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revision 1.2, Tue Jun 12 16:51:53 2007 UTC revision 1.3, Tue Jun 12 20:17:44 2007 UTC
# Line 100  Line 100 
100    
101  =over 9  =over 9
102    
103  =item sim (seq)  =item SIM (seq)
104    
105  =item bbh (seq)  =item BBH (seq)
106    
107  =item pch (fc)  =item PCH (fc)
108    
109  =item figfam (seq)  =item FIGFAM (seq)
110    
111  =item ipr (dom)  =item IPR (dom)
112    
113  =item cdd (dom)  =item CDD (dom)
114    
115  =item pfam (dom)  =item PFAM (dom)
116    
117  =item signalp (dom)  =item SIGNALP (dom)
118    
119  =item cello (loc)  =item  CELLO(loc)
120    
121  =item tmhmm (loc)  =item TMHMM (loc)
122    
123  =item hmmtop (loc)  =item HMMTOP (loc)
124    
125  =back  =back
126    
# Line 324  Line 324 
324      my $objects = [];      my $objects = [];
325    my @matched_datasets=();    my @matched_datasets=();
326    
327    # call function that fetches attribut based observations    # call function that fetches attribute based observations
328    # returns an array of arrays of hashes    # returns an array of arrays of hashes
329    #    #
330    get_attribute_based_observations($fid,\@matched_datasets);    get_attribute_based_observations($fid,\@matched_datasets);
331    
332      # read sims
333      get_sims_observations($fid,\@matched_datasets);
334    
335    # read sims + bbh (enrich BBHs with sims coordindates etc)    # read sims + bbh (enrich BBHs with sims coordindates etc)
336    # read pchs    # read pchs
337    # read figfam match data from 48hr directory (BobO knows how do do this!)    # read figfam match data from 48hr directory (BobO knows how do do this!)
# Line 487  Line 490 
490      }      }
491  }  }
492    
493    =head3 get_sims_observations() (internal)
494    
495    This methods retrieves sims fills the internal data structures.
496    
497    =cut
498    
499    sub get_sims_observations{
500    
501        my ($fid,$datasets_ref) = (@_);
502        my $fig =
503        my @sims= $fig->nsims($fid,100,1e-5);
504        foreach my $sim (@sims){
505            $hit = $sim->[1];
506            $evalue = $sim->[10];
507            $from = $sim->[8];
508            $to = $sim->[9];
509            my $dataset = [ { name => 'class', value => "SIM" },
510                            { name => 'acc' , value => $hit},
511                            { name => 'type', value => "seq"} ,
512                            { name => 'evalue', value => $evalue },
513                            { name => 'start', value => $from},
514                            { name => 'stop' , value => $to}
515                            ];
516        }
517        push (@{$datasets_ref} ,$dataset);
518    
519    }
520    
521  =head3 get_sims_and_bbhs() (internal)  =head3 get_sims_and_bbhs() (internal)
522    
523  This methods retrieves sims and also BBHs and fills the internal data structures.  This methods retrieves sims and also BBHs and fills the internal data structures.

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