org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter

public class MultipleAlignmentXMLConverter extends Object

Helper methods to convert all the hierarchy levels of a MultipleAlignment into an XML format.

To convert a MultipleAlignment to an XML String use the MultipleAlignmentWriter.toXML(MultipleAlignmentEnsemble) method.

Constructor Details
- MultipleAlignmentXMLConverter
  
  public MultipleAlignmentXMLConverter()
Method Details
- printXMLensemble
  
  public static void printXMLensemble(PrettyXMLWriter xml, MultipleAlignmentEnsemble ensemble) throws IOException
  
  Throws:
  
  IOException
- printXMLalignment
  
  public static void printXMLalignment(PrettyXMLWriter xml, MultipleAlignment msa) throws IOException
  
  Throws:
  
  IOException
- printXMLblockSet
  
  public static void printXMLblockSet(PrettyXMLWriter xml, BlockSet bs) throws IOException
  
  Throws:
  
  IOException
- printXMLblock
  
  public static void printXMLblock(PrettyXMLWriter xml, Block b) throws IOException
  
  Throws:
  
  IOException
- printXMLmatrix4d
  
  public static void printXMLmatrix4d(PrettyXMLWriter xml, javax.vecmath.Matrix4d transform) throws IOException
  
  Throws:
  
  IOException
- printXMLscoresCache
  
  public static void printXMLscoresCache(PrettyXMLWriter xml, ScoresCache cache) throws IOException
  
  Throws:
  
  IOException
- printXMLheader
  
  public static void printXMLheader(PrettyXMLWriter xml, MultipleAlignmentEnsemble ensemble) throws IOException
  
  Throws:
  
  IOException

Class MultipleAlignmentXMLConverter

Constructor Summary