * level node if tree is unrooted).
   * 
   * @return
   */
  public TreeNodeI getFurthestNode();

  /**
   * Returns the longest total branch length from the root to a leaf node.
   * 
   * @param adjustForCollapsedSubtrees
   *          true if nodes part of a collapsed (hidden) subtree should be
   *          considered.
   * @return
   */
  public double getMaximumLength(boolean adjustForCollapsedSubtrees);

  public List<SequenceI> getNodeSequences();

  public TreeNodeI getNodeWithName(String name);

  public TreeNodeI getRoot();

  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 Iterator<TreeNodeI> iterateInLevelOrder();

  public Iterator<TreeNodeI> iterateInPostOrder();

  public Iterator<TreeNodeI> iterateInPreOrder();

  /**
   * 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 void setRerootable(boolean b);

  public void setRoot(TreeNodeI rootNode);

  public void setRooted(boolean b);

  public void setTreeName(String treeTitle);

}