htsjdk.samtools.reference

Class FastaSequenceIndex

java.lang.Object

htsjdk.samtools.reference.FastaSequenceIndex

All Implemented Interfaces:

java.lang.Iterable<htsjdk.samtools.reference.FastaSequenceIndexEntry>

public class FastaSequenceIndex
extends java.lang.Object
implements java.lang.Iterable<htsjdk.samtools.reference.FastaSequenceIndexEntry>

Reads a fasta index file (.fai), as generated by `samtools faidx`.

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	FastaSequenceIndex() Empty, protected constructor for unit testing.
	FastaSequenceIndex(java.io.File indexFile) Build a sequence index from the specified file.

Method Summary

Methods

Modifier and Type	Method and Description
protected void	add(htsjdk.samtools.reference.FastaSequenceIndexEntry indexEntry) Add a new index entry to the list.
boolean	equals(java.lang.Object other) Compare two FastaSequenceIndex objects for equality.
htsjdk.samtools.reference.FastaSequenceIndexEntry	getIndexEntry(java.lang.String contigName) Retrieve the index entry associated with the given contig.
boolean	hasIndexEntry(java.lang.String contigName) Does the given contig name have a corresponding entry?
java.util.Iterator<htsjdk.samtools.reference.FastaSequenceIndexEntry>	iterator() Creates an iterator which can iterate through all entries in a fasta index.
protected void	rename(htsjdk.samtools.reference.FastaSequenceIndexEntry entry, java.lang.String newName) Renames the existing index entry to the new index entry with the specified name.
int	size() Returns the number of elements in the index.

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

FastaSequenceIndex

public FastaSequenceIndex(java.io.File indexFile)

Build a sequence index from the specified file.

Parameters:

indexFile - File to open.

Throws:

java.io.FileNotFoundException - if the index file cannot be found.

FastaSequenceIndex

protected FastaSequenceIndex()

Empty, protected constructor for unit testing.

Method Detail

add

protected void add(htsjdk.samtools.reference.FastaSequenceIndexEntry indexEntry)

Add a new index entry to the list. Protected for unit testing.

Parameters:

indexEntry - New index entry to add.

rename

protected void rename(htsjdk.samtools.reference.FastaSequenceIndexEntry entry,
          java.lang.String newName)

Renames the existing index entry to the new index entry with the specified name.

Parameters:

entry - entry to update.

newName - New name for the index entry.

equals

public boolean equals(java.lang.Object other)

Compare two FastaSequenceIndex objects for equality.

Overrides:

equals in class java.lang.Object

Parameters:

other - Another FastaSequenceIndex to compare

Returns:

True if index has the same entries as other instance, in the same order

hasIndexEntry

public boolean hasIndexEntry(java.lang.String contigName)

Does the given contig name have a corresponding entry?

Parameters:

contigName - The contig name for which to search.

Returns:

True if contig name is present; false otherwise.

getIndexEntry

public htsjdk.samtools.reference.FastaSequenceIndexEntry getIndexEntry(java.lang.String contigName)

Retrieve the index entry associated with the given contig.

Parameters:

contigName - Name of the contig for which to search.

Returns:

Index entry associated with the given contig.

Throws:

SAMException - if the associated index entry can't be found.

iterator

public java.util.Iterator<htsjdk.samtools.reference.FastaSequenceIndexEntry> iterator()

Creates an iterator which can iterate through all entries in a fasta index.

Specified by:

iterator in interface java.lang.Iterable<htsjdk.samtools.reference.FastaSequenceIndexEntry>

Returns:

iterator over all fasta index entries.

size

public int size()

Returns the number of elements in the index.

Returns:

Number of elements in the index.