Package org.snpeff.interval

Class Chromosome

java.lang.Object

org.snpeff.interval.Interval

org.snpeff.interval.Marker

org.snpeff.interval.Chromosome

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

Field Summary

Fields inherited from class org.snpeff.interval.Marker

type

Fields inherited from class org.snpeff.interval.Interval

chromosomeNameOri, end, id, parent, start, strandMinus

Constructor Summary

Constructors

Constructor	Description
Chromosome()
Chromosome(Genome parent, int start, int end, java.lang.String id)

Method Summary

Modifier and Type	Method	Description
Chromosome	cloneShallow()	Perform a shallow clone
static int	compare(java.lang.String chr1, java.lang.String chr2)	Compare chromosome names
int	compareChromoName(Interval interval)	Compare only chromosome's name
boolean	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 name
protected 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 file
java.lang.String	serializeSave(MarkerSerializer markerSerializer)	Create a string to serialize to a file
void	setCircular(boolean circular)
void	setLength(int len)
void	setSequence(java.lang.String sequenceStr)	Set sequence for this chromosome
static java.lang.String	simpleName(java.lang.String chrName)	Simplify chromosome name
java.lang.String	toString()

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

Methods inherited from class java.lang.Object

equals, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Chromosome

public Chromosome()

Chromosome

public Chromosome(Genome parent,
                  int start,
                  int end,
                  java.lang.String id)

Method Detail

compare

public static int compare(java.lang.String chr1,
                          java.lang.String chr2)

Compare chromosome names

number

public static int number(java.lang.String chrName)

Convert to chromosome number (return '0' if it cannot be converted)

simpleName

public static java.lang.String simpleName(java.lang.String chrName)

Simplify chromosome name

cloneShallow

public Chromosome cloneShallow()

Description copied from class: Marker

Perform a shallow clone

Overrides:

cloneShallow in class Marker

compareChromoName

public int compareChromoName(Interval interval)

Compare only chromosome's name

detectCircular

public boolean detectCircular()

Is this a circular chromosome? See if any exon has evidence of 'circular coordinates'

Returns:

getCodonTable

public CodonTable getCodonTable()

getDnaSequence

public DnaSequence getDnaSequence()

getSequence

public java.lang.String getSequence()

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 class Interval

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 class Marker

serializeParse

public void serializeParse(MarkerSerializer markerSerializer)

Parse a line from a serialized file

Specified by:

serializeParse in interface TxtSerializable

Overrides:

serializeParse in class Marker

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 interface TxtSerializable

Overrides:

serializeSave in class Marker

setCircular

public void setCircular(boolean circular)

setLength

public void setLength(int len)

setSequence

public void setSequence(java.lang.String sequenceStr)

Set sequence for this chromosome

Parameters:

sequenceStr -

toString

public java.lang.String toString()

Overrides:

toString in class Marker