[Bioperl-guts-l] [15222] bioperl-live/trunk/Bio/Tools: add deprecation messagess

Christopher John Fields cjfields at dev.open-bio.org
Sun Dec 21 01:30:17 EST 2008


Revision: 15222
Author:   cjfields
Date:     2008-12-21 01:30:17 -0500 (Sun, 21 Dec 2008)

Log Message:
-----------
add deprecation messagess

Modified Paths:
--------------
    bioperl-live/trunk/Bio/Tools/ERPIN.pm
    bioperl-live/trunk/Bio/Tools/Infernal.pm
    bioperl-live/trunk/Bio/Tools/RNAMotif.pm

Modified: bioperl-live/trunk/Bio/Tools/ERPIN.pm
===================================================================
--- bioperl-live/trunk/Bio/Tools/ERPIN.pm	2008-12-21 06:29:55 UTC (rev 15221)
+++ bioperl-live/trunk/Bio/Tools/ERPIN.pm	2008-12-21 06:30:17 UTC (rev 15222)
@@ -115,6 +115,7 @@
 
 sub _initialize {
     my($self, at args) = @_;
+    $self->warn('Use of this module is deprecated.  Use Bio::SearchIO::erpin instead');    
     $self->SUPER::_initialize(@args);
     my ($motiftag,$desctag,$srctag) =  $self->SUPER::_rearrange([qw(MOTIFTAG
                                                                     DESCTAG

Modified: bioperl-live/trunk/Bio/Tools/Infernal.pm
===================================================================
--- bioperl-live/trunk/Bio/Tools/Infernal.pm	2008-12-21 06:29:55 UTC (rev 15221)
+++ bioperl-live/trunk/Bio/Tools/Infernal.pm	2008-12-21 06:30:17 UTC (rev 15222)
@@ -158,6 +158,7 @@
 
 sub _initialize {
   my($self, at args) = @_;
+  $self->warn('Use of this module is deprecated.  Use Bio::SearchIO::infernal instead');  
   $self->SUPER::_initialize(@args);
   my ($motiftag,$desctag,$srctag,$rfam,$cm,$ms,$ver) =
         $self->SUPER::_rearrange([qw(MOTIFTAG

Modified: bioperl-live/trunk/Bio/Tools/RNAMotif.pm
===================================================================
--- bioperl-live/trunk/Bio/Tools/RNAMotif.pm	2008-12-21 06:29:55 UTC (rev 15221)
+++ bioperl-live/trunk/Bio/Tools/RNAMotif.pm	2008-12-21 06:30:17 UTC (rev 15222)
@@ -163,6 +163,7 @@
 
 sub _initialize {
   my($self, at args) = @_;
+  $self->warn('Use of this module is deprecated.  Use Bio::SearchIO::rnamotif instead');
   $self->SUPER::_initialize(@args);
   my ($motiftag,$desctag,$srctag) =  $self->SUPER::_rearrange([qw(MOTIFTAG
                                                                   DESCTAG




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