Package org.snpeff.interval
Class Chromosome
- 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.Chromosome
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
,TxtSerializable
public class Chromosome extends Marker
Interval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalid- 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 Chromosome()
Chromosome(Genome parent, int start, int end, java.lang.String id)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description Chromosome
cloneShallow()
Perform a shallow clonestatic int
compare(java.lang.String chr1, java.lang.String chr2)
Compare chromosome namesint
compareChromoName(Interval interval)
Compare only chromosome's nameboolean
detectCircular()
Is this a circular chromosome? See if any exon has evidence of 'circular coordinates'CodonTable
getCodonTable()
DnaSequence
getDnaSequence()
java.lang.String
getSequence()
boolean
isCircular()
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
isShowWarningIfParentDoesNotInclude()
Show an error if parent does not include child?static int
number(java.lang.String chrName)
Convert to chromosome number (return '0' if it cannot be converted)void
serializeParse(MarkerSerializer markerSerializer)
Parse a line from a serialized filejava.lang.String
serializeSave(MarkerSerializer markerSerializer)
Create a string to serialize to a filevoid
setCircular(boolean circular)
void
setLength(int len)
void
setSequence(java.lang.String sequenceStr)
Set sequence for this chromosomestatic java.lang.String
simpleName(java.lang.String chrName)
Simplify chromosome namejava.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, 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, 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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Chromosome
public Chromosome()
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Chromosome
public Chromosome(Genome parent, int start, int end, java.lang.String id)
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Method Detail
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compare
public static int compare(java.lang.String chr1, java.lang.String chr2)
Compare chromosome names
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number
public static int number(java.lang.String chrName)
Convert to chromosome number (return '0' if it cannot be converted)
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simpleName
public static java.lang.String simpleName(java.lang.String chrName)
Simplify chromosome name
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cloneShallow
public Chromosome cloneShallow()
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classMarker
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compareChromoName
public int compareChromoName(Interval interval)
Compare only chromosome's name
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detectCircular
public boolean detectCircular()
Is this a circular chromosome? See if any exon has evidence of 'circular coordinates'- Returns:
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getCodonTable
public CodonTable getCodonTable()
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getDnaSequence
public DnaSequence getDnaSequence()
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getSequence
public java.lang.String 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
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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
public void serializeParse(MarkerSerializer markerSerializer)
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)
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)
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setLength
public void setLength(int len)
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setSequence
public void setSequence(java.lang.String sequenceStr)
Set sequence for this chromosome- Parameters:
sequenceStr
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