Package org.snpeff.stats
Class GeneCountByTypeTable
- java.lang.Object
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- org.snpeff.stats.GeneCountByTypeTable
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Iterable<java.lang.String>
public class GeneCountByTypeTable extends java.lang.Object implements java.lang.Iterable<java.lang.String>, java.io.Serializable
Count for each 'type' and 'gene'. Tries to avoid multiple counting by comparing to latest seqChanges. WARNING: This strategy does not work if changeEffect are out of order.- Author:
- pcingola
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description static boolean
debug
static int
GENE_CPG_NUM_BINS
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Constructor Summary
Constructors Constructor Description GeneCountByTypeTable()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
getBioType(java.lang.String key)
CountByType
getCounter(java.lang.String type)
Get counter for this typeCountByType
getCounterSize(java.lang.String type)
Get size counter for this typejava.util.List<java.lang.String>
getKeyList()
Get a sorted list of keysint
getSizeByType(java.lang.String key, java.lang.String type)
java.util.List<java.lang.String>
getTypeList()
Get a sorted list of keysjava.util.Iterator<java.lang.String>
iterator()
void
sample(Gene gene, Transcript tr, java.lang.String type, VariantEffect variantEffect)
Sample thistuple to update statistics
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Method Detail
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getBioType
public java.lang.String getBioType(java.lang.String key)
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getCounter
public CountByType getCounter(java.lang.String type)
Get counter for this type
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getCounterSize
public CountByType getCounterSize(java.lang.String type)
Get size counter for this type
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getKeyList
public java.util.List<java.lang.String> getKeyList()
Get a sorted list of keys
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getSizeByType
public int getSizeByType(java.lang.String key, java.lang.String type)
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getTypeList
public java.util.List<java.lang.String> getTypeList()
Get a sorted list of keys
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iterator
public java.util.Iterator<java.lang.String> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<java.lang.String>
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sample
public void sample(Gene gene, Transcript tr, java.lang.String type, VariantEffect variantEffect)
Sample thistuple to update statistics
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