edu.cornell.med.alignments
Class ClustalwParser

java.lang.Object
  extended by edu.cornell.med.alignments.ClustalwParser
All Implemented Interfaces:
AlignmentParser

public class ClustalwParser
extends Object
implements AlignmentParser

Takes in an alignment in ClustalW format, parses it into a BiologicalAlignment, and calculates at each position whether the alignment reaches a user-specified conservation cutoff value.

Author:
luce

Constructor Summary
ClustalwParser()
           
 
Method Summary
 edu.mssm.crover.representation.BiologicalAlignment readAlignment(Reader reader)
          Reads a ClustalW alignment and converts it into a BiologicalAlignment.
 edu.mssm.crover.representation.BiologicalAlignment readAlignmentFile(String filename)
          Reads a ClustalW alignment from a file and converts it into a BiologicalAlignment.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ClustalwParser

public ClustalwParser()
Method Detail

readAlignment

public final edu.mssm.crover.representation.BiologicalAlignment readAlignment(Reader reader)
                                                                       throws IOException
Reads a ClustalW alignment and converts it into a BiologicalAlignment.

Specified by:
readAlignment in interface AlignmentParser
Parameters:
reader - The alignment reader
Returns:
The BiologicalAlignment
Throws:
IOException - if the reader cannot be read

readAlignmentFile

public final edu.mssm.crover.representation.BiologicalAlignment readAlignmentFile(String filename)
                                                                           throws IOException
Reads a ClustalW alignment from a file and converts it into a BiologicalAlignment.

Specified by:
readAlignmentFile in interface AlignmentParser
Parameters:
filename - The alignment reader
Returns:
The BiologicalAlignment
Throws:
IOException - if the file cannot be read


Copyright © 2007 Institute for Computational Biomedicine, All Rights Reserved.