com.milaboratory.core.io.sequence.fasta

Class RandomAccessFastaIndex

java.lang.Object

com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex

public final class RandomAccessFastaIndex
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	RandomAccessFastaIndex.IndexBuilder
class	RandomAccessFastaIndex.IndexRecord
static class	RandomAccessFastaIndex.MultipleMatchingRecordsException
static class	RandomAccessFastaIndex.NoSuchRecordException
static class	RandomAccessFastaIndex.StreamIndexBuilder

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_INDEX_STEP Default index step = the most common HDD cluster size
static int	FILE_POSITION_OFFSET Bit-shift that should be applied to encoded file position to get "file position" field.
static String	INDEX_SUFFIX
static int	MAGIC Magic integer written before serialized index
static long	SKIP_MASK Bit mask for encoded file position.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object o)
static long	extractFilePosition(long p) Extracts file position part from value returned by RandomAccessFastaIndex.IndexRecord.queryPosition(long)
static int	extractSkipLetters(long p) Extracts number of letters to skip from value returned by RandomAccessFastaIndex.IndexRecord.queryPosition(long)
int	getIndexStep()
RandomAccessFastaIndex.IndexRecord	getRecordById(String id)
RandomAccessFastaIndex.IndexRecord	getRecordByIdCheck(String id)
RandomAccessFastaIndex.IndexRecord	getRecordByIndex(int i)
int	hashCode()
static RandomAccessFastaIndex	index(Path file) Index fasta file with automatic step selection or load previously created index
static RandomAccessFastaIndex	index(Path file, boolean save) Index fasta file with automatic step selection or load previously created index
static RandomAccessFastaIndex	index(Path file, boolean save, LongProcessReporter reporter) Index fasta file with automatic step selection or load previously created index
static RandomAccessFastaIndex	index(Path file, int indexStep, boolean save) Index fasta file or loads previously created index
static RandomAccessFastaIndex	index(Path file, int indexStep, boolean save, LongProcessReporter reporter) Index fasta file or loads previously created index
static RandomAccessFastaIndex	read(InputStream stream)
int	size()
void	write(OutputStream stream)

Methods inherited from class java.lang.Object

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

Field Detail

INDEX_SUFFIX

public static final String INDEX_SUFFIX

See Also:

Constant Field Values

MAGIC

public static int MAGIC

Magic integer written before serialized index

DEFAULT_INDEX_STEP

public static final int DEFAULT_INDEX_STEP

Default index step = the most common HDD cluster size

See Also:

Constant Field Values

SKIP_MASK

public static final long SKIP_MASK

Bit mask for encoded file position. Masks "letters to skip" field.

See Also:

Constant Field Values

FILE_POSITION_OFFSET

public static final int FILE_POSITION_OFFSET

Bit-shift that should be applied to encoded file position to get "file position" field.

See Also:

Constant Field Values

Method Detail

getIndexStep

public int getIndexStep()

size

public int size()

getRecordByIndex

public RandomAccessFastaIndex.IndexRecord getRecordByIndex(int i)

getRecordById

public RandomAccessFastaIndex.IndexRecord getRecordById(String id)

getRecordByIdCheck

public RandomAccessFastaIndex.IndexRecord getRecordByIdCheck(String id)

write

public void write(OutputStream stream)

read

public static RandomAccessFastaIndex read(InputStream stream)

extractFilePosition

public static long extractFilePosition(long p)

Extracts file position part from value returned by RandomAccessFastaIndex.IndexRecord.queryPosition(long)

Parameters:

p - value returned by RandomAccessFastaIndex.IndexRecord.queryPosition(long)

Returns:

file positions

extractSkipLetters

public static int extractSkipLetters(long p)

Extracts number of letters to skip from value returned by RandomAccessFastaIndex.IndexRecord.queryPosition(long)

Parameters:

p - value returned by RandomAccessFastaIndex.IndexRecord.queryPosition(long)

Returns:

umber of letters to skip

index

public static RandomAccessFastaIndex index(Path file)

Index fasta file with automatic step selection or load previously created index

Parameters:

file - file to index

Returns:

index

index

public static RandomAccessFastaIndex index(Path file,
                           boolean save)

Index fasta file with automatic step selection or load previously created index

Parameters:

file - file to index

save - whether to save index to {input_file_name}.mifdx file

Returns:

index

index

public static RandomAccessFastaIndex index(Path file,
                           boolean save,
                           LongProcessReporter reporter)

Index fasta file with automatic step selection or load previously created index

Parameters:

file - file to index

save - whether to save index to {input_file_name}.mifdx file

reporter - indexing reporter

Returns:

index

index

public static RandomAccessFastaIndex index(Path file,
                           int indexStep,
                           boolean save)

Index fasta file or loads previously created index

Parameters:

file - file to index

indexStep - index step

save - whether to save index to {input_file_name}.mifdx file

Returns:

index

index

public static RandomAccessFastaIndex index(Path file,
                           int indexStep,
                           boolean save,
                           LongProcessReporter reporter)

Index fasta file or loads previously created index

Parameters:

file - file to index

indexStep - index step

save - whether to save index to {input_file_name}.mifdx file

reporter - reporter

Returns:

index

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object