[Bio] / FigKernelPackages / SeedUtils.pm Repository:
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revision 1.30, Fri Jan 29 23:25:55 2010 UTC revision 1.31, Fri Feb 26 15:22:31 2010 UTC
# Line 930  Line 930 
930    
931  =head3 sims  =head3 sims
932    
933      my $sims = sims($id, $maxN, $maxP, $select, $max_expand, $filters);      my @sims = sims($id, $maxN, $maxP, 'fig');
934    
935    or
936    
937        my @sims = sims($id, $maxN, $maxP, 'all);
938    
939    
940  Retrieve similarities from the network similarity server. The similarity retrieval  Retrieve similarities from the network similarity server. The similarity retrieval
941  is performed using an HTTP user agent that returns similarity data in multiple  is performed using an HTTP user agent that returns similarity data in multiple
# Line 952  Line 957 
957  ID of the feature whose similarities are desired, or reference to a list  ID of the feature whose similarities are desired, or reference to a list
958  of the IDs of the features whose similarities are desired.  of the IDs of the features whose similarities are desired.
959    
960  =item maxN  =item maxN (optional)
961    
962  Maximum number of similarities to return for each incoming feature.  Maximum number of similarities to return for each incoming feature.
963    
964  =item maxP  =item maxP (optional)
965    
966  The maximum allowable similarity score.  The maximum allowable similarity score.
967    
968  =item select  =item select (optional)
969    
970  Selection criterion: C<raw> means only raw similarities are returned; C<fig>  Selection criterion: C<raw> means only raw similarities are returned; C<fig>
971  means only similarities to FIG features are returned; C<all> means all expanded  means only similarities to FIG features are returned; C<all> means all expanded
972  similarities are returned; and C<figx> means similarities are expanded until the  similarities are returned; and C<figx> means similarities are expanded until the
973  number of FIG features equals the maximum.  number of FIG features equals the maximum.
974    
975  =item max_expand  =item max_expand (optional)
976    
977  The maximum number of features to expand.  The maximum number of features to expand.
978    
979  =item filters  =item filters (optional)
980    
981  Reference to a hash containing filter information, or a subroutine that can be  Reference to a hash containing filter information, or a subroutine that can be
982  used to filter the sims.  used to filter the sims.

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