Class FastaAFPChainConverter

Method Details

• 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