'STRAP:multiple sequence alignments '

charite.christo.interfaces
Interface SequenceAligner


public interface SequenceAligner

Classes that provide a calculation of sequence alignments. PACKAGE:charite.christo.interfaces. PACKAGE:charite.christo. With JAVADOC:SequenceAligner#setSequences(String[]) the amino acid sequences of the proteins are set. Alignment starts on invoking JAVADOC:SequenceAligner#compute() STRAP retrieves the result by calling JAVADOC:SequenceAligner#getAlignedSequences(). JAVADOC:SequenceAligner#getMaxNumberOfSequences()may return 2 if the procedure is capable of only pair alignments or the number of allowed proteins. A container of GUI elements for the user is provided on pressing ICON:IC_CONTROLPANEL when the class implements JAVADOC:HasControlPanel. The GUI elements may be used to select gap-panalties or BLOSUM matrices.


Field Summary
static int OPTION_USE_SECONDARY_STRUCTURE
           
 
Method Summary
 void compute()
          The time consuming computation.
 byte[][] getAlignedSequences()
           
 int getMaxNumberOfSequences()
          Multiple aligners are usually not limited in the number of sequences.
 byte[][] getSequences()
          Return the sequences that have been set with setSequences(String[])
 boolean isLocal()
          Local alignment procedures do not align the entire sequences.
 void setOptions(long flags)
           
 void setSequences(byte[]... ss)
           
 

Field Detail

OPTION_USE_SECONDARY_STRUCTURE

static final int OPTION_USE_SECONDARY_STRUCTURE
See Also:
Constant Field Values
Method Detail

setSequences

void setSequences(byte[]... ss)

getSequences

byte[][] getSequences()
Return the sequences that have been set with setSequences(String[])


compute

void compute()
The time consuming computation.


setOptions

void setOptions(long flags)

getAlignedSequences

byte[][] getAlignedSequences()

getMaxNumberOfSequences

int getMaxNumberOfSequences()
Multiple aligners are usually not limited in the number of sequences. Pair aligners should return "2". See JAVADOC:charite.christo.strap.extensions.MultiFromPairAligner


isLocal

boolean isLocal()
Local alignment procedures do not align the entire sequences. They identify sequence regions which match best.


'STRAP:multiple sequence alignments '

'The most important classes are StrapAlign, StrapProtein and StrapEvent.'