Package VCF
Class PositionMeta
- java.lang.Object
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- VCF.PositionMeta
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public class PositionMeta extends java.lang.Object
Represents the meta data for a position
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Constructor Summary
Constructors Constructor Description PositionMeta(java.lang.String meta)
Constructor from a string representing the meta data (tab delimited)PositionMeta(java.lang.String[] parts)
Constructor from an array of strings representing the meta data
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
equals(java.lang.Object o)
Are two positions equal - based only on chromosome and positionjava.lang.String[]
getAlt()
Get the alternative allelesjava.lang.String
getChrom()
Get the chromosomejava.lang.String
getFilter()
Get the filtersjava.util.List<java.lang.String>
getFormat()
Get a list of formatsjava.lang.String
getID()
Get the IDjava.lang.String
getInfo()
Get the infojava.lang.String
getPosition()
Get the position (within a chromosome) of the positionjava.lang.String
getQual()
Get the qualityjava.lang.String
getRef()
Get the reference alleleint
hashCode()
java.lang.String
toString()
Gets a string representing just the chromosome and the position of the position.java.lang.String
toText()
Get a string for all the meta data for the position
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Constructor Detail
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PositionMeta
public PositionMeta(java.lang.String meta)
Constructor from a string representing the meta data (tab delimited)- Parameters:
meta
- String representing the meta data
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PositionMeta
public PositionMeta(java.lang.String[] parts)
Constructor from an array of strings representing the meta data- Parameters:
parts
- Array of strings representing the meta data
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Method Detail
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toString
public java.lang.String toString()
Gets a string representing just the chromosome and the position of the position.- Overrides:
toString
in classjava.lang.Object
- Returns:
- The string
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toText
public java.lang.String toText()
Get a string for all the meta data for the position- Returns:
- The string
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getChrom
public java.lang.String getChrom()
Get the chromosome- Returns:
- The chromosome
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getPosition
public java.lang.String getPosition()
Get the position (within a chromosome) of the position- Returns:
- The position
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getID
public java.lang.String getID()
Get the ID- Returns:
- The ID
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getRef
public java.lang.String getRef()
Get the reference allele- Returns:
- The reference allele
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getAlt
public java.lang.String[] getAlt()
Get the alternative alleles- Returns:
- Array of the alternative alleles
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getQual
public java.lang.String getQual()
Get the quality- Returns:
- The quality
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getFilter
public java.lang.String getFilter()
Get the filters- Returns:
- The filters
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getInfo
public java.lang.String getInfo()
Get the info- Returns:
- The info
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getFormat
public java.util.List<java.lang.String> getFormat()
Get a list of formats- Returns:
- List of formats
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equals
public boolean equals(java.lang.Object o)
Are two positions equal - based only on chromosome and position- Overrides:
equals
in classjava.lang.Object
- Parameters:
o
- The position to compare to- Returns:
- Whether the two positions are equal
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hashCode
public int hashCode()
- Overrides:
hashCode
in classjava.lang.Object
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