de.zimek.proteinfeatures.parser
Class ManifoldParser

java.lang.Object
  extended byde.zimek.proteinfeatures.parser.AbstractParser
      extended byde.zimek.proteinfeatures.parser.ManifoldParser
All Implemented Interfaces:
Parser

public class ManifoldParser
extends AbstractParser

Author:
Arthur Zimek

Field Summary
 java.util.Properties DOMAIN2SCOP
           
 
Constructor Summary
ManifoldParser()
           
 
Method Summary
 Protein[] parse(java.io.File in)
           
 Protein parseSingleProtein(java.io.File in)
          Parses the proteins as given in the MANIFOLD directory.
 
Methods inherited from class de.zimek.proteinfeatures.parser.AbstractParser
print, printForMotifScan
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

DOMAIN2SCOP

public final java.util.Properties DOMAIN2SCOP
Constructor Detail

ManifoldParser

public ManifoldParser()
Method Detail

parse

public Protein[] parse(java.io.File in)
                throws java.text.ParseException,
                       java.io.FileNotFoundException
Throws:
java.text.ParseException
java.io.FileNotFoundException
See Also:
Parser.parse(java.io.File)

parseSingleProtein

public Protein parseSingleProtein(java.io.File in)
                           throws java.text.ParseException,
                                  java.io.FileNotFoundException
Parses the proteins as given in the MANIFOLD directory. Secondary structure is assigned as dummy C. Refer to secondary-structure-based features to the features defined by Ding and Dubchak.

Parameters:
in -
Returns:
Protein
Throws:
java.text.ParseException
java.io.FileNotFoundException