Package org.snpeff.interval
Class Gtf2Marker
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.Custom
org.snpeff.interval.GffMarker
org.snpeff.interval.Gtf2Marker
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,Iterable<KeyValue<String,
,String>> TxtSerializable
An interval intended as a mark
- Author:
- pcingola
- See Also:
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Field Summary
Fields inherited from class org.snpeff.interval.GffMarker
FIELD_BIOTYPE, FIELD_DB_XREF, FIELD_EXON_ID, FIELD_GENE, FIELD_GENE_BIOTYPE, FIELD_GENE_ID, FIELD_GENE_NAME, FIELD_GENE_TYPE, FIELD_ID, FIELD_NAME, FIELD_NAMEU, FIELD_PARENT, FIELD_PROTEIN_ID, FIELD_TAG, FIELD_TRANSCRIPT_ID, FIELD_TRANSCRIPT_TSL, FIELD_TRANSCRIPT_VERSION, MULTIPLE_VALUES_SEPARATOR
Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
ConstructorsConstructorDescriptionGtf2Marker
(Genome genome, String line) Gtf2Marker
(Marker parent, int start, int end, boolean strandMinus, String id) -
Method Summary
Modifier and TypeMethodDescriptionboolean
isMultipleValues
(String key) Does the key have mutiple valuesprotected void
parseAttributes
(String attrStr) Parse attributesMethods inherited from class org.snpeff.interval.GffMarker
add, canParseLine, getAttr, getBiotype, getBioType, getBiotypeGeneric, getFrame, getGeneBiotype, getGeneId, getGeneName, getGffParentId, getGffParentIds, getGffType, getProteinId, getTags, getTranscriptBiotype, getTranscriptId, getTranscriptTsl, getTranscriptVersion, hasAnnotations, hasAttr, isProteingCoding, iterator, parse, parseId, toString
Methods inherited from class org.snpeff.interval.Custom
cloneShallow, getLabel, getScore, setLabel, setScore, variantEffect
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
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
Methods inherited from class java.lang.Object
equals, finalize, getClass, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Constructor Details
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Gtf2Marker
public Gtf2Marker() -
Gtf2Marker
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Gtf2Marker
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Method Details
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isMultipleValues
Does the key have mutiple values- Overrides:
isMultipleValues
in classGffMarker
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parseAttributes
Parse attributes- Overrides:
parseAttributes
in classGffMarker
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