edu.cornell.med.icb.goby.alignments
Class ConcatAlignmentReader

java.lang.Object
  edu.cornell.med.icb.goby.alignments.AbstractAlignmentReader
      edu.cornell.med.icb.goby.alignments.AbstractConcatAlignmentReader
          edu.cornell.med.icb.goby.alignments.ConcatAlignmentReader

All Implemented Interfaces:

Closeable, Iterable<Alignments.AlignmentEntry>, Iterator<Alignments.AlignmentEntry>

Direct Known Subclasses:

ConcatSortedAlignmentReader

public class ConcatAlignmentReader
extends AbstractConcatAlignmentReader

Read over a set of alignments. This aligner concatenates entries from the input alignment. Reference sequences must match exactly across the input alignments. Query are assumed to be entirely distinct and will be treated as independent observations (e.g., reads from multiple independent samples). To this effect, alignment entries read from different input basenames, which would otherwise share an identical query index, are renumbered with distinct query indices.

Author:

Fabien Campagne Date: May 20, 2009 Time: 5:06:01 PM

Field Summary

protected int	activeIndex
protected boolean	adjustQueryIndices
protected AlignmentReader[]	readers
protected IntSet	readersWithMoreEntries

Fields inherited from class edu.cornell.med.icb.goby.alignments.AbstractConcatAlignmentReader

adjustSampleIndices

Fields inherited from class edu.cornell.med.icb.goby.alignments.AbstractAlignmentReader

alignerName, alignerVersion, constantLength, constantQueryLengths, largestQueryIndex, numberOfQueries, numberOfTargets, queryIdentifiers, sampleBasenames, smallestQueryIndex, targetIdentifiers, targetLengths

Constructor Summary

ConcatAlignmentReader(AlignmentReaderFactory alignmentReaderFactory, boolean adjustQueryIndices, int startReferenceIndex, int startPosition, int endReferenceIndex, int endPosition, String... basenames)
Construct an alignment reader over a set of alignments.

ConcatAlignmentReader(AlignmentReaderFactory alignmentReaderFactory, boolean adjustQueryIndices, String... basenames)
Construct an alignment reader over a set of alignments.

ConcatAlignmentReader(boolean adjustQueryIndices, String... basenames)
Construct an alignment reader over a set of alignments.

ConcatAlignmentReader(String... basenames)
Construct an alignment reader over a set of alignments.

Method Summary

void	close() Close the underlying readers.
String	getAlignerName()
String	getAlignerVersion()
ObjectList<ReferenceLocation>	getLocations(int modulo)
int	getNumberOfAlignedReads()
Properties	getStatistics() Obtain statistics about this alignment as a Java property instance.
boolean	hasNext() Returns true if the input has more entries.
Iterator<Alignments.AlignmentEntry>	iterator() Iterator over alignment entries.
protected int	mergedQueryIndex(int queryIndex)
Alignments.AlignmentEntry	next() Returns the next alignment entry from the input stream.
void	readHeader() Read the header of this alignment.
void	remove() This operation is not supported by this iterator.
void	setAdjustQueryIndices(boolean adjustQueryIndices) Deprecated.

Methods inherited from class edu.cornell.med.icb.goby.alignments.AbstractConcatAlignmentReader

setAdjustSampleIndices

Methods inherited from class edu.cornell.med.icb.goby.alignments.AbstractAlignmentReader

getBasename, getBasenames, getLargestSplitQueryIndex, getNumberOfQueries, getNumberOfTargets, getQueryIdentifiers, getSampleBasename, getSmallestSplitQueryIndex, getTargetIdentifiers, getTargetLength, getTargetLength, isConstantQueryLengths, isHeaderLoaded, setHeaderLoaded

Methods inherited from class java.lang.Object

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

Field Detail

readers

protected final AlignmentReader[] readers

readersWithMoreEntries

protected final IntSet readersWithMoreEntries

activeIndex

protected int activeIndex

adjustQueryIndices

protected boolean adjustQueryIndices

Constructor Detail

ConcatAlignmentReader

public ConcatAlignmentReader(String... basenames)
                      throws IOException

Construct an alignment reader over a set of alignments. Please note that the constructor access the header of each individual alignment to check reference sequence identity and obtain the number of queries in each input alignment. This version uses adjustQueryIndices as the default true.

Parameters:

basenames - Basenames of the individual alignemnts to combine.

Throws:

IOException - If an error occurs reading the header of the alignments.

ConcatAlignmentReader

public ConcatAlignmentReader(boolean adjustQueryIndices,
                             String... basenames)
                      throws IOException

Construct an alignment reader over a set of alignments. Please note that the constructor access the header of each individual alignment to check reference sequence identity and obtain the number of queries in each input alignment. This version uses adjustQueryIndices as the default true.

Parameters:

basenames - Basenames of the individual alignemnts to combine.

adjustQueryIndices - if we need to adjustQueryIndices

Throws:

IOException - If an error occurs reading the header of the alignments.

ConcatAlignmentReader

public ConcatAlignmentReader(AlignmentReaderFactory alignmentReaderFactory,
                             boolean adjustQueryIndices,
                             String... basenames)
                      throws IOException

Construct an alignment reader over a set of alignments. Please note that the constructor access the header of each individual alignment to check reference sequence identity and obtain the number of queries in each input alignment.

Parameters:

alignmentReaderFactory - Factory to create new alignmentReaders.

adjustQueryIndices - if we need to adjustQueryIndices

basenames - Basenames of the individual alignemnts to combine.

Throws:

IOException - If an error occurs reading the header of the alignments.

ConcatAlignmentReader

public ConcatAlignmentReader(AlignmentReaderFactory alignmentReaderFactory,
                             boolean adjustQueryIndices,
                             int startReferenceIndex,
                             int startPosition,
                             int endReferenceIndex,
                             int endPosition,
                             String... basenames)
                      throws IOException

Construct an alignment reader over a set of alignments. Please note that the constructor access the header of each individual alignment to check reference sequence identity and obtain the number of queries in each input alignment.

Parameters:

alignmentReaderFactory - Factory to create new alignmentReaders.

adjustQueryIndices - if we need to adjustQueryIndices

startReferenceIndex - Index of the reference for the start position.

startPosition - Position on the reference for the start position.

endReferenceIndex - Index of the reference for the end position.

endPosition - Position on the reference for the end position.

basenames - Basenames of the individual alignemnts to combine.

Throws:

IOException - If an error occurs reading the header of the alignments.

Method Detail

readHeader

public final void readHeader()
                      throws IOException

Read the header of this alignment.

Specified by:

readHeader in class AbstractAlignmentReader

Throws:

IOException - If an error occurs.

mergedQueryIndex

protected int mergedQueryIndex(int queryIndex)

iterator

public final Iterator<Alignments.AlignmentEntry> iterator()

Iterator over alignment entries.

Returns:

an iterator over the alignment entries.

hasNext

public boolean hasNext()

Returns true if the input has more entries.

Returns:

true if the input has more entries, false otherwise.

getAlignerName

public String getAlignerName()

Overrides:

getAlignerName in class AbstractAlignmentReader

Returns:

The list of aligner names with duplicates removed

getAlignerVersion

public String getAlignerVersion()

Overrides:

getAlignerVersion in class AbstractAlignmentReader

Returns:

The list of aligner versions with duplicates removed

next

public Alignments.AlignmentEntry next()

Returns the next alignment entry from the input stream.

Returns:

the alignment read entry from the input stream.

remove

public void remove()

This operation is not supported by this iterator.

setAdjustQueryIndices

@Deprecated
public void setAdjustQueryIndices(boolean adjustQueryIndices)

Deprecated.

getStatistics

public Properties getStatistics()

Obtain statistics about this alignment as a Java property instance.

Returns:

statistics about this alignment

getNumberOfAlignedReads

public int getNumberOfAlignedReads()

close

public void close()
           throws IOException

Close the underlying readers.

Throws:

IOException - if an I/O error occurs

getLocations

public ObjectList<ReferenceLocation> getLocations(int modulo)
                                           throws IOException

Throws:

IOException