Package org.snpeff.interval
Class Gtf2Marker
- 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.Custom
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- org.snpeff.interval.GffMarker
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- org.snpeff.interval.Gtf2Marker
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,java.lang.Iterable<KeyValue<java.lang.String,java.lang.String>>
,TxtSerializable
public class Gtf2Marker extends GffMarker
An interval intended as a mark- Author:
- pcingola
- See Also:
- Serialized Form
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Field Summary
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Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
Constructors Constructor Description Gtf2Marker()
Gtf2Marker(Genome genome, java.lang.String line)
Gtf2Marker(Marker parent, int start, int end, boolean strandMinus, java.lang.String id)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
parseAttributes(java.lang.String attrStr)
Parse attributes-
Methods inherited from class org.snpeff.interval.GffMarker
add, canParseLine, getAttr, getBiotype, getBioType, getBiotypeGeneric, getFrame, getGeneBiotype, getGeneId, getGeneName, getGffParentId, getGffParentIds, getGffType, getTranscriptBiotype, getTranscriptId, getTranscriptVersion, hasAnnotations, hasAttr, isProteingCoding, iterator, parse, parseId, toString
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Methods inherited from class org.snpeff.interval.Custom
cloneShallow, getLabel, getScore, setLabel, setScore, variantEffect
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Methods inherited from class org.snpeff.interval.Marker
adjust, apply, applyDel, applyDup, applyIns, applyMixed, clone, codonTable, compareTo, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isDeferredAnalysis, isShowWarningIfParentDoesNotInclude, minus, query, query, readTxt, serializeParse, serializeSave, shouldApply, union, 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, hashCode, 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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Method Detail
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parseAttributes
protected void parseAttributes(java.lang.String attrStr)
Parse attributes- Overrides:
parseAttributes
in classGffMarker
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