Class MultipleAlignmentWriter
- java.lang.Object
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- org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter
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public class MultipleAlignmentWriter extends Object
This class contains functions for the conversion ofMultipleAlignment
to various String outputs.Supported formats: FASTA, FatCat, Aligned Residues, Transformation Matrices, XML, 3D format.
- Since:
- 4.1.0
- Author:
- Aleix Lafita
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Constructor Summary
Constructors Constructor Description MultipleAlignmentWriter()
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Method Summary
All Methods Static Methods Concrete Methods 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.htmlstatic String
toAlignedResidues(MultipleAlignment multAln)
Converts the alignment to its simplest form: a list of groups of aligned residues.static String
toFASTA(MultipleAlignment alignment)
Converts theMultipleAlignment
into a multiple sequence alignment String in FASTA format.static String
toFatCat(MultipleAlignment alignment)
Converts theMultipleAlignment
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.
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Constructor Detail
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MultipleAlignmentWriter
public MultipleAlignmentWriter()
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Method Detail
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toFASTA
public static String toFASTA(MultipleAlignment alignment)
Converts theMultipleAlignment
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)
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toFatCat
public static String toFatCat(MultipleAlignment alignment)
Converts theMultipleAlignment
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)
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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)
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.
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toTransformMatrices
public static String toTransformMatrices(MultipleAlignment alignment)
Converts the transformation Matrices of the alignment into a String output.- Parameters:
afpChain
-- Returns:
- String transformation Matrices
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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
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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.htmlThe 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 proteinsqueryIndex
- index of the query within the multiple alignmenttemplateIndex
- 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
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