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revision 1.430, Wed Jan 25 18:57:05 2006 UTC revision 1.431, Sat Jan 28 04:23:47 2006 UTC
# Line 6491  Line 6491 
6491    
6492  =head3 sims  =head3 sims
6493    
6494  usage: @sims = $fig->sims($peg,$maxN,$maxP,$select)  usage: @sims = $fig->sims($peg,$maxN,$maxP,$select,$max_expand, $filters)
6495    
6496  Returns a list of similarities for $peg such that  Returns a list of similarities for $peg such that
6497    
# Line 6504  Line 6504 
6504          "raw" means that the similarities will not be expanded (by far fastest option)          "raw" means that the similarities will not be expanded (by far fastest option)
6505          "fig" means return only similarities to fig genes          "fig" means return only similarities to fig genes
6506          "all" means that you want all the expanded similarities.          "all" means that you want all the expanded similarities.
6507            "figx" means exapand until the maximum number of fig sims
6508    
6509  By "expanded", we refer to taking a "raw similarity" against an entry in the non-redundant  By "expanded", we refer to taking a "raw similarity" against an entry in the non-redundant
6510  protein collection, and converting it to a set of similarities (one for each of the  protein collection, and converting it to a set of similarities (one for each of the
# Line 12543  Line 12544 
12544      }      }
12545  }  }
12546    
12547    =head3 subsystems_for_ec
12548    
12549    Return a list of subsystems, roles, and proteins containing an EC number.
12550    
12551    Returns an arrray. Each item in the array is a reference to a three-ple of subsystem, role, and peg.
12552    
12553    =cut
12554    
12555    sub subsystems_for_ec
12556    {
12557        my($self, $ec) = @_;
12558    
12559        my $rdbH = $self->db_handle;
12560    
12561        my $q = "SELECT DISTINCT subsystem, role, protein FROM subsystem_index WHERE role like \'\%$ec\%\'";
12562    
12563        my $relational_db_response;
12564        if (($relational_db_response = $rdbH->SQL($q)) &&
12565                (@$relational_db_response > 0))
12566        {
12567            return @$relational_db_response;
12568        }
12569        else
12570        {
12571            return ();
12572        }
12573    }
12574    
12575    
12576    

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