edu.cornell.med.icb.tissueinfo.similarity
Class TiSimOptions

java.lang.Object
  edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions

public class TiSimOptions
extends Object

Regroups options for tiSimilarity.

Author:

Fabien Campagne Date: Jul 8, 2007 Time: 12:07:11 PM

Field Summary

protected boolean	accumulateScoresPerQuery
protected String	basename
protected int	blockSizeOption
int	crossValidationFoldNumber
protected int	endIndex
protected TiSimilaritySearchEngine	engine
protected int[]	focusGroup
int	k
int	maxSequenceIndex
int	numberOfGenesWithTranscripts The number of genes with non-zero count transcripts.
PrintWriter	output
Int2ObjectMap<IntSet>	pairs
CountPreprocessor[]	preProcessorChain
protected int[]	queryAccessionCodeIndices
protected ObjectSet<String>	queryAccessionCodes
int	randomSeed
boolean	rankByScore Rank by sum of score if true, by sum of inverse rank if false.
boolean	rankFusionWithSpecificityRank
protected ExpressionProfileSimilarityScorer	scorer
protected int	startIndex
PrintWriter	stats Writes to a statistics file.
protected boolean	useWeights

Constructor Summary

TiSimOptions()

Method Summary

void	addPair(int index1, int index2)
boolean	hasPair(int index1, int index2)
void	setRankFusionWithSpecificityRank(boolean rankFusionWithSpecificityRank)

Methods inherited from class java.lang.Object

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

Field Detail

scorer

protected ExpressionProfileSimilarityScorer scorer

accumulateScoresPerQuery

protected boolean accumulateScoresPerQuery

useWeights

protected boolean useWeights

blockSizeOption

protected int blockSizeOption

startIndex

protected int startIndex

endIndex

protected int endIndex

focusGroup

protected int[] focusGroup

queryAccessionCodeIndices

protected int[] queryAccessionCodeIndices

queryAccessionCodes

protected ObjectSet<String> queryAccessionCodes

engine

protected TiSimilaritySearchEngine engine

basename

protected String basename

k

public int k

output

public PrintWriter output

maxSequenceIndex

public int maxSequenceIndex

pairs

public Int2ObjectMap<IntSet> pairs

crossValidationFoldNumber

public int crossValidationFoldNumber

randomSeed

public int randomSeed

rankByScore

public boolean rankByScore

Rank by sum of score if true, by sum of inverse rank if false.

preProcessorChain

public CountPreprocessor[] preProcessorChain

rankFusionWithSpecificityRank

public boolean rankFusionWithSpecificityRank

numberOfGenesWithTranscripts

public int numberOfGenesWithTranscripts

The number of genes with non-zero count transcripts.

stats

public PrintWriter stats

Writes to a statistics file. Format of the file depends on the TEPSS mode used, but is a human readable format.

Constructor Detail

TiSimOptions

public TiSimOptions()

Method Detail

setRankFusionWithSpecificityRank

public void setRankFusionWithSpecificityRank(boolean rankFusionWithSpecificityRank)

addPair

public void addPair(int index1,
                    int index2)

hasPair

public boolean hasPair(int index1,
                       int index2)