Class MultipleAlignmentWriter

Method Details

• 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