edu.cornell.med.alignments
Interface AlignmentWriter

All Known Implementing Classes:
ClustalwWriter

public interface AlignmentWriter

Writes a BiologicalAlignment.

Author:
luce

Method Summary
 String getConservationLine()
          Gets the line indicating conservation at each position of the alignment.
 void setConservationLine(String conservationLine)
          Sets the line indicating conservation at each position of the alignment.
 void writeAlignment(edu.mssm.crover.representation.BiologicalAlignment aln, Writer writer)
          Writes the BiologicalAlignment to a file.
 String writeAlignmentFile(edu.mssm.crover.representation.BiologicalAlignment aln)
          Writes the BiologicalAlignment as a ClustalW formnatted alignment to a String.
 

Method Detail

getConservationLine

String getConservationLine()
Gets the line indicating conservation at each position of the alignment.

Returns:
the conservation line

setConservationLine

void setConservationLine(String conservationLine)
Sets the line indicating conservation at each position of the alignment.

Parameters:
conservationLine - the conservation line

writeAlignment

void writeAlignment(edu.mssm.crover.representation.BiologicalAlignment aln,
                    Writer writer)
                    throws IOException
Writes the BiologicalAlignment to a file.

Parameters:
aln - The BiologicalAlignment to be written
writer - The file to write the alignment to.
Throws:
IOException - if the file cannot be written to

writeAlignmentFile

String writeAlignmentFile(edu.mssm.crover.representation.BiologicalAlignment aln)
Writes the BiologicalAlignment as a ClustalW formnatted alignment to a String.

Parameters:
aln - The BiologicalAlignment
Returns:
the String representation of the alignment in ClustalW format


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