Class BestTreeMP

java.lang.Object
  |
  +--BestTreeMP

public class BestTreeMP
extends java.lang.Object

This class keeps the best tree information in the MP algorithm.


Constructor Summary
BestTreeMP()
          Constructs a default best tree object in the MP algorithm
 
Method Summary
 int[][] getAllNumOfSubs()
          Gets the number of substitutions table in all sites in the MP algorithm.
 int getAllSitesSubs()
          Gets the total number of substitutions in all sites in the MP algorithm.
 java.lang.String[][] getBestCharacters()
          Gets the character sequences for all nodes in the best tree in the MP algorithm.
 java.util.Vector getBestInterNodes()
          Gets the interior nodes in the best tree in the MP algorithm.
 TreeDisplay getBestTreeDisplay()
          Gets the tree drawing object in the best tree in the MP algorithm.
 javax.swing.JFrame getBestTreeFrame()
          Gets the best tree window in the MP algorithm.
 void setAllNumOfSubs(int[][] allNumOfSubsOthers)
          Sets the total number of substitutions in all sites in the MP algorithm.
 void setBestCharacters(java.lang.String[][] bestCharactersOthers)
          Sets the character sequences for all nodes in the best tree in the MP algorithm.
 void setBestInterNodes(java.util.Vector bestInterNodesOthers)
          Sets the interior nodes in the best tree in the MP algorithm.
 void setBestTreeDisplay(TreeDisplay bestTreeDisplayOthers)
          Sets the tree drawing object in the best tree in the MP algorithm.
 void setBestTreeFrame(javax.swing.JFrame bestTreeFrameOthers)
          Sets the best tree window in the MP algorithm.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

BestTreeMP

public BestTreeMP()
Constructs a default best tree object in the MP algorithm

Method Detail

getAllSitesSubs

public int getAllSitesSubs()
Gets the total number of substitutions in all sites in the MP algorithm.

Returns:
the total number of substitutions in all sites in the MP algorithm

getAllNumOfSubs

public int[][] getAllNumOfSubs()
Gets the number of substitutions table in all sites in the MP algorithm.

Returns:
the number of substitutions table in all sites in the MP algorithm

getBestInterNodes

public java.util.Vector getBestInterNodes()
Gets the interior nodes in the best tree in the MP algorithm.

Returns:
the interior nodes in the best tree in the MP algorithm

getBestCharacters

public java.lang.String[][] getBestCharacters()
Gets the character sequences for all nodes in the best tree in the MP algorithm.

Returns:
the character sequences for all nodes in the best tree in the MP algorithm

getBestTreeDisplay

public TreeDisplay getBestTreeDisplay()
Gets the tree drawing object in the best tree in the MP algorithm.

Returns:
the tree drawing object in the best tree in the MP algorithm

getBestTreeFrame

public javax.swing.JFrame getBestTreeFrame()
Gets the best tree window in the MP algorithm.

Returns:
the best tree window in the MP algorithm

setAllNumOfSubs

public void setAllNumOfSubs(int[][] allNumOfSubsOthers)
Sets the total number of substitutions in all sites in the MP algorithm.

Parameters:
allNumOfSubsOthers - the total number of substitutions in all sites in the MP algorithm

setBestInterNodes

public void setBestInterNodes(java.util.Vector bestInterNodesOthers)
Sets the interior nodes in the best tree in the MP algorithm.

Parameters:
bestInterNodesOthers - the interior nodes in the best tree in the MP algorithm

setBestCharacters

public void setBestCharacters(java.lang.String[][] bestCharactersOthers)
Sets the character sequences for all nodes in the best tree in the MP algorithm.

Parameters:
bestCharactersOthers - the character sequences for all nodes in the best tree in the MP algorithm

setBestTreeDisplay

public void setBestTreeDisplay(TreeDisplay bestTreeDisplayOthers)
Sets the tree drawing object in the best tree in the MP algorithm.

Parameters:
bestTreeDisplayOthers - the tree drawing object in the best tree in the MP algorithm

setBestTreeFrame

public void setBestTreeFrame(javax.swing.JFrame bestTreeFrameOthers)
Sets the best tree window in the MP algorithm.

Parameters:
bestTreeFrameOthers - the best tree window in the MP algorithm