org.snpeff.interval.Gtf2Marker

All Implemented Interfaces:: Serializable, Cloneable, Comparable<Interval>, Iterable<KeyValue<String,String>>, TxtSerializable

public class Gtf2Marker extends GffMarker

An interval intended as a mark

Author:

pcingola

See Also:

Serialized Form

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.Marker
type

Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
Constructor Summary

Constructors

Constructor

Description

Gtf2Marker()

Gtf2Marker(Genome genome, String line)

Gtf2Marker(Marker parent, int start, int end, boolean strandMinus, String id)
Method Summary

Modifier and Type

Method

Description

boolean

isMultipleValues(String key)

Does the key have mutiple values

protected void

parseAttributes(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, 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

Constructor Details
- Gtf2Marker
  
  public Gtf2Marker()
- Gtf2Marker
  
  public Gtf2Marker(Genome genome, String line)
- Gtf2Marker
  
  public Gtf2Marker(Marker parent, int start, int end, boolean strandMinus, String id)
Method Details
- isMultipleValues
  
  public boolean isMultipleValues(String key)
  
  Does the key have mutiple values
  
  Overrides:
  
  isMultipleValues in class GffMarker
- parseAttributes
  
  protected void parseAttributes(String attrStr)
  
  Parse attributes
  
  Overrides:
  
  parseAttributes in class GffMarker

Class Gtf2Marker

Field Summary

Fields inherited from class org.snpeff.interval.GffMarker

Fields inherited from class org.snpeff.interval.Marker

Fields inherited from class org.snpeff.interval.Interval

Constructor Summary

Method Summary

Methods inherited from class org.snpeff.interval.GffMarker

Methods inherited from class org.snpeff.interval.Custom

Methods inherited from class org.snpeff.interval.Marker

Methods inherited from class org.snpeff.interval.Interval

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Iterable

Constructor Details

Gtf2Marker

Gtf2Marker

Gtf2Marker

Method Details

isMultipleValues

parseAttributes