[Bioperl-guts-l] [16606] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run: refactor

Mark Allen Jensen maj at dev.open-bio.org
Wed Jan 6 08:57:49 EST 2010


Revision: 16606
Author:   maj
Date:     2010-01-06 08:57:49 -0500 (Wed, 06 Jan 2010)
Log Message:
-----------
refactor

Added Paths:
-----------
    bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/SoapEUtilities/FetchAdaptor/
    bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/SoapEUtilities/FetchAdaptor.pm

Removed Paths:
-------------
    bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap/FetchAdaptor/
    bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap/FetchAdaptor.pm

Deleted: bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap/FetchAdaptor.pm
===================================================================
--- bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap/FetchAdaptor.pm	2010-01-06 13:51:15 UTC (rev 16605)
+++ bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap/FetchAdaptor.pm	2010-01-06 13:57:49 UTC (rev 16606)
@@ -1,176 +0,0 @@
-# $Id$
-#
-# BioPerl module for Bio::Tools::Run::ESoap::FetchAdaptor
-#
-# Please direct questions and support issues to <bioperl-l at bioperl.org>
-#
-# Cared for by Mark A. Jensen <maj -at- fortinbras -dot- us>
-#
-# Copyright Mark A. Jensen
-#
-# You may distribute this module under the same terms as perl itself
-
-# POD documentation - main docs before the code
-
-=head1 NAME
-
-Bio::Tools::Run::ESoap::FetchAdaptor - Conversion of Entrez SOAP messages to BioPerl objects
-
-=head1 SYNOPSIS
-
-Give standard usage here
-
-=head1 DESCRIPTION
-
-Describe the object here
-
-=head1 FEEDBACK
-
-=head2 Mailing Lists
-
-User feedback is an integral part of the evolution of this and other
-Bioperl modules. Send your comments and suggestions preferably to
-the Bioperl mailing list.  Your participation is much appreciated.
-
-  bioperl-l at bioperl.org                  - General discussion
-http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
-
-=head2 Support
-
-Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l at bioperl.org>
-
-rather than to the module maintainer directly. Many experienced and
-reponsive experts will be able look at the problem and quickly
-address it. Please include a thorough description of the problem
-with code and data examples if at all possible.
-
-=head2 Reporting Bugs
-
-Report bugs to the Bioperl bug tracking system to help us keep track
-of the bugs and their resolution. Bug reports can be submitted via
-the web:
-
-  http://bugzilla.open-bio.org/
-
-=head1 AUTHOR - Mark A. Jensen
-
-Email maj -at- fortinbras -dot- us
-
-=head1 APPENDIX
-
-The rest of the documentation details each of the object methods.
-Internal methods are usually preceded with a _
-
-=cut
-
-package Bio::Tools::Run::ESoap::FetchAdaptor;
-use strict;
-
-use Bio::Root::Root;
-
-use base qw(Bio::Root::Root );
-
-our %TYPE_MODULE_XLT = (
-    
-    );
-
-=head2 new
-
- Title   : new
- Usage   : my $obj = new Bio::Tools::Run::ESoap::FetchAdaptor();
- Function: Builds a new Bio::Tools::Run::ESoap::FetchAdaptor object
- Returns : an instance of Bio::Tools::Run::ESoap::FetchAdaptor
- Args    : named arguments
-           -som => $soap_som_object (soap message)
-           -type => $type ( optional, forces loading of $type adaptor )
-
-=cut
-
-sub new {
-    my ($class, at args) = @_;
-    my $self = $class->SUPER::new(@args);
-    my ($som, $type) = $self->_rearrange([qw( SOM TYPE )], @args);
-    $self->throw("SOM argument required") unless $som;
-    $self->throw("SOM argument must be a SOAP::SOM object") unless
-	ref($som) eq 'SOAP::SOM';
-    # identify the correct adaptor module to load using SOM info
-    # if no module available, return raw message with warning
-    
-
-    # $type ultimately contains a FetchAdaptor subclass
-    return unless( $class->_load_adaptor($type) );
-    return "Bio::Tools::Run::ESoap::FetchAdaptor::$type"->new(@args);
-}
-
-=head2 _load_adaptor()
-
- Title   : _load_adaptor
- Usage   : 
- Function: loads a FetchAdaptor subclass
- Returns : 
- Args    : adaptor type (subclass name)
-
-=cut
-
-sub _load_adaptor {
-    my ($self, $type) = @_;
-    return unless $type;
-    my $module = "Bio::Tools::Run::ESoap::FetchAdaptor::".$type;
-    my $ok;
-    eval {
-	$ok = $self->_load_module($module);
-    };
-    for ($@) {
-	/^$/ && do {
-	    return $ok;
-	};
-	/Can't locate/ && do {
-	    $self->throw("Fetch adaptor for '$type' not found");
-	};
-	do { # else 
-	    $self->throw("Error in fetch adaptor for '$type' : $@");
-	};
-    }
-}
-
-=head2 obj_class()
-
- Title   : obj_class
- Usage   : $adaptor->obj_class
- Function: Returns the fully qualified BioPerl classname
-           of the objects returned by next_obj()
- Returns : scalar string (class name)
- Args    : none
-
-=cut
-
-sub obj_class { shift->throw_not_implemented }
-
-=head2 next_obj()
-
- Title   : next_obj
- Usage   : $obj = $adaptor->next_obj
- Function: Returns the next parsed BioPerl object from the 
-           adaptor
- Returns : object of class obj_class()
- Args    : none
-
-=cut
-
-sub next_obj { shift->throw_not_implemented }
-
-=head2 rewind()
-
- Title   : rewind
- Usage   : 
- Function: Rewind the adaptor's iterator
- Returns : 
- Args    : none
-
-=cut
-
-sub rewind { shift->throw_not_implemented }
-    
-1;

Copied: bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/SoapEUtilities/FetchAdaptor (from rev 16584, bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap/FetchAdaptor)

Copied: bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/SoapEUtilities/FetchAdaptor.pm (from rev 16605, bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap/FetchAdaptor.pm)
===================================================================
--- bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/SoapEUtilities/FetchAdaptor.pm	                        (rev 0)
+++ bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/SoapEUtilities/FetchAdaptor.pm	2010-01-06 13:57:49 UTC (rev 16606)
@@ -0,0 +1,176 @@
+# $Id$
+#
+# BioPerl module for Bio::Tools::Run::ESoap::FetchAdaptor
+#
+# Please direct questions and support issues to <bioperl-l at bioperl.org>
+#
+# Cared for by Mark A. Jensen <maj -at- fortinbras -dot- us>
+#
+# Copyright Mark A. Jensen
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Tools::Run::ESoap::FetchAdaptor - Conversion of Entrez SOAP messages to BioPerl objects
+
+=head1 SYNOPSIS
+
+Give standard usage here
+
+=head1 DESCRIPTION
+
+Describe the object here
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to
+the Bioperl mailing list.  Your participation is much appreciated.
+
+  bioperl-l at bioperl.org                  - General discussion
+http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
+
+=head2 Support
+
+Please direct usage questions or support issues to the mailing list:
+
+L<bioperl-l at bioperl.org>
+
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
+with code and data examples if at all possible.
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+of the bugs and their resolution. Bug reports can be submitted via
+the web:
+
+  http://bugzilla.open-bio.org/
+
+=head1 AUTHOR - Mark A. Jensen
+
+Email maj -at- fortinbras -dot- us
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+package Bio::Tools::Run::ESoap::FetchAdaptor;
+use strict;
+
+use Bio::Root::Root;
+
+use base qw(Bio::Root::Root );
+
+our %TYPE_MODULE_XLT = (
+    
+    );
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Tools::Run::ESoap::FetchAdaptor();
+ Function: Builds a new Bio::Tools::Run::ESoap::FetchAdaptor object
+ Returns : an instance of Bio::Tools::Run::ESoap::FetchAdaptor
+ Args    : named arguments
+           -som => $soap_som_object (soap message)
+           -type => $type ( optional, forces loading of $type adaptor )
+
+=cut
+
+sub new {
+    my ($class, at args) = @_;
+    my $self = $class->SUPER::new(@args);
+    my ($som, $type) = $self->_rearrange([qw( SOM TYPE )], @args);
+    $self->throw("SOM argument required") unless $som;
+    $self->throw("SOM argument must be a SOAP::SOM object") unless
+	ref($som) eq 'SOAP::SOM';
+    # identify the correct adaptor module to load using SOM info
+    # if no module available, return raw message with warning
+    
+
+    # $type ultimately contains a FetchAdaptor subclass
+    return unless( $class->_load_adaptor($type) );
+    return "Bio::Tools::Run::ESoap::FetchAdaptor::$type"->new(@args);
+}
+
+=head2 _load_adaptor()
+
+ Title   : _load_adaptor
+ Usage   : 
+ Function: loads a FetchAdaptor subclass
+ Returns : 
+ Args    : adaptor type (subclass name)
+
+=cut
+
+sub _load_adaptor {
+    my ($self, $type) = @_;
+    return unless $type;
+    my $module = "Bio::Tools::Run::ESoap::FetchAdaptor::".$type;
+    my $ok;
+    eval {
+	$ok = $self->_load_module($module);
+    };
+    for ($@) {
+	/^$/ && do {
+	    return $ok;
+	};
+	/Can't locate/ && do {
+	    $self->throw("Fetch adaptor for '$type' not found");
+	};
+	do { # else 
+	    $self->throw("Error in fetch adaptor for '$type' : $@");
+	};
+    }
+}
+
+=head2 obj_class()
+
+ Title   : obj_class
+ Usage   : $adaptor->obj_class
+ Function: Returns the fully qualified BioPerl classname
+           of the objects returned by next_obj()
+ Returns : scalar string (class name)
+ Args    : none
+
+=cut
+
+sub obj_class { shift->throw_not_implemented }
+
+=head2 next_obj()
+
+ Title   : next_obj
+ Usage   : $obj = $adaptor->next_obj
+ Function: Returns the next parsed BioPerl object from the 
+           adaptor
+ Returns : object of class obj_class()
+ Args    : none
+
+=cut
+
+sub next_obj { shift->throw_not_implemented }
+
+=head2 rewind()
+
+ Title   : rewind
+ Usage   : 
+ Function: Rewind the adaptor's iterator
+ Returns : 
+ Args    : none
+
+=cut
+
+sub rewind { shift->throw_not_implemented }
+    
+1;



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