All Implemented Interfaces:

Serializable, Alignment, SymbolList, Changeable

public class AlignmentPair
extends SimpleAlignment 

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

  All 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