edu.cornell.med.alignments
Interface AlignmentParser

All Known Implementing Classes:
ClustalwParser

public interface AlignmentParser

Reads an alignment and converts it into a BiologicalAlignment.

Author:
luce

Method Summary
 edu.mssm.crover.representation.BiologicalAlignment readAlignment(Reader reader)
          Reads an alignment and converts it into a BiologicalAlignment.
 edu.mssm.crover.representation.BiologicalAlignment readAlignmentFile(String filename)
          Reads an alignment from a file and converts it into a BiologicalAlignment.
 

Method Detail

readAlignment

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

Parameters:
reader - The alignment reader
Returns:
The alignment as a BiologicalAlignment
Throws:
IOException - if the reader cannot be read

readAlignmentFile

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

Parameters:
filename - The alignment reader
Returns:
The alignment as a BiologicalAlignment
Throws:
IOException - if the file cannot be read


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