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public interface Align
Method Summary | |
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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 |
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double align(List<String> sequences)
sequences
- list of sequences in FASTA format
double getIdentity()
double getASPscore(String alnFile, int numSequences)
List<String> getAlignment()
alignedSequences
- list of aligned sequences
String getHTMLAlignment(List<String> alignedSequences)
alignedSequences
- list of aligned sequences
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