dasp.algorithms
Class ClustalAlign

java.lang.Object
  extended by dasp.algorithms.ClustalAlign
All Implemented Interfaces:
Align

public class ClustalAlign
extends Object
implements Align


Constructor Summary
ClustalAlign()
          Will need to store the alignment or files the alignemnt is saved to?
 
Method Summary
 double align(List<String> sequences)
          align actually performs the alignment.
 List<String> getAlignment()
          Return the alignment itself with each sequence as a single string and with dashes inserted 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> alignment)
          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.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ClustalAlign

public ClustalAlign()
Will need to store the alignment or files the alignemnt is saved to?

Method Detail

align

public 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

Specified by:
align in interface Align
Parameters:
model - the data model we're using
Returns:
the alignment score

getASPscore

public double getASPscore(String alnFile,
                          int numSequences)
Return the ASP score as defined in Cammer et al for this alignment. method basically parses the .aln file and processes it by blocks. Is there an easier way to do this? Try to find out later as this should work for now. Need to look closer at this as it came from the identityTableMaker class which is pairwise ASP scores. It looks like it will work for the full alignment though, so not sure why the DASP code does it differently.

Specified by:
getASPscore in interface Align
Returns:
the ASP score

getIdentity

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

Specified by:
getIdentity in interface Align
Returns:
the % identity

getAlignment

public List<String> getAlignment()
Return the alignment itself with each sequence as a single string and with dashes inserted to account for insertions. Need to include the PDB id or structure id at the start of each line followed by some delimiter like spaces. findProfileFragments() currently assumes spaces. Basically reads in the .aln file and formats it appropriatly. Should we do the fragment thing here or elsewhere? We have the fragments, so why not do them at this step?

Specified by:
getAlignment in interface Align
Returns:
the alignment

getHTMLAlignment

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

Specified by:
getHTMLAlignment in interface Align
Parameters:
alignment - the string alignment
Returns:
the HTML formatted alignment