Package VCF

Class PositionMeta


  • public class PositionMeta
    extends java.lang.Object
    Represents the meta data for a position
    • 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
    • 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 position
      java.lang.String[] getAlt()
      Get the alternative alleles
      java.lang.String getChrom()
      Get the chromosome
      java.lang.String getFilter()
      Get the filters
      java.util.List<java.lang.String> getFormat()
      Get a list of formats
      java.lang.String getID()
      Get the ID
      java.lang.String getInfo()
      Get the info
      java.lang.String getPosition()
      Get the position (within a chromosome) of the position
      java.lang.String getQual()
      Get the quality
      java.lang.String getRef()
      Get the reference allele
      int 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
      • Methods inherited from class java.lang.Object

        getClass, notify, notifyAll, wait, wait, wait
    • Constructor Detail

      • PositionMeta

        public PositionMeta​(java.lang.String meta)
        Constructor from a string representing the meta data (tab delimited)
        Parameters:
        meta - String representing the meta data
      • 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
    • Method Detail

      • toString

        public java.lang.String toString()
        Gets a string representing just the chromosome and the position of the position.
        Overrides:
        toString in class java.lang.Object
        Returns:
        The string
      • toText

        public java.lang.String toText()
        Get a string for all the meta data for the position
        Returns:
        The string
      • getChrom

        public java.lang.String getChrom()
        Get the chromosome
        Returns:
        The chromosome
      • getPosition

        public java.lang.String getPosition()
        Get the position (within a chromosome) of the position
        Returns:
        The position
      • getID

        public java.lang.String getID()
        Get the ID
        Returns:
        The ID
      • getRef

        public java.lang.String getRef()
        Get the reference allele
        Returns:
        The reference allele
      • getAlt

        public java.lang.String[] getAlt()
        Get the alternative alleles
        Returns:
        Array of the alternative alleles
      • getQual

        public java.lang.String getQual()
        Get the quality
        Returns:
        The quality
      • getFilter

        public java.lang.String getFilter()
        Get the filters
        Returns:
        The filters
      • getInfo

        public java.lang.String getInfo()
        Get the info
        Returns:
        The info
      • getFormat

        public java.util.List<java.lang.String> getFormat()
        Get a list of formats
        Returns:
        List of formats
      • equals

        public boolean equals​(java.lang.Object o)
        Are two positions equal - based only on chromosome and position
        Overrides:
        equals in class java.lang.Object
        Parameters:
        o - The position to compare to
        Returns:
        Whether the two positions are equal
      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class java.lang.Object