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)
CompactACGT	getSequence(String chr, int start, int end, boolean isReverse)
int	getSequenceLength(String chr)
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:

getSequenceLength

public int getSequenceLength(String chr)

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

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)