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
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Field Summary
Fields inherited from class 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_SEPARATORFields inherited from class Interval
chromosomeNameOri, end, id, parent, start, strandMinus -
Constructor Summary
ConstructorsConstructorDescriptionGtf2Marker(Genome genome, String line) Gtf2Marker(Marker parent, int start, int end, boolean strandMinus, String id) -
Method Summary
Modifier and TypeMethodDescriptionbooleanisMultipleValues(String key) Does the key have mutiple valuesprotected voidparseAttributes(String attrStr) Parse attributesMethods inherited from class 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, toStringMethods inherited from class Custom
cloneShallow, getLabel, getScore, setLabel, setScore, variantEffectMethods inherited from class 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, variantEffectNonRefMethods inherited from class 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, toStrPosMethods inherited from interface 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:
isMultipleValuesin classGffMarker
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parseAttributes
Parse attributes- Overrides:
parseAttributesin classGffMarker
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