[Bioperl-l] Missing methods in SearchUtils and GenericHit

Steve_Chervitz Steve_Chervitz at affymetrix.com
Mon Mar 20 19:35:18 EST 2006


My local copies of from Bio::Search::SearchUtils and  
Bio::Search::Hit::GenericHit have some extra methods relative to  
what's in the CVS head. Looking at CVS logs, it doesn't appear they  
were removed, so it's likely they were new things I never committed  
to CVS:

Methods in Bio::Search::Hit::GenericHit:
     num_unknown_residues
     frac_aligned_query
     percent_conserved
     percent_identical

Methods in Bio::Search::SearchUtils:
     mol_type

Looks like I may have added them to provide additional data output  
via Bio::SearchIO::Writer::HitTableWriter (which is also modified on  
my local copy).

It's been a while since I worked on these. Can anyone remember add/ 
removing/modifying these methods?  If not, I'll go ahead and commit  
them. They look like they could be generally useful.

Steve



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