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revision 1.720, Thu Sep 11 14:46:03 2008 UTC revision 1.721, Thu Sep 11 14:57:59 2008 UTC
# Line 7892  Line 7892 
7892    
7893  usage: $fig->possibly_truncated($feature_id) or $fig->possibly_truncated($genome, $loc)  usage: $fig->possibly_truncated($feature_id) or $fig->possibly_truncated($genome, $loc)
7894    
7895  Returns true iff the feature or location occurs near the end of a contig.  
7896    Returns the empty string if the feature or location is not near either end of a contig.
7897    
7898    Returns 'stop' if the feature or location is on the 'plus' strand and near the end of a contig,
7899    or is on the 'minus' starnd and near the beginning of the contig.
7900    
7901    Returns 'start' if the feature or location is on the 'plus' strand and near the beginning of a contig,
7902    or is on the 'minus' starnd and near the end of the contig.
7903    
7904    Possibly truncated STOPs have return priority over possibly truncated STARTs.
7905    
7906  =cut  =cut
7907    
# Line 7946  Line 7955 
7955      if (  (($strand > 0) && ($end > ($self->contig_ln($genome,$contig) - 300)))      if (  (($strand > 0) && ($end > ($self->contig_ln($genome,$contig) - 300)))
7956         || (($strand < 0) && ($end < 300))         || (($strand < 0) && ($end < 300))
7957         ) {         ) {
7958          return qq(start);          return qq(stop);
7959      }      }
7960      return qq();      return qq();
7961  }  }

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