Package org.snpeff.interval
Class Chromosome
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.Chromosome
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,TxtSerializable
Interval for the whole chromosome
If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalid
- 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
Constructors -
Method Summary
Modifier and TypeMethodDescriptionPerform a shallow clonestatic int
Compare chromosome namesint
compareChromoName
(Interval interval) Compare only chromosome's nameboolean
Is this a circular chromosome? See if any exon has evidence of 'circular coordinates'boolean
Is this interval part of a circular chromosome and it spans the 'chromosome zero / chromosome end' line?boolean
isMt()
Is this a mitochondrial chromosome? Note: This is a wild guess just by looking at the nameprotected boolean
Show an error if parent does not include child?static int
Convert to chromosome number (return '0' if it cannot be converted)void
serializeParse
(MarkerSerializer markerSerializer) Parse a line from a serialized fileserializeSave
(MarkerSerializer markerSerializer) Create a string to serialize to a filevoid
setCircular
(boolean circular) void
setLength
(int len) void
setSequence
(String sequenceStr) Set sequence for this chromosomestatic String
simpleName
(String chrName) Simplify chromosome nametoString()
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, 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, 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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Chromosome
public Chromosome() -
Chromosome
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Method Details
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compare
Compare chromosome names -
number
Convert to chromosome number (return '0' if it cannot be converted) -
simpleName
Simplify chromosome name -
cloneShallow
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarker
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compareChromoName
Compare only chromosome's name -
detectCircular
public boolean detectCircular()Is this a circular chromosome? See if any exon has evidence of 'circular coordinates'- Returns:
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getCodonTable
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getDnaSequence
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getSequence
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isCircular
public boolean isCircular()Description copied from class:Interval
Is this interval part of a circular chromosome and it spans the 'chromosome zero / chromosome end' line?- Overrides:
isCircular
in classInterval
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isMt
public boolean isMt()Is this a mitochondrial chromosome? Note: This is a wild guess just by looking at the name -
isShowWarningIfParentDoesNotInclude
protected boolean isShowWarningIfParentDoesNotInclude()Description copied from class:Marker
Show an error if parent does not include child?- Overrides:
isShowWarningIfParentDoesNotInclude
in classMarker
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serializeParse
Parse a line from a serialized file- Specified by:
serializeParse
in interfaceTxtSerializable
- Overrides:
serializeParse
in classMarker
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serializeSave
Description copied from class:Marker
Create a string to serialize to a file- Specified by:
serializeSave
in interfaceTxtSerializable
- Overrides:
serializeSave
in classMarker
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setCircular
public void setCircular(boolean circular) -
setLength
public void setLength(int len) -
setSequence
Set sequence for this chromosome- Parameters:
sequenceStr
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toString
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