org.biojava.nbio.structure.align.multiple

Class MultipleAlignmentTools

java.lang.Object

org.biojava.nbio.structure.align.multiple.MultipleAlignmentTools

public class MultipleAlignmentTools
extends java.lang.Object

Utility functions for working with MultipleAlignment.

Supported functions:

• Multiple Sequence Alignment Calculation Methods
• Map from Sequence Alignment Position to Structure Atom
• Map from Sequence Alignment Position to Block Number

Author:

Spencer Bliven, Aleix Lafita

Constructor Summary

Constructors

Constructor and Description
MultipleAlignmentTools()

Method Summary

Methods

Modifier and Type	Method and Description
static Atom	getAtomForSequencePosition(MultipleAlignment multAln, java.util.List<java.lang.Integer> mapSeqToStruct, int structure, int sequencePos) Returns the Atom of the specified structure that is aligned in the sequence alignment position specified.
static Matrix	getAverageResidueDistances(MultipleAlignment alignment) The average residue distance Matrix contains the average distance from each residue to all other residues aligned with it.
static int	getBlockForSequencePosition(MultipleAlignment multAln, java.util.List<java.lang.Integer> mapSeqToStruct, int sequencePos) Returns the block number of a specified position in the sequence alignment.
static java.util.List<java.lang.String>	getBlockSequenceAlignment(MultipleAlignment alignment) Calculate the sequence alignment Strings for the alignment Blocks in an alignment.
static java.util.List<java.lang.String>	getBlockSequenceAlignment(MultipleAlignment alignment, java.util.List<java.lang.Integer> mapSeqToStruct) Calculate the sequence alignment Strings for the alignment Blocks in an alignment.
static java.util.List<java.lang.String>	getSequenceAlignment(MultipleAlignment alignment) Calculate the sequence alignment Strings for the whole alignment.
static java.util.List<java.lang.String>	getSequenceAlignment(MultipleAlignment alignment, java.util.List<java.lang.Integer> mapSeqToStruct) Calculate the sequence alignment Strings for the whole alignment.

Methods inherited from class java.lang.Object

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

Constructor Detail

MultipleAlignmentTools

public MultipleAlignmentTools()

Method Detail

getSequenceAlignment

public static java.util.List<java.lang.String> getSequenceAlignment(MultipleAlignment alignment,
                                                    java.util.List<java.lang.Integer> mapSeqToStruct)

Calculate the sequence alignment Strings for the whole alignment. This method creates a sequence alignment where aligned residues are in uppercase and unaligned residues are in lowercase, thus providing a more compact way to represent the alignment.

Blocks are concatenated in the order returned by MultipleAlignment.getBlocks(), so sequences may not be sequential. Gaps are represented by '-'. Separation between different Blocks is indicated by a gap in all positions, meaning that there is a possible discontinuity.

Parameters:

alignment - input MultipleAlignment

mapSeqToStruct - provides a link from the sequence alignment position to the structure alignment position. Specially designed for the GUI. Has to be initialized previously and will be overwritten.

Returns:

a string for each row in the alignment, giving the 1-letter code for each aligned residue.

getSequenceAlignment

public static java.util.List<java.lang.String> getSequenceAlignment(MultipleAlignment alignment)

Calculate the sequence alignment Strings for the whole alignment. This method creates a sequence alignment where aligned residues are in uppercase and unaligned residues are in lowercase, thus providing a more compact way to represent the alignment.

Blocks are concatenated in the order returned by MultipleAlignment.getBlocks(), so sequences may not be sequential. Gaps are represented by '-'. Separation between different Blocks is indicated by a gap in all positions, meaning that there is a possible discontinuity.

Parameters:

alignment - input MultipleAlignment

Returns:

String for each row in the alignment, giving the 1-letter code for each aligned residue.

getBlockSequenceAlignment

public static java.util.List<java.lang.String> getBlockSequenceAlignment(MultipleAlignment alignment,
                                                         java.util.List<java.lang.Integer> mapSeqToStruct)

Calculate the sequence alignment Strings for the alignment Blocks in an alignment. This method creates a sequence alignment where all residues are in uppercase and a residue alone with gaps in all the other structures represents unaligned residues. Because of this latter constraint only the residues within the Blocks are represented, for a more compact alignment. For a sequence alignment of the full protein use getSequenceAlignment(MultipleAlignment).

Blocks are concatenated in the order returned by MultipleAlignment.getBlocks(), so sequences may not be sequential. Gaps between blocks are omitted, while gaps within blocks are represented by '-'. Separation between different Blocks is indicated by a gap in all positions, meaning that there is something unaligned inbetween.

Parameters:

alignment - input MultipleAlignment

mapSeqToStruct - provides a link from the sequence alignment position to the structure alignment position. Specially designed for the GUI. Has to be initialized previously and will be overwritten.

Returns:

a string for each row in the alignment, giving the 1-letter code for each aligned residue.

getBlockSequenceAlignment

public static java.util.List<java.lang.String> getBlockSequenceAlignment(MultipleAlignment alignment)

Calculate the sequence alignment Strings for the alignment Blocks in an alignment. This method creates a sequence alignment where all residues are in uppercase and a residue alone with gaps in all the other structures represents unaligned residues. Because of this latter constraint only the residues within the Blocks are represented, for a more compact alignment. For a sequence alignment of the full protein use getSequenceAlignment(MultipleAlignment).

Blocks are concatenated in the order returned by MultipleAlignment.getBlocks(), so sequences may not be sequential. Gaps between blocks are omitted, while gaps within blocks are represented by '-'. Separation between different Blocks is indicated by a gap in all positions, meaning that there is something unaligned inbetween.

Parameters:

alignment - input MultipleAlignment

Returns:

String for each row in the alignment, giving the 1-letter code for each aligned residue.

getAtomForSequencePosition

public static Atom getAtomForSequencePosition(MultipleAlignment multAln,
                              java.util.List<java.lang.Integer> mapSeqToStruct,
                              int structure,
                              int sequencePos)

Returns the Atom of the specified structure that is aligned in the sequence alignment position specified.

Parameters:

multAln - the MultipleAlignment object from where the sequence alignment has been generated

mapSeqToStruct - the mapping between sequence and structure generated with the sequence alignment

structure - the structure index of the alignment (row)

sequencePos - the sequence alignment position (column)

Returns:

Atom the atom in that position or null if there is a gap

getBlockForSequencePosition

public static int getBlockForSequencePosition(MultipleAlignment multAln,
                              java.util.List<java.lang.Integer> mapSeqToStruct,
                              int sequencePos)

Returns the block number of a specified position in the sequence alignment.

Parameters:

multAln - the MultipleAlignment object from where the sequence alignment has been generated

mapSeqToStruct - the mapping between sequence and structure generated with the sequence alignment

sequencePos - the position in the sequence alignment (column)

Returns:

int the block index, or -1 if the position is not aligned

getAverageResidueDistances

public static Matrix getAverageResidueDistances(MultipleAlignment alignment)

The average residue distance Matrix contains the average distance from each residue to all other residues aligned with it.

Complexity: T(n,l) = O(l*n^2), if n=number of structures and l=alignment length.

Parameters:

alignment - MultipleAlignment

Returns:

Matrix containing all average residue distances in alignmed columns