dasp.model
Class ActiveSiteProfile
java.lang.Object
dasp.model.Alignment
dasp.model.ActiveSiteProfile
public class ActiveSiteProfile
- extends Alignment
Methods inherited from class dasp.model.Alignment |
addSequence, addSequences, deleteSequence, doAlign, getAlignment, getAlignmentAsString, getAlignmentByIndex, getAlignmentByName, getHTMLAlignment, getIdentity, getScore, getSequences |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
ActiveSiteProfile
public ActiveSiteProfile(List<ActiveSiteSignature> signatures,
Align alignmentMethod)
getFragFormattedAlignment
public List<String> getFragFormattedAlignment()
- Modify alignment to reflect fragments of signatures.
The sequences stored in seq already have the upper and lower case format of fragments.
2 ways to do this:
1) take each aligned signature in 'alignment' and compare to original in 'seqs' and covert to upper or lower case where necessary
2) take each original signature and compare to alignment and insert dashes where necessary
Not sure which way is easier. I think I implemented #2 in the FormatDaspAlignment.pl script, so should look at that algorithm.