[Bioperl-guts-l] [15002] bioperl-live/trunk: * fix POD

[Christopher John Fields]

Revision: 15002
Author:   cjfields
Date:     2008-11-17 21:43:47 -0500 (Mon, 17 Nov 2008)

Log Message:
-----------
* fix POD
* make verbose to trip evals

Modified Paths:
--------------
    bioperl-live/trunk/Bio/Search/Hit/ModelHit.pm
    bioperl-live/trunk/t/SearchIO_infernal.t

Modified: bioperl-live/trunk/Bio/Search/Hit/ModelHit.pm
===================================================================
--- bioperl-live/trunk/Bio/Search/Hit/ModelHit.pm	2008-11-17 22:59:46 UTC (rev 15001)
+++ bioperl-live/trunk/Bio/Search/Hit/ModelHit.pm	2008-11-18 02:43:47 UTC (rev 15002)
@@ -31,17 +31,17 @@
 This object handles the hit data from a database search using models or
 descriptors instead of sequences, such as Infernal, HMMER, RNAMotif, etc.
 
-Unless you're writing a parser, you won't ever need to create a GenericHit or
+Unless you're writing a parser, you won't ever need to create a ModelHit or
 any other HitI-implementing object. If you use the SearchIO system, HitI objects
 are created automatically from a SearchIO stream which returns
 Bio::Search::Hit::HitI objects.
 
-Note that several HitI-based methods have been overridden from GenericHit due to
+Note that several HitI-based methods have been overridden from ModelHit due to
 their unreliability when dealing with queries that aren't sequence-based. It may
 be possible to reimplement these at a later point, but for the time being they
 will throw warnings and return w/o results.
 
-For documentation on what you can do with GenericHit (and other HitI objects),
+For documentation on what you can do with ModelHit (and other HitI objects),
 please see the API documentation in
 L<Bio::Search::Hit::HitI|Bio::Search::Hit::HitI>.
 
@@ -83,14 +83,14 @@
 
 use base qw(Bio::Search::Hit::GenericHit);
 
-=head1 HitI methods implemented in parent class Bio::Search::Hit::GenericHit
+=head1 HitI methods implemented in parent class Bio::Search::Hit::ModelHit
 
 =head2 new
 
  Title   : new
- Usage   : my $obj = Bio::Search::Hit::GenericHit->new();
- Function: Builds a new Bio::Search::Hit::GenericHit object 
- Returns : Bio::Search::Hit::GenericHit
+ Usage   : my $obj = Bio::Search::Hit::ModelHit->new();
+ Function: Builds a new Bio::Search::Hit::ModelHit object 
+ Returns : Bio::Search::Hit::ModelHit
  Args    : -name         => Name of Hit (required)
            -description  => Description (optional)
            -accession    => Accession number (optional)
@@ -584,7 +584,7 @@
         return $previous;
 }
 
-=head1 GenericHit methods overridden in ModelHit
+=head1 ModelHit methods overridden in ModelHit
 
 The following methods have been overridden due to their current reliance on
 sequence-based queries. They may be implemented in future versions of this class.

Modified: bioperl-live/trunk/t/SearchIO_infernal.t
===================================================================
--- bioperl-live/trunk/t/SearchIO_infernal.t	2008-11-17 22:59:46 UTC (rev 15001)
+++ bioperl-live/trunk/t/SearchIO_infernal.t	2008-11-18 02:43:47 UTC (rev 15002)
@@ -26,7 +26,6 @@
                                 -database => 'b_sub.fas',
                                 -hsp_minscore => 40,
                                 -convert_meta => 0,
-                                -verbose => 2
                                );
 
 $result = $searchio->next_result;
@@ -48,6 +47,8 @@
 is($result->query_name, 'Purine', "Result query_name");
 
 $hit = $result->next_hit;
+$hit->verbose(2);
+
 isa_ok($hit, 'Bio::Search::Hit::HitI');
 is($hit->ncbi_gi, '2239287', "Hit GI");
 is($hit->accession, 'U51115.1', "Hit accession");
@@ -153,7 +154,7 @@
 is($hsp->significance, undef, "HSP significance");
 is($hsp->end, 102, "HSP end");
 is($hsp->expect, undef, "HSP expect");
-
+$hsp->verbose(2);
 # These Bio::Search::HSP::HSPI methods are currently unimplemented in
 # Bio::Search::HSP::ModelHSP; they may be integrated over time but will require
 # some reconfiguring for Model-based searches
@@ -316,7 +317,7 @@
                                 -database => 'b_sub.fas',
                                 -hsp_minscore => 40,
                                 -convert_meta => 1,
-                                -symbols => $symbols
+                                -symbols => $symbols,
                                );
 
 $result = $searchio->next_result;
@@ -370,6 +371,7 @@
 is($result->query_name, 'Purine', "Result query_name");
 
 $hit = $result->next_hit;
+$hit->verbose(2);
 isa_ok($hit, 'Bio::Search::Hit::HitI');
 is($hit->ncbi_gi, '633168', "Hit GI");
 is($hit->accession, 'X83878.1', "Hit accession");
@@ -475,6 +477,7 @@
 is($hsp->significance, 1.945e-07, "HSP significance");
 is($hsp->end, 102, "HSP end");
 is($hsp->expect, 1.945e-07, "HSP expect");
+$hsp->verbose(2);
 
 # These Bio::Search::HSP::HSPI methods are currently unimplemented in
 # Bio::Search::HSP::ModelHSP; they may be integrated over time but will require