Package org.biojava.nbio.structure.align.multiple.util

Class MultipleAlignmentWriter

java.lang.Object

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

public class MultipleAlignmentWriter
extends Object

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

Supported formats: FASTA, FatCat, Aligned Residues, Transformation Matrices, XML, 3D format.

Since:

4.1.0

Author:

Aleix Lafita

Constructor Summary

Constructors

Constructor	Description
MultipleAlignmentWriter()

Method Summary

Modifier and Type	Method	Description
static String	to3DFormat(MultipleAlignment alignment, int queryIndex, int templateIndex)	Outputs a pairwise alignment in I-TASSER's 3D Format for target-template alignment. http://zhanglab.ccmb.med.umich.edu/I-TASSER/option4.html
static String	toAlignedResidues(MultipleAlignment multAln)	Converts the alignment to its simplest form: a list of groups of aligned residues.
static String	toFASTA(MultipleAlignment alignment)	Converts the MultipleAlignment into a multiple sequence alignment String in FASTA format.
static String	toFatCat(MultipleAlignment alignment)	Converts the MultipleAlignment into a FatCat String format.
static String	toTransformMatrices(MultipleAlignment alignment)	Converts the transformation Matrices of the alignment into a String output.
static String	toXML(MultipleAlignmentEnsemble ensemble)	Converts all the information of a multiple alignment ensemble into an XML String format.

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 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

See Also:

MultipleAlignmentTools.getSequenceAlignment(MultipleAlignment)

toFatCat

public static 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

See Also:

MultipleAlignmentTools.getSequenceAlignment(MultipleAlignment)

toAlignedResidues

public static 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 String toTransformMatrices(MultipleAlignment alignment)

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

Parameters:

afpChain -

Returns:

String transformation Matrices

toXML

public static String toXML(MultipleAlignmentEnsemble ensemble)
                    throws IOException

Converts all the information of a multiple alignment ensemble into an XML String format. Cached variables, like transformation matrices and scores, are also converted.

Parameters:

ensemble - the MultipleAlignmentEnsemble to convert.

Returns:

String XML representation of the ensemble

Throws:

IOException

See Also:

Helper methods for XML conversion

to3DFormat

public static String to3DFormat(MultipleAlignment alignment,
                                int queryIndex,
                                int templateIndex)
                         throws StructureException

Outputs a pairwise alignment in I-TASSER's 3D Format for target-template alignment. http://zhanglab.ccmb.med.umich.edu/I-TASSER/option4.html

The format is closely related to a standard PDB file, but contains only CA atoms and adds two columns for specifying the alignment:

 ATOM   2001  CA  MET     1      41.116 -30.727   6.866  129 THR
 ATOM   2002  CA  ALA     2      39.261 -27.408   6.496  130 ARG
 ATOM   2003  CA  ALA     3      35.665 -27.370   7.726  131 THR
 ATOM   2004  CA  ARG     4      32.662 -25.111   7.172  132 ARG
 ATOM   2005  CA  GLY     5      29.121 -25.194   8.602  133 ARG

 Column 1 -30: Atom & Residue records of query sequence.
 Column 31-54: Coordinates of atoms in query copied from corresponding atoms in template.
 Column 55-59: Corresponding residue number in template based on alignment
 Column 60-64: Corresponding residue name in template
 

Note that the output is a pairwise alignment. Only the first and second rows in the MultipleAlignment will be used, others ignored.

This method supports topology-independent alignments. The output will have sequence order matching the query, but include atoms from the template.

Parameters:

alignment - A full multiple alignment between proteins

queryIndex - index of the query within the multiple alignment

templateIndex - index of the template within the multiple alignment

Returns:

The file contents as a string

Throws:

StructureException - If an error occurs parsing the alignment's structure names