org.utgenome.format.fasta
Class CompactFASTA

java.lang.Object
  org.utgenome.format.fasta.CompactFASTA

public class CompactFASTA
extends Object

CompactFASTA is a packed FASTA file, supporting random accesses to sub sequences of a specified chromosome.

Author:

leo

Nested Class Summary

class	CompactFASTA.OnDiskAccess
class	CompactFASTA.OnMemoryBuffer
static interface	CompactFASTA.PacFileAccess

Field Summary

static String	PAC_FILE_SUFFIX
static String	PAC_INDEX_FILE_SUFFIX
static String	PAC_N_FILE_SUFFIX

Constructor Summary

CompactFASTA(String fastaFile)

Method Summary

void	close()
boolean	containsChr(String chr) Test the specified chromosome name is in this FASTA
Set<String>	getChrSet() Get the set of chromosome names
GenomeSequence	getSequence(String chr)
GenomeSequence	getSequence(String chr, int start)
CompactACGT	getSequence(String chr, int start, int end) Retrieves a genome sequence of the specified range [start, end)
static CompactFASTA	loadIntoMemory(String fastaFilePrefix)
static String	pickSequenceName(String descriptionLine)

Methods inherited from class java.lang.Object

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

Field Detail

PAC_FILE_SUFFIX

public static final String PAC_FILE_SUFFIX

See Also:

Constant Field Values

PAC_N_FILE_SUFFIX

public static final String PAC_N_FILE_SUFFIX

See Also:

Constant Field Values

PAC_INDEX_FILE_SUFFIX

public static final String PAC_INDEX_FILE_SUFFIX

See Also:

Constant Field Values

Constructor Detail

CompactFASTA

public CompactFASTA(String fastaFile)
             throws org.xerial.core.XerialException,
                    IOException

Parameters:

fastaFilePrefix -

Throws:

org.xerial.core.XerialException

IOException

Method Detail

getChrSet

public Set<String> getChrSet()

Get the set of chromosome names

Returns:

containsChr

public boolean containsChr(String chr)

Test the specified chromosome name is in this FASTA

Parameters:

chr -

Returns:

loadIntoMemory

public static CompactFASTA loadIntoMemory(String fastaFilePrefix)
                                   throws org.xerial.core.XerialException,
                                          IOException

Throws:

org.xerial.core.XerialException

IOException

close

public void close()
           throws IOException

Throws:

IOException

getSequence

public CompactACGT getSequence(String chr,
                               int start,
                               int end)
                        throws IOException,
                               UTGBException

Retrieves a genome sequence of the specified range [start, end)

Parameters:

chr - sequence name

start - start position on the genome (0-origin)

end - end position on genome (0-origin, exclusive)

Returns:

genome sequence of the specified range, or null if no entry found for the given sequence name

Throws:

IOException

UTGBException

getSequence

public GenomeSequence getSequence(String chr,
                                  int start)
                           throws IOException,
                                  UTGBException

Throws:

IOException

UTGBException

getSequence

public GenomeSequence getSequence(String chr)
                           throws IOException,
                                  UTGBException

Throws:

IOException

UTGBException

pickSequenceName

public static String pickSequenceName(String descriptionLine)