org.biojava.nbio.structure.io

Class FastaAFPChainConverter

java.lang.Object

org.biojava.nbio.structure.io.FastaAFPChainConverter

public class FastaAFPChainConverter
extends Object

A collection of static utilities to convert between AFPChains and FastaSequences.

Author:

dmyersturnbull

See Also:

StructureSequenceMatcher, FastaStructureParser, SeqRes2AtomAligner

Constructor Summary

Constructors

Constructor and Description
FastaAFPChainConverter()

Method Summary

Modifier and Type	Method and Description
static AFPChain	cpFastaToAfpChain(File fastaFile, Structure structure, int cpSite) Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site cpSite residues to the right.
static AFPChain	cpFastaToAfpChain(ProteinSequence first, ProteinSequence second, Structure structure, int cpSite) Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site cpSite residues to the right.
static AFPChain	cpFastaToAfpChain(String first, String second, Structure structure, int cpSite)
static AFPChain	fastaFileToAfpChain(File fastaFile, Structure structure1, Structure structure2) Reads the file fastaFile, expecting exactly two sequences which give a pairwise alignment.
static AFPChain	fastaStringToAfpChain(String sequence1, String sequence2, Structure structure1, Structure structure2) Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2.
static AFPChain	fastaToAfpChain(Map<String,ProteinSequence> sequences, Structure structure1, Structure structure2) Uses two sequences each with a corresponding structure to create an AFPChain corresponding to the alignment.
static AFPChain	fastaToAfpChain(ProteinSequence sequence1, ProteinSequence sequence2, Structure structure1, Structure structure2) Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2.
static AFPChain	fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>,AminoAcidCompound> alignment, Structure structure1, Structure structure2) Provided only for convenience.
static AFPChain	fastaToAfpChain(String sequence1, String sequence2, Structure structure1, Structure structure2) TODO Write comment
static List<Object>	getAlignedUserCollection(String sequence) Takes a protein sequence string with capital and lowercase letters and sets its user collection to record which letters are uppercase (aligned) and which are lowercase (unaligned).
static void	main(String[] args) Prints out the XML representation of an AFPChain from a file containing exactly two FASTA sequences.

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaAFPChainConverter

public FastaAFPChainConverter()

Method Detail

cpFastaToAfpChain

public static AFPChain cpFastaToAfpChain(String first,
                                         String second,
                                         Structure structure,
                                         int cpSite)
                                  throws StructureException,
                                         CompoundNotFoundException

Throws:

StructureException

CompoundNotFoundException

cpFastaToAfpChain

public static AFPChain cpFastaToAfpChain(File fastaFile,
                                         Structure structure,
                                         int cpSite)
                                  throws IOException,
                                         StructureException

Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site cpSite residues to the right.

Parameters:

fastaFile - A FASTA file containing exactly 2 sequences, the first unpermuted and the second permuted

cpSite - The number of residues from the beginning of the sequence at which the circular permutation site occurs; can be positive or negative; values greater than the length of the sequence are acceptable

Throws:

IOException

StructureException

cpFastaToAfpChain

public static AFPChain cpFastaToAfpChain(ProteinSequence first,
                                         ProteinSequence second,
                                         Structure structure,
                                         int cpSite)
                                  throws StructureException

Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site cpSite residues to the right.

Parameters:

first - The unpermuted sequence

second - The sequence permuted by cpSite

cpSite - The number of residues from the beginning of the sequence at which the circular permutation site occurs; can be positive or negative; values greater than the length of the sequence are acceptable

Throws:

StructureException

fastaFileToAfpChain

public static AFPChain fastaFileToAfpChain(File fastaFile,
                                           Structure structure1,
                                           Structure structure2)
                                    throws IOException,
                                           StructureException

Reads the file fastaFile, expecting exactly two sequences which give a pairwise alignment. Uses this and two structures to create an AFPChain corresponding to the alignment. Uses a CasePreservingProteinSequenceCreator and assumes that a residue is aligned if and only if it is given by an uppercase letter.

Throws:

IOException

StructureException

See Also:

fastaToAfpChain(ProteinSequence, ProteinSequence, Structure, Structure)

fastaStringToAfpChain

public static AFPChain fastaStringToAfpChain(String sequence1,
                                             String sequence2,
                                             Structure structure1,
                                             Structure structure2)
                                      throws StructureException,
                                             CompoundNotFoundException

Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2. The sequences need not correspond to the entire structures, since local alignment is performed to match the sequences to structures.

Throws:

StructureException

CompoundNotFoundException

fastaToAfpChain

public static AFPChain fastaToAfpChain(Map<String,ProteinSequence> sequences,
                                       Structure structure1,
                                       Structure structure2)
                                throws StructureException

Uses two sequences each with a corresponding structure to create an AFPChain corresponding to the alignment. Provided only for convenience since FastaReaders return such maps.

Parameters:

sequences - A Map containing exactly two entries from sequence names as Strings to gapped ProteinSequences; the name is ignored

Throws:

StructureException

See Also:

fastaToAfpChain(ProteinSequence, ProteinSequence, Structure, Structure)

fastaToAfpChain

public static AFPChain fastaToAfpChain(String sequence1,
                                       String sequence2,
                                       Structure structure1,
                                       Structure structure2)
                                throws StructureException,
                                       CompoundNotFoundException

TODO Write comment

Parameters:

sequence1 -

sequence2 -

structure1 -

structure2 -

Returns:

Throws:

StructureException

CompoundNotFoundException

fastaToAfpChain

public static AFPChain fastaToAfpChain(ProteinSequence sequence1,
                                       ProteinSequence sequence2,
                                       Structure structure1,
                                       Structure structure2)
                                throws StructureException

Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2. The sequences need not correspond to the entire structures, since local alignment is performed to match the sequences to structures. Assumes that a residue is aligned if and only if it is given by an uppercase letter.

Parameters:

sequence1 - Must have AbstractSequence.getUserCollection() set to document upper- and lower-case as aligned and unaligned; see getAlignedUserCollection(String)

Throws:

StructureException

fastaToAfpChain

public static AFPChain fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>,AminoAcidCompound> alignment,
                                       Structure structure1,
                                       Structure structure2)
                                throws StructureException

Provided only for convenience.

Throws:

StructureException

See Also:

fastaToAfpChain(ProteinSequence, ProteinSequence, Structure, Structure)

getAlignedUserCollection

public static List<Object> getAlignedUserCollection(String sequence)

Takes a protein sequence string with capital and lowercase letters and sets its user collection to record which letters are uppercase (aligned) and which are lowercase (unaligned).

Parameters:

sequence - Make sure not to use AbstractSequence.getSequenceAsString() for this, as it won't preserve upper- and lower-case

main

public static void main(String[] args)
                 throws StructureException,
                        IOException

Prints out the XML representation of an AFPChain from a file containing exactly two FASTA sequences.

Parameters:

args - A String array of fasta-file structure-1-name structure-2-name

Throws:

StructureException

IOException