uk.ac.kent.dover.fastGraph

Class ExactMotifFinder

java.lang.Object

uk.ac.kent.dover.fastGraph.ExactMotifFinder

public class ExactMotifFinder
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	ExactMotifFinder.IsoHolder Class to hold a FastGraph key and the number of instances of that FastGraph for a particular key. Graphs are loaded from disk.
class	ExactMotifFinder.MotifResultHolder Inner class to hold details of motifs ready for output

Constructor Summary

Constructors

Constructor and Description
ExactMotifFinder(FastGraph g, boolean saveAll) Trivial contructor
ExactMotifFinder(FastGraph g, uk.ac.kent.dover.fastGraph.Gui.MotifTask mt, boolean saveAll) Trivial constructor

Method Summary

Modifier and Type	Method and Description
void	buildRewires(int numOfRewires) Builds a list of rewired graphs, each one built from the previous and saved to disk
java.util.ArrayList<ExactMotifFinder.MotifResultHolder>	compareAndExportResults(int size, int minSize, int maxSize) Compares the results from the reference set to the real set. Exports these in a user friendly manner
void	compareMotifDatas(int minSize, int maxSize) Runs the comparison of motif data for each size given
java.util.HashMap<java.lang.String,ExactMotifFinder.IsoHolder>	extractGraphLists(java.util.HashMap<java.lang.String,java.util.LinkedList<ExactMotifFinder.IsoHolder>> hashBuckets) This extracts the lists of isomorphic graphs.
void	findMotifs(int k, double q, java.util.HashMap<java.lang.String,java.util.LinkedList<ExactMotifFinder.IsoHolder>> hashBuckets) Run the motif finder.
void	findMotifsRealSet(int minSize, int maxSize) Finds all motifs from the real set.
void	findMotifsReferenceSet(int rewires, int minSize, int maxSize) Finds all motifs from the reference set.
java.util.HashMap<java.lang.String,java.util.LinkedList<ExactMotifFinder.IsoHolder>>	getHashBuckets() Returns the hashbuckets from this instance
int	getNumOfResults()
FastGraph	getReferenceGraph()
boolean	isSaveAll() If the saveAll option is specified
java.util.HashMap<java.lang.String,ExactMotifFinder.IsoHolder>	mergeIsoLists(java.util.HashMap<java.lang.String,ExactMotifFinder.IsoHolder> oldList, java.util.HashMap<java.lang.String,ExactMotifFinder.IsoHolder> newList) Merges two isoLists together, and returns the enlarged list
void	outputHashBuckets(java.util.HashMap<java.lang.String,java.util.LinkedList<ExactMotifFinder.IsoHolder>> hashBuckets) Outputs a given map hashBuckets to the screen.
void	setReferenceGraph(FastGraph referenceGraph)
void	setSaveAll(boolean saveAll) Sets if the saveAll option is specified

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ExactMotifFinder

public ExactMotifFinder(FastGraph g,
                        boolean saveAll)

Trivial contructor

Parameters:

g - the FastGraph to find motifs in

saveAll - If every example is to be saved

ExactMotifFinder

public ExactMotifFinder(FastGraph g,
                        uk.ac.kent.dover.fastGraph.Gui.MotifTask mt,
                        boolean saveAll)

Trivial constructor

Parameters:

g - the FastGraph to find motifs in

mt - The MotifTask to report progress to

saveAll - If every example is to be saved

Method Detail

findMotifsReferenceSet

public void findMotifsReferenceSet(int rewires,
                                   int minSize,
                                   int maxSize)
                            throws java.io.IOException,
                                   FastGraphException

Finds all motifs from the reference set. Will rewire a reference set if one has not been given.

Parameters:

rewires - The number of rewires needed. If 0, then main set.

minSize - The minimum size of motifs to be found

maxSize - The maximum size of motifs to be found

Throws:

java.io.IOException - If the output data cannot be written

FastGraphException

findMotifsRealSet

public void findMotifsRealSet(int minSize,
                              int maxSize)
                       throws java.io.IOException,
                              FastGraphException

Finds all motifs from the real set.

Parameters:

minSize - The minimum size of motifs to be found

maxSize - The maximum size of motifs to be found

Throws:

java.io.IOException - If the output data cannot be written

FastGraphException

isSaveAll

public boolean isSaveAll()

If the saveAll option is specified

Returns:

saveAll

setSaveAll

public void setSaveAll(boolean saveAll)

Sets if the saveAll option is specified

Parameters:

saveAll - to save all motifs?

compareMotifDatas

public void compareMotifDatas(int minSize,
                              int maxSize)
                       throws java.io.FileNotFoundException,
                              java.io.IOException

Runs the comparison of motif data for each size given

Parameters:

minSize - The minimum size of motifs found

maxSize - The maximum size of motifs found

Throws:

java.io.FileNotFoundException - If the files cannot be loaded

java.io.IOException - Any other IO problems

buildRewires

public void buildRewires(int numOfRewires)
                  throws java.io.IOException

Builds a list of rewired graphs, each one built from the previous and saved to disk

Parameters:

numOfRewires - The number of rewires to perform

Throws:

java.io.IOException - If the rewired graph cannot be saved

outputHashBuckets

public void outputHashBuckets(java.util.HashMap<java.lang.String,java.util.LinkedList<ExactMotifFinder.IsoHolder>> hashBuckets)

Outputs a given map hashBuckets to the screen. Note: Not to a file!

Parameters:

hashBuckets - The hashbuckets to output

mergeIsoLists

public java.util.HashMap<java.lang.String,ExactMotifFinder.IsoHolder> mergeIsoLists(java.util.HashMap<java.lang.String,ExactMotifFinder.IsoHolder> oldList,
                                                                                    java.util.HashMap<java.lang.String,ExactMotifFinder.IsoHolder> newList)

Merges two isoLists together, and returns the enlarged list

Parameters:

oldList - The first list

newList - The second list

Returns:

The new list contains elements from both.

getHashBuckets

public java.util.HashMap<java.lang.String,java.util.LinkedList<ExactMotifFinder.IsoHolder>> getHashBuckets()

Returns the hashbuckets from this instance

Returns:

The hashbuckets

extractGraphLists

public java.util.HashMap<java.lang.String,ExactMotifFinder.IsoHolder> extractGraphLists(java.util.HashMap<java.lang.String,java.util.LinkedList<ExactMotifFinder.IsoHolder>> hashBuckets)

This extracts the lists of isomorphic graphs. Each element in a list is isomorphic. Call after running findMotifs.

Parameters:

hashBuckets - The buckets to store the results in

Returns:

collection of lists, all graphs in a single list are isomorphic

findMotifs

public void findMotifs(int k,
                       double q,
                       java.util.HashMap<java.lang.String,java.util.LinkedList<ExactMotifFinder.IsoHolder>> hashBuckets)
                throws java.io.IOException,
                       FastGraphException

Run the motif finder.

Parameters:

k - the size of motifs in terms of number of nodes.

q - the fraction of nodes to sample.

hashBuckets - The buckets to store the results in

Throws:

java.io.IOException - If the output files cannot be written

FastGraphException

compareAndExportResults

public java.util.ArrayList<ExactMotifFinder.MotifResultHolder> compareAndExportResults(int size,
                                                                                       int minSize,
                                                                                       int maxSize)
                                                                                throws java.io.FileNotFoundException,
                                                                                       java.io.IOException

Compares the results from the reference set to the real set.
Exports these in a user friendly manner

Parameters:

size - The size of motif being compared

minSize - The minimum size of motifs

maxSize - The maximum size of motifs

Returns:

The results

Throws:

java.io.IOException - If the File cannot be read

java.io.FileNotFoundException - If the file cannot be found

getNumOfResults

public int getNumOfResults()

Returns:

the numOfResults

getReferenceGraph

public FastGraph getReferenceGraph()

Returns:

the referenceGraph

setReferenceGraph

public void setReferenceGraph(FastGraph referenceGraph)

Parameters:

referenceGraph - the referenceGraph to set