org.biojava.nbio.structure.align.multiple

Class MultipleAlignmentWriter

java.lang.Object

org.biojava.nbio.structure.align.multiple.MultipleAlignmentWriter

public class MultipleAlignmentWriter
extends java.lang.Object

This class contains functions for the conversion of MultipleAlignment to various String outputs.

Supported formats: FASTA, FatCat, Aligned Residues

Author:

Aleix Lafita

Constructor Summary

Constructors

Constructor and Description
MultipleAlignmentWriter()

Method Summary

Methods

Modifier and Type	Method and Description
static java.lang.String	toAlignedResidues(MultipleAlignment multAln) Converts the alignment to its simplest form: a list of groups of aligned residues.
static java.lang.String	toFASTA(MultipleAlignment alignment) Converts the MultipleAlignment into a multiple sequence alignment String in FASTA format.
static java.lang.String	toFatCat(MultipleAlignment alignment) Converts the MultipleAlignment into a FatCat String format.
static java.lang.String	toTransformMatrices(MultipleAlignment alignment) Converts the transformation Matrices of the alignment into a String output.

Methods inherited from class java.lang.Object

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

Constructor Detail

MultipleAlignmentWriter

public MultipleAlignmentWriter()

Method Detail

toFASTA

public static java.lang.String toFASTA(MultipleAlignment alignment)

Converts the MultipleAlignment into a multiple sequence alignment String in FASTA format.

Parameters:

alignment - MultipleAlignment

Returns:

String multiple sequence alignment in FASTA format

toFatCat

public static java.lang.String toFatCat(MultipleAlignment alignment)

Converts the MultipleAlignment into a FatCat String format. Includes summary information about the alignment in the top and a multiple sequence alignment at the bottom.

Parameters:

alignment - MultipleAlignment

Returns:

String multiple sequence alignment in FASTA format

toAlignedResidues

public static java.lang.String toAlignedResidues(MultipleAlignment multAln)

Converts the alignment to its simplest form: a list of groups of aligned residues. Format is one line per residue group, tab delimited:

• PDB number (includes insertion code)
• Chain
• Amino Acid (three letter code)

Example: 52 A ALA 102 A VAL 154 A THR

Note that this format loses information about blocks.

Parameters:

multAln - MultipleAlignment object

Returns:

a String representation of the aligned residues.

toTransformMatrices

public static java.lang.String toTransformMatrices(MultipleAlignment alignment)

Converts the transformation Matrices of the alignment into a String output.

Parameters:

afpChain -

Returns:

String transformation Matrices