Package org.snpeff.interval

Class Cds

java.lang.Object

org.snpeff.interval.Interval

org.snpeff.interval.Marker

org.snpeff.interval.Cds

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<Interval>, MarkerWithFrame, TxtSerializable

public class Cds
extends Marker
implements MarkerWithFrame

CDS: The coding region of a gene, also known as the coding sequence or CDS (from Coding DNA Sequence), is that portion of a gene's DNA or RNA, composed of exons, that codes for protein.

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
Cds()
Cds(Transcript parent, int start, int end, boolean strandMinus, java.lang.String id)

Method Summary

Modifier and Type	Method	Description
Cds	cloneShallow()	Perform a shallow clone
boolean	frameCorrection(int frameCorrection)	Correct coordinates according to frame differences
int	getFrame()
void	serializeParse(MarkerSerializer markerSerializer)	Parse a line from a serialized file
java.lang.String	serializeSave(MarkerSerializer markerSerializer)	Create a string to serialize to a file
void	setFrame(int frame)	Frame can be {-1, 0, 1, 2}, where '-1' means unknown
java.lang.String	toString()

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, shouldApply, union, variantEffect, 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

Constructor Detail

Cds

public Cds()

Cds

public Cds(Transcript parent,
           int start,
           int end,
           boolean strandMinus,
           java.lang.String id)

Method Detail

cloneShallow

public Cds cloneShallow()

Description copied from class: Marker

Perform a shallow clone

Overrides:

cloneShallow in class Marker

frameCorrection

public boolean frameCorrection(int frameCorrection)

Correct coordinates according to frame differences

Parameters:

frameCorrection -

getFrame

public int getFrame()

Specified by:

getFrame in interface MarkerWithFrame

serializeParse

public void serializeParse(MarkerSerializer markerSerializer)

Description copied from class: Marker

Parse a line from a serialized file

Specified by:

serializeParse in interface TxtSerializable

Overrides:

serializeParse in class Marker

serializeSave

public java.lang.String serializeSave(MarkerSerializer markerSerializer)

Create a string to serialize to a file

Specified by:

serializeSave in interface TxtSerializable

Overrides:

serializeSave in class Marker

Returns:

setFrame

public void setFrame(int frame)

Frame can be {-1, 0, 1, 2}, where '-1' means unknown

Specified by:

setFrame in interface MarkerWithFrame

Parameters:

frame -

toString

public java.lang.String toString()

Overrides:

toString in class Marker