dasp.model
Class ActiveSiteProfile

java.lang.Object
  extended by dasp.model.Alignment
      extended by dasp.model.ActiveSiteProfile

public class ActiveSiteProfile
extends Alignment


Field Summary
 
Fields inherited from class dasp.model.Alignment
alignment, method, nameMap, seqs
 
Constructor Summary
ActiveSiteProfile(List<ActiveSiteSignature> signatures, Align alignmentMethod)
           
 
Method Summary
 List<String> getFragFormattedAlignment()
          Modify alignment to reflect fragments of signatures.
 
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
 

Constructor Detail

ActiveSiteProfile

public ActiveSiteProfile(List<ActiveSiteSignature> signatures,
                         Align alignmentMethod)
Method Detail

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.