edu.mssm.crover.representation
Interface BiologicalAlignment

All Superinterfaces:

RootObject

All Known Implementing Classes:

Alignment

public interface BiologicalAlignment

extends RootObject

Interface to represent a biological alignment of protein sequences.

Author:

Fabien Campagne

See Also:

RandomAccessAlignment

Method Summary

BiologicalSequence	findGappedSequence(java.lang.String shortname) Returns the first sequence of this alignment which name matches shortname (the order of the search is reversed).
BiologicalSequence[]	getGappedSequences()
java.lang.String[]	getPositions() returns the positions of this alignments as an array of String.
BiologicalSequence[]	getSequenceSet() Obtain the set of sequences that constitute this alignment as an array of object that support the BiologicalSequence interface
java.lang.String	getShortName()
int	longer() Computes and returns the length of the longer sequence of this alignment.
void	removeSequence(BiologicalSequence seq) Removes the specified sequence from the alignment.
void	setSequenceSet(BiologicalSequence[] new_set) Replace the set of sequences that constitute this alignment by new_set
void	setShortName(java.lang.String x)

Method Detail

setSequenceSet

public void setSequenceSet(BiologicalSequence[] new_set)

Replace the set of sequences that constitute this alignment by new_set

getSequenceSet

public BiologicalSequence[] getSequenceSet()

Obtain the set of sequences that constitute this alignment as an array of object that support the BiologicalSequence interface

removeSequence

public void removeSequence(BiologicalSequence seq)

Removes the specified sequence from the alignment. The gap arrangement is not disturbed by this operation in the other gapped sequences.

findGappedSequence

public BiologicalSequence findGappedSequence(java.lang.String shortname)

Returns the first sequence of this alignment which name matches shortname (the order of the search is reversed). If no sequence with the given shortname is found in this alignment, then null is returned.

longer

public int longer()

Computes and returns the length of the longer sequence of this alignment.

getPositions

public java.lang.String[] getPositions()

returns the positions of this alignments as an array of String.

See Also:

String

getGappedSequences

public BiologicalSequence[] getGappedSequences()

getShortName

public java.lang.String getShortName()

setShortName

public void setShortName(java.lang.String x)