[Bioperl-guts-l] [15048] bioperl-live/trunk: verbose mistakenly left on in PrimarySeq->new, which was causing RootIO to be verbose about its tempfile handling after.

Dave Messina dave_messina at dev.open-bio.org
Fri Nov 28 08:24:34 EST 2008


Revision: 15048
Author:   dave_messina
Date:     2008-11-28 08:24:34 -0500 (Fri, 28 Nov 2008)

Log Message:
-----------
verbose mistakenly left on in PrimarySeq->new, which was causing RootIO to be verbose about its tempfile handling after. I noticed this from running SeqIO/largefasta.t. Reverting r15026, wherein Heikki went after the same problem in Bio::Seq::LargeLocatableSeq. Also minor cleanup in t/SeqIO/largefasta.t and t/EUtilities.t

Modified Paths:
--------------
    bioperl-live/trunk/Bio/PrimarySeq.pm
    bioperl-live/trunk/Bio/Seq/LargeLocatableSeq.pm
    bioperl-live/trunk/t/EUtilities.t
    bioperl-live/trunk/t/SeqIO/largefasta.t

Modified: bioperl-live/trunk/Bio/PrimarySeq.pm
===================================================================
--- bioperl-live/trunk/Bio/PrimarySeq.pm	2008-11-28 10:00:33 UTC (rev 15047)
+++ bioperl-live/trunk/Bio/PrimarySeq.pm	2008-11-28 13:24:34 UTC (rev 15048)
@@ -161,7 +161,6 @@
 sub new {
     my ($class, @args) = @_;
     my $self = $class->SUPER::new(@args);
-    $self->verbose(1);
 
     my($seq,$id,$acc,$pid,$ns,$auth,$v,$oid,
        $desc,$description,

Modified: bioperl-live/trunk/Bio/Seq/LargeLocatableSeq.pm
===================================================================
--- bioperl-live/trunk/Bio/Seq/LargeLocatableSeq.pm	2008-11-28 10:00:33 UTC (rev 15047)
+++ bioperl-live/trunk/Bio/Seq/LargeLocatableSeq.pm	2008-11-28 13:24:34 UTC (rev 15048)
@@ -320,14 +320,11 @@
 
 sub DESTROY {
     my $self = shift;
-    my $verbose = $self->verbose();
-    $self->verbose(-1);
     my $fh = $self->_fh();
     close($fh) if( defined $fh );
     # this should be handled by Tempfile removal, but we'll unlink anyways.
     unlink $self->_filename() if defined $self->_filename() && -e $self->_filename;
     $self->SUPER::DESTROY();
-    $self->verbose($verbose);
 }
 
 1;

Modified: bioperl-live/trunk/t/EUtilities.t
===================================================================
--- bioperl-live/trunk/t/EUtilities.t	2008-11-28 10:00:33 UTC (rev 15047)
+++ bioperl-live/trunk/t/EUtilities.t	2008-11-28 13:24:34 UTC (rev 15048)
@@ -1,7 +1,5 @@
 # -*-Perl-*- Test Harness script for Bioperl
 # $Id$
-
-#$Id$
 #
 # Note this uses Test::More; this should catch the few perl versions w/o
 # this test suite

Modified: bioperl-live/trunk/t/SeqIO/largefasta.t
===================================================================
--- bioperl-live/trunk/t/SeqIO/largefasta.t	2008-11-28 10:00:33 UTC (rev 15047)
+++ bioperl-live/trunk/t/SeqIO/largefasta.t	2008-11-28 13:24:34 UTC (rev 15048)
@@ -14,8 +14,9 @@
 
 my $tmpfile = test_output_file();
 
-my $seqio = Bio::SeqIO->new('-format'=>'largefasta',
-							'-file'  =>test_input_file('genomic-seq.fasta'));
+my $seqio = Bio::SeqIO->new('-format' => 'largefasta',
+							'-file'   => test_input_file('genomic-seq.fasta'),
+						   );
 isa_ok($seqio, 'Bio::SeqIO');
 
 my $pseq = $seqio->next_seq();




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