Package org.snpeff.geneSets.algorithm
Class EnrichmentAlgorithm
- java.lang.Object
-
- org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
-
- Direct Known Subclasses:
EnrichmentAlgorithmGreedy
,FisherPValueAlgorithm
,NoneAlgorithm
,RankSumPValueAlgorithm
public abstract class EnrichmentAlgorithm extends java.lang.Object
A generic enrichment algorithm for selecting gene-sets from a collection of gene-sets- Author:
- pcingola
-
-
Nested Class Summary
Nested Classes Modifier and Type Class Description static class
EnrichmentAlgorithm.EnrichmentAlgorithmType
-
Field Summary
Fields Modifier and Type Field Description static java.lang.String[]
HTML_BG_COLOR
static java.lang.String
HTML_BG_COLOR_TITLE
static int
HTML_TD_GENES_MAX_LEN
static long
PRINT_SOMETHING_TIME
-
Constructor Summary
Constructors Constructor Description EnrichmentAlgorithm(GeneSets geneSets, int numberToSelect)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double
getMaxPvalueAdjusted()
java.lang.StringBuilder
getOutput()
protected boolean
isShow(Result result)
Showld we show this result or should the output be filtered?protected void
print(java.lang.String str)
Result
select()
Select the 'best' gene setsvoid
setDebug(boolean debug)
void
setFilterOutputGeneSets(java.util.Set<java.lang.String> filterOutputGeneSets)
void
setHtmlTable(boolean htmlTable)
void
setMaxGeneSetSize(int maxGeneSetSize)
void
setMaxPValue(double maxPValue)
void
setMaxPvalueAdjusted(double maxPvalueAdjusted)
void
setMinGeneSetSize(int minGeneSetSize)
void
setVerbose(boolean verbose)
-
-
-
Field Detail
-
HTML_TD_GENES_MAX_LEN
public static final int HTML_TD_GENES_MAX_LEN
- See Also:
- Constant Field Values
-
HTML_BG_COLOR
public static final java.lang.String[] HTML_BG_COLOR
-
HTML_BG_COLOR_TITLE
public static final java.lang.String HTML_BG_COLOR_TITLE
- See Also:
- Constant Field Values
-
PRINT_SOMETHING_TIME
public static long PRINT_SOMETHING_TIME
-
-
Constructor Detail
-
EnrichmentAlgorithm
public EnrichmentAlgorithm(GeneSets geneSets, int numberToSelect)
-
-
Method Detail
-
getMaxPvalueAdjusted
public double getMaxPvalueAdjusted()
-
getOutput
public java.lang.StringBuilder getOutput()
-
isShow
protected boolean isShow(Result result)
Showld we show this result or should the output be filtered?- Parameters:
result
-- Returns:
-
print
protected void print(java.lang.String str)
-
select
public Result select()
Select the 'best' gene sets- Returns:
-
setDebug
public void setDebug(boolean debug)
-
setFilterOutputGeneSets
public void setFilterOutputGeneSets(java.util.Set<java.lang.String> filterOutputGeneSets)
-
setHtmlTable
public void setHtmlTable(boolean htmlTable)
-
setMaxGeneSetSize
public void setMaxGeneSetSize(int maxGeneSetSize)
-
setMaxPValue
public void setMaxPValue(double maxPValue)
-
setMaxPvalueAdjusted
public void setMaxPvalueAdjusted(double maxPvalueAdjusted)
-
setMinGeneSetSize
public void setMinGeneSetSize(int minGeneSetSize)
-
setVerbose
public void setVerbose(boolean verbose)
-
-