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revision 1.3, Tue Oct 23 15:48:08 2007 UTC revision 1.4, Thu Oct 25 22:21:28 2007 UTC
# Line 377  Line 377 
377          return $return_value;          return $return_value;
378  }  }
379    
380    
381    =begin WSDL
382    _IN pat1 $string
383    _RETURN @string
384    _DOC Input is a pattern to search for, output is tab separated list of pegs and roles
385    =cut
386    sub simple_search {
387            my ($class, $arg1)=@_;
388    
389            my $fig = new FIG;
390    
391            my ($pegs, $roles) =  $fig->search_index($arg1);
392    
393            my (@result_list, $entry);
394    
395            for $entry (@$pegs) {
396                    push (@result_list, (join("\t", @$entry)));
397            }
398    
399            push (@result_list, (join("\t", @$roles)));
400            chomp @result_list;
401            my $return_value = join ("\n", @result_list);
402            return $return_value;
403    }
404    
405    
406  =begin WSDL  =begin WSDL
407  _RETURN $string list of families  _RETURN $string list of families
408  _DOC No Input, output is list of all families  _DOC No Input, output is list of all families
# Line 518  Line 544 
544          $return_value = join ("", @std_out);          $return_value = join ("", @std_out);
545          return $return_value;          return $return_value;
546  }  }
547    
548    
549    
550    =begin WSDL
551    _IN genome $string
552    _IN location1 $string
553    _IN location2 $string
554    _RETURN @string
555    _DOC Input is a genome ID and one or more locations in the form contig_start_stop, output is the DNA sequence
556    =cut
557    sub dna_sequence {
558            my ($class, $genome, @locations)=@_;
559            my $fig = new FIG;
560            my $seq=$fig->dna_seq($genome,@locations);
561            return $seq;
562    }
563    

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