private void updateMultipleAlignment ( ) throws StructureException , RefinerFailedException { msa . clear ( ) ; // Override the alignment with the new information Block b = msa . getBlock ( 0 ) ; b . setAlignRes ( block ) ; repeatCore = b . getCoreLength ( ) ; if ( repeatCore < 1 ) throw new RefinerFailedException ( "Optimization converged to length 0" ) ; SymmetryTools . updateSymmetryTransformation ( axes , msa ) ; }
This method translates the internal data structures to a MultipleAlignment of the repeats in order to use the methods to score MultipleAlignments .