dasp.algorithms
Interface Align

All Known Implementing Classes:
ClustalAlign

public interface Align


Method Summary
 double align(List<String> sequences)
          align actually performs the alignment.
 List<String> getAlignment()
          Return the alignment itself as a list of aligned sequences with dashes to account for insertions.
 double getASPscore(String alnFile, int numSequences)
          Return the ASP score as defined in Cammer et al for this alignment.
 String getHTMLAlignment(List<String> alignedSequences)
          Return the alignment itself as an HTML-formatted string to account for insertions.
 double getIdentity()
          Return the % identity for all of the sequences in the alignment.
 

Method Detail

align

double align(List<String> sequences)
align actually performs the alignment. This will almost certainly throw some sort of exception, depending on the alignment algorithm or program

Parameters:
sequences - list of sequences in FASTA format
Returns:
the alignment score

getIdentity

double getIdentity()
Return the % identity for all of the sequences in the alignment.

Returns:
the % identity

getASPscore

double getASPscore(String alnFile,
                   int numSequences)
Return the ASP score as defined in Cammer et al for this alignment.

Returns:
the ASP score

getAlignment

List<String> getAlignment()
Return the alignment itself as a list of aligned sequences with dashes to account for insertions.

Parameters:
alignedSequences - list of aligned sequences
Returns:
list of aligned sequences

getHTMLAlignment

String getHTMLAlignment(List<String> alignedSequences)
Return the alignment itself as an HTML-formatted string to account for insertions.

Parameters:
alignedSequences - list of aligned sequences
Returns:
the HTML formatted alignment