| 
 | FORESTER 1.92 | |||||||
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| SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD | |||||||
java.lang.Object | +--forester.tools.DistanceCalculator
| Field Summary | |
| static double | DEFAULT | 
| Constructor Summary | |
| DistanceCalculator()Default constructor. | |
| DistanceCalculator(Tree t)Constructor. | |
| DistanceCalculator(Tree t,
                   java.util.Vector ext_nodes)Constructor. | |
| Method Summary | |
|  double | getDistanceToLCA(java.lang.String seq_name)Calculates the distance of the Node with seq name seq_name to the LCA of ext_nodes, which has been set either with constructor DistanceCalculator(Tree,Vector) or method setTreeAndExtNodes(Tree,Vector). | 
|  double | getDistanceToNode(Node outer,
                  Node inner)Calculates the distance of Node outer to Node inner. | 
|  double | getDistanceToNode(java.lang.String seq_name,
                  Node inner)Calculates the distance of the Node with seq name seq_name to Node inner. | 
|  double | getDistanceToRoot(Node n)Calculates the distance of Node n to the root of Tree t which has been set either with a constructor, setTree(Tree), or setTreeAndExtNodes(Tree,Vector). | 
|  double | getDistanceToRoot(java.lang.String seq_name)Calculates the distance of the Node with seq name seq_name to the root of Tree t, which has been set either with a constructor, setTree(Tree), or setTreeAndExtNodes(Tree,Vector). | 
|  double | getMean()Returns the mean distance. | 
|  int | getN()Returns the sum of all Nodes used to calculate the mean. | 
|  double | getStandardDeviation()Returns the standard deviation. | 
|  double | getVariance()Returns the variance. | 
| static void | main(java.lang.String[] args) | 
|  void | setTree(Tree t)Sets the rooted Tree t for which the mean distance to the root and its variance and standard deviation are calculated. | 
|  void | setTreeAndExtNodes(Tree t,
                   java.util.ArrayList ext_nodes)Sets the rooted Tree t and the external Nodes ext_nodes for which the mean distance to their lowest common ancestor and its variance and standard deviation are calculated. | 
|  void | setTreeAndExtNodes(Tree t,
                   java.util.Vector ext_nodes)Sets the rooted Tree t and the external Nodes ext_nodes for which the mean distance to their lowest common ancestor and its variance and standard deviation are calculated. | 
| Methods inherited from class java.lang.Object | 
|  | 
| Field Detail | 
public static final double DEFAULT
| Constructor Detail | 
public DistanceCalculator()
public DistanceCalculator(Tree t)
t - the rooted Tree for which the mean distance
to the root and its variance and standard
deviation are calculated
public DistanceCalculator(Tree t,
                          java.util.Vector ext_nodes)
t - the rooted Tree containing Nodes in Vector ext_nodesext_nodes - a Vector of Nodes of t, the mean distance
to their lowest common ancestor and its variance
and standard deviation are calculated| Method Detail | 
public void setTree(Tree t)
t - the rooted Tree for which the mean distance
to the root and its variance and standard
deviation are calculated
public void setTreeAndExtNodes(Tree t,
                               java.util.Vector ext_nodes)
t - the rooted Tree containing Nodes in Vector ext_nodesext_nodes - a Vector of Nodes of t, the mean distance
to their lowest common ancestor and its variance
and standard deviation are calculated
public void setTreeAndExtNodes(Tree t,
                               java.util.ArrayList ext_nodes)
t - the rooted Tree containing Nodes in Vector ext_nodesext_nodes - a ArrayList of Nodes of t, the mean distance
to their lowest common ancestor and its variance
and standard deviation are calculatedpublic double getDistanceToRoot(Node n)
n - the Node for which the distance to the root is to be
calculatedDistanceCalculator(Tree), 
DistanceCalculator(Tree,Vector), 
setTree(Tree), 
setTreeAndExtNodes(Tree,Vector)
public double getDistanceToNode(Node outer,
                                Node inner)
                         throws java.lang.Exception
outer - a Nodeinner - a Node closer to the root than outer
public double getDistanceToRoot(java.lang.String seq_name)
                         throws java.lang.Exception
seq_name - the seq name for the Node for which the distance
to the root is to be calculatedDistanceCalculator(Tree), 
DistanceCalculator(Tree,Vector), 
setTree(Tree), 
setTreeAndExtNodes(Tree,Vector), 
setTreeAndExtNodes(Tree,ArrayList)
public double getDistanceToLCA(java.lang.String seq_name)
                        throws java.lang.Exception
seq_name - the seq name for the Node for which the distance
to the LCA is to be calculatedDistanceCalculator(Tree,Vector), 
setTreeAndExtNodes(Tree,Vector), 
setTreeAndExtNodes(Tree,ArrayList)
public double getDistanceToNode(java.lang.String seq_name,
                                Node inner)
                         throws java.lang.Exception
seq_name - the seq name of a Node further from the root than
Node innerinner - a Nodepublic double getMean()
DistanceCalculator(Tree), 
DistanceCalculator(Tree,Vector), 
setTree(Tree), 
setTreeAndExtNodes(Tree,Vector), 
setTreeAndExtNodes(Tree,ArrayList)public double getVariance()
DistanceCalculator(Tree), 
DistanceCalculator(Tree,Vector), 
setTree(Tree), 
setTreeAndExtNodes(Tree,Vector), 
setTreeAndExtNodes(Tree,ArrayList)public double getStandardDeviation()
DistanceCalculator(Tree), 
DistanceCalculator(Tree,Vector), 
setTree(Tree), 
setTreeAndExtNodes(Tree,Vector), 
setTreeAndExtNodes(Tree,ArrayList)public int getN()
public static void main(java.lang.String[] args)
| 
 | FORESTER 1.92 | |||||||
| PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||
| SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD | |||||||