Package org.snpeff.interval
Class Cds
- java.lang.Object
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- org.snpeff.interval.Interval
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- org.snpeff.interval.Marker
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- org.snpeff.interval.Cds
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- 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
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Field Summary
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Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
Constructors Constructor Description Cds()
Cds(Transcript parent, int start, int end, boolean strandMinus, java.lang.String id)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Cds
cloneShallow()
Perform a shallow cloneboolean
frameCorrection(int frameCorrection)
Correct coordinates according to frame differencesint
getFrame()
void
serializeParse(MarkerSerializer markerSerializer)
Parse a line from a serialized filejava.lang.String
serializeSave(MarkerSerializer markerSerializer)
Create a string to serialize to a filevoid
setFrame(int frame)
Frame can be {-1, 0, 1, 2}, where '-1' means unknownjava.lang.String
toString()
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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
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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
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Constructor Detail
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Cds
public Cds()
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Cds
public Cds(Transcript parent, int start, int end, boolean strandMinus, java.lang.String id)
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Method Detail
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cloneShallow
public Cds cloneShallow()
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarker
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frameCorrection
public boolean frameCorrection(int frameCorrection)
Correct coordinates according to frame differences- Parameters:
frameCorrection
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getFrame
public int getFrame()
- Specified by:
getFrame
in interfaceMarkerWithFrame
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serializeParse
public void serializeParse(MarkerSerializer markerSerializer)
Description copied from class:Marker
Parse a line from a serialized file- Specified by:
serializeParse
in interfaceTxtSerializable
- Overrides:
serializeParse
in classMarker
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serializeSave
public java.lang.String serializeSave(MarkerSerializer markerSerializer)
Create a string to serialize to a file- Specified by:
serializeSave
in interfaceTxtSerializable
- Overrides:
serializeSave
in classMarker
- Returns:
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setFrame
public void setFrame(int frame)
Frame can be {-1, 0, 1, 2}, where '-1' means unknown- Specified by:
setFrame
in interfaceMarkerWithFrame
- Parameters:
frame
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