Package org.snpeff.interval
Class Cds
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.Cds
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,MarkerWithFrame
,TxtSerializable
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:
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Field Summary
Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
ConstructorsConstructorDescriptionCds()
Cds
(Transcript parent, int start, int end, boolean strandMinus, String id) -
Method Summary
Modifier and TypeMethodDescriptionPerform a shallow cloneboolean
frameCorrection
(int frameCorrection) Correct coordinates according to frame differencesint
getFrame()
void
serializeParse
(MarkerSerializer markerSerializer) Parse a line from a serialized fileserializeSave
(MarkerSerializer markerSerializer) Create a string to serialize to a filevoid
setFrame
(int frame) Frame can be {-1, 0, 1, 2}, where '-1' means unknowntoString()
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
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Constructor Details
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Cds
public Cds() -
Cds
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Method Details
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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
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
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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toString
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