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 -
Constructor Summary
ConstructorsConstructorDescriptionCds()Cds(Transcript parent, int start, int end, boolean strandMinus, String id) -
Method Summary
Modifier and TypeMethodDescriptionPerform a shallow clonebooleanframeCorrection(int frameCorrection) Correct coordinates according to frame differencesintgetFrame()voidserializeParse(MarkerSerializer markerSerializer) Parse a line from a serialized fileserializeSave(MarkerSerializer markerSerializer) Create a string to serialize to a filevoidsetFrame(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, variantEffectNonRefMethods 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:MarkerPerform a shallow clone- Overrides:
cloneShallowin 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:
getFramein interfaceMarkerWithFrame
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serializeParse
Description copied from class:MarkerParse a line from a serialized file- Specified by:
serializeParsein interfaceTxtSerializable- Overrides:
serializeParsein classMarker
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serializeSave
Create a string to serialize to a file- Specified by:
serializeSavein interfaceTxtSerializable- Overrides:
serializeSavein 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:
setFramein interfaceMarkerWithFrame- Parameters:
frame-
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toString
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