Class AFPChainXMLParser

Method Details

• fromXML

  public static AFPChain fromXML(String xml, String name1, String name2, Atom[] ca1, Atom[] ca2) throws IOException, StructureException

  new utility method that checks that the order of the pair in the XML alignment is correct and flips the direction if needed

  Parameters:

  xml -

  name1 -

  name1 -

  ca1 -

  ca2 -

  Returns:

  Throws:

  IOException

  StructureException

• fromXML

  public static AFPChain fromXML(String xml, Atom[] ca1, Atom[] ca2) throws IOException

  Throws:

  IOException

• isErrorXML

  public static boolean isErrorXML(String xml)

  returns true if the alignment XML contains an error message

  Parameters:

  xml -

  Returns:

  flag if there was an Error while processing the alignment.

• flipAlignment

  public static String flipAlignment(String xml) throws IOException, StructureException

  Takes an XML representation of the alignment and flips the positions of name1 and name2

  Parameters:

  xml - String representing the alignment

  Returns:

  XML representation of the flipped alignment

  Throws:

  IOException

  StructureException

• rebuildAFPChain

  public static void rebuildAFPChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2)

  replace the PDB res nums with atom positions:

  Parameters:

  afpChain -

  ca1 -

  ca2 -

• parseMultiXML

  public static AFPChain[] parseMultiXML(String xml) throws IOException

  Throws:

  IOException