Package org.snpeff.interval

Class GffMarker

java.lang.Object

org.snpeff.interval.Interval

org.snpeff.interval.Marker

org.snpeff.interval.Custom

org.snpeff.interval.GffMarker

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<Interval>, java.lang.Iterable<KeyValue<java.lang.String,java.lang.String>>, TxtSerializable

Direct Known Subclasses:

Gtf2Marker

public class GffMarker
extends Custom

An interval intended as a mark

Author:

pcingola

See Also:

Serialized Form

Field Summary

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
GffMarker()
GffMarker(Genome genome, java.lang.String line)
GffMarker(Marker parent, int start, int end, boolean strandMinus, java.lang.String id)

Method Summary

Modifier and Type	Method	Description
void	add(java.lang.String key, java.lang.String value)	Add key value pair
static boolean	canParseLine(java.lang.String line)	Can this line (form a GFF file) be parsed? Note: Returns false for headers, empty lines and lines having less number of fields than expected
java.lang.String	getAttr(java.lang.String key)
BioType	getBiotype()
protected java.lang.String	getBioType()
protected BioType	getBiotypeGeneric()
int	getFrame()
BioType	getGeneBiotype()
java.lang.String	getGeneId()
java.lang.String	getGeneName()
java.lang.String	getGffParentId(boolean doNotRecurse)
java.lang.String[]	getGffParentIds()	Parent can have multiple, comma separated entries
GffType	getGffType()
BioType	getTranscriptBiotype()
java.lang.String	getTranscriptId()
java.lang.String	getTranscriptVersion()
boolean	hasAnnotations()	When annotating a VCF file, add fields from this GFF
boolean	hasAttr(java.lang.String key)
boolean	isProteingCoding()	Is biotType considered 'protein coding'?
java.util.Iterator<KeyValue<java.lang.String,java.lang.String>>	iterator()
protected void	parse(Genome genome, java.lang.String line)	Parse an entry (line) from a GFF file
protected void	parseAttributes(java.lang.String attrStr)	Parse attributes (key-value pairs) from a line in a GFF file
protected java.lang.String	parseId()	Obtain or create an ID
java.lang.String	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 Detail

GffMarker

public GffMarker()

GffMarker

public GffMarker(Genome genome,
                 java.lang.String line)

GffMarker

public GffMarker(Marker parent,
                 int start,
                 int end,
                 boolean strandMinus,
                 java.lang.String id)

Method Detail

canParseLine

public static boolean canParseLine(java.lang.String line)

Can this line (form a GFF file) be parsed? Note: Returns false for headers, empty lines and lines having less number of fields than expected

add

public void add(java.lang.String key,
                java.lang.String value)

Add key value pair

getAttr

public java.lang.String getAttr(java.lang.String key)

getBiotype

public BioType getBiotype()

getBioType

protected java.lang.String getBioType()

getBiotypeGeneric

protected BioType getBiotypeGeneric()

getFrame

public int getFrame()

getGeneBiotype

public BioType getGeneBiotype()

getGeneId

public java.lang.String getGeneId()

getGeneName

public java.lang.String getGeneName()

getGffParentId

public java.lang.String getGffParentId(boolean doNotRecurse)

getGffParentIds

public java.lang.String[] getGffParentIds()

Parent can have multiple, comma separated entries

getGffType

public GffType getGffType()

getTranscriptBiotype

public BioType getTranscriptBiotype()

getTranscriptId

public java.lang.String getTranscriptId()

getTranscriptVersion

public java.lang.String getTranscriptVersion()

hasAnnotations

public boolean hasAnnotations()

When annotating a VCF file, add fields from this GFF

Overrides:

hasAnnotations in class Custom

hasAttr

public boolean hasAttr(java.lang.String key)

isProteingCoding

public boolean isProteingCoding()

Is biotType considered 'protein coding'?

iterator

public java.util.Iterator<KeyValue<java.lang.String,java.lang.String>> iterator()

Specified by:

iterator in interface java.lang.Iterable<KeyValue<java.lang.String,java.lang.String>>

Overrides:

iterator in class Custom

parse

protected void parse(Genome genome,
                     java.lang.String line)

Parse an entry (line) from a GFF file

parseAttributes

protected void parseAttributes(java.lang.String attrStr)

Parse attributes (key-value pairs) from a line in a GFF file

parseId

protected java.lang.String parseId()

Obtain or create an ID

toString

public java.lang.String toString()

Overrides:

toString in class Custom