org.biojava.bio.alignment

Class AlignmentPair

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.AbstractSymbolList

org.biojava.bio.alignment.SimpleAlignment

org.biojava.bio.alignment.AlignmentPair

All Implemented Interfaces:

Serializable, Alignment, SymbolList, Changeable

public class AlignmentPair
extends SimpleAlignment

This class stores the result of an alignment procedure that creates a pairwise alignment of two sequences. Currently, these sequences must have the identical length (this may be changed in the future). A format routine produces a BLAST-like output for the sequences but all necessary information to visualize the alignment are contained in this class.

Author:

Andreas Dräger

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.bio.symbol.AbstractSymbolList

AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater

Nested classes/interfaces inherited from interface org.biojava.bio.alignment.Alignment

Alignment.SymbolListIterator

Field Summary

Fields inherited from interface org.biojava.bio.alignment.Alignment

CONTENT

Fields inherited from interface org.biojava.bio.symbol.SymbolList

EDIT, EMPTY_LIST

Constructor Summary

Constructors

Constructor and Description
AlignmentPair(Sequence query, Sequence subject, int queryStart, int queryEnd, int subjectStart, int subjectEnd, SubstitutionMatrix subMatrix)
AlignmentPair(Sequence query, Sequence subject, SubstitutionMatrix subMatrix)

Method Summary

Methods

Modifier and Type	Method and Description
static AlignmentPair	align(Sequence query, Sequence subject, AlignmentAlgorithm algorithm)
String	formatOutput()
String	formatOutput(int width) This method provides a BLAST-like formated alignment from the given Strings, in which the sequence coordinates and the information "Query" or "Sbjct", respectively is added to each line.
long	getComputationTime()
int	getNumGapsInQuery()
int	getNumGapsInSubject()
int	getNumIdenticals()
int	getNumSimilars()
float	getPercentGapsQuery()
float	getPercentGapsTarget()
float	getPercentIdentityQuery()
float	getPercentIdentitySubject()
float	getPercentSimilarityQuery()
float	getPercentSimilaritySubject()
GappedSequence	getQuery() Return the query sequence as a gapped sequence.
int	getQueryEnd()
int	getQueryLength()
int	getQueryStart()
GappedSequence	getSubject() Return the subject sequence as a gapped sequence.
int	getSubjectEnd()
int	getSubjectLength()
int	getSubjectStart()
SubstitutionMatrix	getSubstitutionMatrix()

Methods inherited from class org.biojava.bio.alignment.SimpleAlignment

finalize, getAlphabet, getLabels, getScore, length, setScore, subAlignment, symbolAt, symbolAt, symbolListForLabel, symbolListIterator

Methods inherited from class org.biojava.bio.symbol.AbstractSymbolList

edit, equals, hashCode, iterator, seqString, subList, subStr, toList, toString

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.bio.symbol.SymbolList

edit, iterator, seqString, subList, subStr, toList

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

AlignmentPair

public AlignmentPair(Sequence query,
             Sequence subject,
             int queryStart,
             int queryEnd,
             int subjectStart,
             int subjectEnd,
             SubstitutionMatrix subMatrix)
              throws IllegalArgumentException,
                     BioException

Parameters:

queryStart - the start position in the query, where the alignment starts. For example zero for normal Needleman-Wunsch-Alignments.

queryEnd - the end position, that means the sequence coordinate, which is the last symbol of the query sequence. Counting starts at zero!

queryLength - The length of the query sequence without gaps.

subjectStart - These are all the same for the target. Have a look at these above.

subjectEnd -

subMatrix - the subsitution Matrix used for calculating the alignment

Throws:

IllegalArgumentException

BioException

AlignmentPair

public AlignmentPair(Sequence query,
             Sequence subject,
             SubstitutionMatrix subMatrix)
              throws IllegalArgumentException,
                     BioException

Parameters:

query -

subject -

subMatrix -

Throws:

IllegalArgumentException

BioException

Method Detail

align

public static AlignmentPair align(Sequence query,
                  Sequence subject,
                  AlignmentAlgorithm algorithm)
                           throws Exception

Parameters:

query -

subject -

algorithm -

Returns:

Throws:

Exception

getQueryStart

public int getQueryStart()

Returns:

the queryStart

getQueryEnd

public int getQueryEnd()

Returns:

the queryEnd

getSubjectStart

public int getSubjectStart()

Returns:

the subjectStart

getSubjectEnd

public int getSubjectEnd()

Returns:

the subjectEnd

getComputationTime

public long getComputationTime()

Returns:

the time

getNumGapsInQuery

public int getNumGapsInQuery()

Returns:

the ngapsq

getNumGapsInSubject

public int getNumGapsInSubject()

Returns:

the ngapst

getNumIdenticals

public int getNumIdenticals()

Returns:

the identicals

getNumSimilars

public int getNumSimilars()

Returns:

the similars

getPercentIdentityQuery

public float getPercentIdentityQuery()

Returns:

getPercentIdentitySubject

public float getPercentIdentitySubject()

Returns:

getPercentSimilarityQuery

public float getPercentSimilarityQuery()

Returns:

getPercentSimilaritySubject

public float getPercentSimilaritySubject()

Returns:

getQueryLength

public int getQueryLength()

Returns:

getSubjectLength

public int getSubjectLength()

Returns:

getSubstitutionMatrix

public SubstitutionMatrix getSubstitutionMatrix()

Returns:

the subMatrix

formatOutput

public String formatOutput()
                    throws BioException

Returns:

Throws:

BioException

formatOutput

public String formatOutput(int width)
                    throws BioException

This method provides a BLAST-like formated alignment from the given Strings, in which the sequence coordinates and the information "Query" or "Sbjct", respectively is added to each line. Each line contains width sequence characters including the gap symbols plus the meta information. There is one white line between two pairs of sequences.

Parameters:

width - the number of symbols to be displayed per line.

Returns:

formated String.

Throws:

BioException

getPercentGapsTarget

public float getPercentGapsTarget()

Returns:

getPercentGapsQuery

public float getPercentGapsQuery()

Returns:

getQuery

public GappedSequence getQuery()

Return the query sequence as a gapped sequence.

Returns:

the query sequence as a gapped sequence

getSubject

public GappedSequence getSubject()

Return the subject sequence as a gapped sequence.

Returns:

the subject sequence as a gapped sequence