Package htsjdk.samtools.reference

Class FastaSequenceIndexEntry

java.lang.Object
htsjdk.samtools.reference.FastaSequenceIndexEntry
public class FastaSequenceIndexEntry extends Object
Hold an individual entry in a fasta sequence index file.

  • Constructor Summary

    Constructors
    Constructor
    Description
    FastaSequenceIndexEntry(String contig, long location, long size, int basesPerLine, int bytesPerLine, int sequenceIndex)
    Create a new entry with the given parameters.

  • Method Summary

    Modifier and Type
    Method
    Description
    boolean
    equals(Object other)
    Compare this index entry to another index entry.
    int
    getBasesPerLine()
    Gets the number of bases in a given line.
    int
    getBytesPerLine()
    How many bytes (bases + whitespace) are consumed by the given line?
    String
    getContig()
    Gets the contig associated with this entry.
    long
    getLocation()
    Gets the location of this contig within the fasta.
    int
    getSequenceIndex()
     
    long
    getSize()
    Gets the size, in bytes, of the data in the contig.
    int
    hashCode()
    In general, we expect one entry per contig, so compute the hash based only on the contig.
    protected void
    setContig(String contig)
    Sometimes contigs need to be adjusted on-the-fly to match sequence dictionary entries.
    String
    toString()
    For debugging.

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait

  • Constructor Details

    • FastaSequenceIndexEntry

      public FastaSequenceIndexEntry(String contig, long location, long size, int basesPerLine, int bytesPerLine, int sequenceIndex)
      Create a new entry with the given parameters.
      Parameters:
      contig - Contig this entry represents.
      location - Location (byte coordinate) in the fasta file.
      size - The number of bases in the contig.
      basesPerLine - How many bases are on each line.
      bytesPerLine - How many bytes are on each line (includes newline characters).

  • Method Details

    • getContig

      public String getContig()
      Gets the contig associated with this entry.
      Returns:
      String representation of the contig.

    • setContig

      protected void setContig(String contig)
      Sometimes contigs need to be adjusted on-the-fly to match sequence dictionary entries. Provide that capability to other classes w/i the package.
      Parameters:
      contig - New value for the contig.

    • getLocation

      public long getLocation()
      Gets the location of this contig within the fasta.
      Returns:
      seek position within the fasta.

    • getSize

      public long getSize()
      Gets the size, in bytes, of the data in the contig.
      Returns:
      size of the contig bases in bytes.

    • getBasesPerLine

      public int getBasesPerLine()
      Gets the number of bases in a given line.
      Returns:
      Number of bases in the fasta line.

    • getBytesPerLine

      public int getBytesPerLine()
      How many bytes (bases + whitespace) are consumed by the given line?
      Returns:
      Number of bytes in a line.

    • getSequenceIndex

      public int getSequenceIndex()

    • toString

      public String toString()
      For debugging. Emit the contents of each contig line.
      Overrides:
      toString in class Object
      Returns:
      A string representation of the contig line.

    • equals

      public boolean equals(Object other)
      Compare this index entry to another index entry.
      Overrides:
      equals in class Object
      Parameters:
      other - another FastaSequenceIndexEntry
      Returns:
      True if each has the same name, location, size, basesPerLine and bytesPerLine

    • hashCode

      public int hashCode()
      In general, we expect one entry per contig, so compute the hash based only on the contig.
      Overrides:
      hashCode in class Object
      Returns:
      A unique hash code representing this object.