Package org.snpsift.fileIterator
Class DbNsfpEntry
- java.lang.Object
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- org.snpeff.interval.Interval
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- org.snpeff.interval.Marker
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- org.snpeff.interval.Variant
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- org.snpsift.fileIterator.DbNsfpEntry
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<org.snpeff.interval.Interval>
,org.snpeff.serializer.TxtSerializable
public class DbNsfpEntry extends org.snpeff.interval.Variant
DbNSFP database entry: Reference https://sites.google.com/site/jpopgen/dbNSFP Added lazy parsing of key/value pairs- Author:
- lletourn
- See Also:
- Serialized Form
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Constructor Summary
Constructors Constructor Description DbNsfpEntry(DbNsfp dbNsfp, java.lang.String line)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
add(java.lang.String columnName, java.lang.String valuesToAdd)
Add a valueDbNsfpEntry
cloneShallow()
java.lang.String
getVcfInfo(java.lang.String key)
Get data in a VCF INFO field compatible formatboolean
hasValues(java.lang.String allele)
Do we have values for this alleleprotected void
parseChrPosRefAlt()
Parse dbSNFP 'Chr, pos, ref, alt' values from a single lineprotected void
parseKeyValues()
Parse dbSNFP ALL values from a single line and store them in 'values' hashint
parsePosition(java.lang.String posStr)
Parse a string as a 'position'.static java.lang.String[]
splitValuesField(java.lang.String value)
java.lang.String
toString()
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Methods inherited from class org.snpeff.interval.Variant
clone, compareTo, decompose, factory, getAlt, getGenotype, getReference, getVariantType, hashCode, isBnd, isDel, isDup, isElongation, isImprecise, isInDel, isIns, isInterval, isInv, isMixed, isMnp, isNonRef, isShowWarningIfParentDoesNotInclude, isSnp, isStructural, isStructuralHuge, isTruncation, isVariant, lengthChange, netChange, netChange, realignLeft, reverse, setGenotype, setImprecise, setVariantType, toStringEnsembl, toStringOld
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Methods inherited from class org.snpeff.interval.Marker
adjust, apply, applyDel, applyDup, applyIns, applyMixed, codonTable, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isDeferredAnalysis, minus, query, query, readTxt, serializeParse, serializeSave, shouldApply, union, variantEffect, variantEffectNonRef
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Methods inherited from class org.snpeff.interval.Interval
equals, findParent, getChromosome, getChromosomeName, getChromosomeNameOri, getChromosomeNum, getEnd, getGenome, getGenomeName, getId, getStart, getStrand, intersects, intersects, intersects, intersects, intersectSize, isCircular, isSameChromo, isStrandMinus, isStrandPlus, isValid, setChromosomeNameOri, setEnd, setId, setParent, setStart, setStrandMinus, shiftCoordinates, size, toStr, toStringAsciiArt, toStrPos
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Constructor Detail
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DbNsfpEntry
public DbNsfpEntry(DbNsfp dbNsfp, java.lang.String line)
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Method Detail
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splitValuesField
public static java.lang.String[] splitValuesField(java.lang.String value)
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add
public void add(java.lang.String columnName, java.lang.String valuesToAdd)
Add a value
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cloneShallow
public DbNsfpEntry cloneShallow()
- Overrides:
cloneShallow
in classorg.snpeff.interval.Variant
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getVcfInfo
public java.lang.String getVcfInfo(java.lang.String key)
Get data in a VCF INFO field compatible format
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hasValues
public boolean hasValues(java.lang.String allele)
Do we have values for this allele
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parseChrPosRefAlt
protected void parseChrPosRefAlt()
Parse dbSNFP 'Chr, pos, ref, alt' values from a single line
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parseKeyValues
protected void parseKeyValues()
Parse dbSNFP ALL values from a single line and store them in 'values' hashNote: This method is supposed to be a lazy parsing of the key/value pairs, so it DOES NOT store 'chr, pos, ref, alt'. You can use `parseChrPosRefAlt()` for that.
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parsePosition
public int parsePosition(java.lang.String posStr)
Parse a string as a 'position'.
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toString
public java.lang.String toString()
- Overrides:
toString
in classorg.snpeff.interval.Variant
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