org.gersteinlab.tyna.core.operators
Class ChainMotifMiner

java.lang.Object
  extended by org.gersteinlab.tyna.core.operators.MotifMiner
      extended by org.gersteinlab.tyna.core.operators.ChainMotifMiner
All Implemented Interfaces:
UnaryOperator

public class ChainMotifMiner
extends MotifMiner

        This class defines the chain motif miner. It takes a graph as input, and
        returns a graph that contains the set of all chains that satisfy some
        requirements.
        

Version:
1.0 (December 9, 2005) Change History: 1.0 - Initial version
Author:
Kevin Yuk-Lap Yip

Field Summary
protected  int maxSize
          The maximum size
protected  int minSize
          The minimum size
protected  java.lang.String motifType
          The motif type
 
Fields inherited from class org.gersteinlab.tyna.core.operators.MotifMiner
INTEGRATED, MAXIMAL, MINIMAL, outputType, SEPARATED
 
Constructor Summary
ChainMotifMiner(java.lang.String outputType, int minSize, int maxSize, java.lang.String motifType)
          Create a new chain motif miner.
 
Method Summary
 Graph operate(Graph graph)
          Perform the operation on a graph.
 
Methods inherited from class org.gersteinlab.tyna.core.operators.MotifMiner
createOutputGraph
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

minSize

protected int minSize
The minimum size


maxSize

protected int maxSize
The maximum size


motifType

protected java.lang.String motifType
The motif type

Constructor Detail

ChainMotifMiner

public ChainMotifMiner(java.lang.String outputType,
                       int minSize,
                       int maxSize,
                       java.lang.String motifType)
Create a new chain motif miner.

Parameters:
outputType - The output type (separated or integrated)
minSize - The minimum size of each chain
maxSize - The maximum size of each chain
motifType - The motif type (minimal or maximal)
Method Detail

operate

public Graph operate(Graph graph)
              throws GraphTypeException
Description copied from interface: UnaryOperator
Perform the operation on a graph.

Parameters:
graph - The graph
Returns:
The resulting graph
Throws:
GraphTypeException - If there are problems with the type of the input graph