[Bioperl-guts-l] bioperl-live/Bio/Biblio Article.pm, 1.16, 1.17 Book.pm, 1.16, 1.17 BookArticle.pm, 1.15, 1.16 IO.pm, 1.19, 1.20 Journal.pm, 1.15, 1.16 JournalArticle.pm, 1.16, 1.17 MedlineArticle.pm, 1.13, 1.14 MedlineBook.pm, 1.12, 1.13 MedlineBookArticle.pm, 1.12, 1.13 MedlineJournal.pm, 1.11, 1.12 MedlineJournalArticle.pm, 1.12, 1.13 Organisation.pm, 1.15, 1.16 Patent.pm, 1.15, 1.16 Person.pm, 1.17, 1.18 Proceeding.pm, 1.14, 1.15 Provider.pm, 1.12, 1.13 PubmedArticle.pm, 1.11, 1.12 PubmedBookArticle.pm, 1.11, 1.12 PubmedJournalArticle.pm, 1.12, 1.13 Ref.pm, 1.14, 1.15 Service.pm, 1.14, 1.15 TechReport.pm, 1.14, 1.15 Thesis.pm, 1.13, 1.14 WebResource.pm, 1.15, 1.16

Senduran Balasubramaniam sendu at dev.open-bio.org
Thu Jun 14 10:16:12 EDT 2007


Update of /home/repository/bioperl/bioperl-live/Bio/Biblio
In directory dev.open-bio.org:/tmp/cvs-serv22328/Bio/Biblio

Modified Files:
	Article.pm Book.pm BookArticle.pm IO.pm Journal.pm 
	JournalArticle.pm MedlineArticle.pm MedlineBook.pm 
	MedlineBookArticle.pm MedlineJournal.pm 
	MedlineJournalArticle.pm Organisation.pm Patent.pm Person.pm 
	Proceeding.pm Provider.pm PubmedArticle.pm 
	PubmedBookArticle.pm PubmedJournalArticle.pm Ref.pm Service.pm 
	TechReport.pm Thesis.pm WebResource.pm 
Log Message:
removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"

Index: Article.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/Article.pm,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** Article.pm	26 Sep 2006 22:03:05 -0000	1.16
--- Article.pm	14 Jun 2007 14:16:10 -0000	1.17
***************
*** 14,23 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::Article (-identifier => '123abc',
                                       -first_page => 23,
                                       -last_page  => 68);
    #--- OR ---
  
!     $obj = new Bio::Biblio::Article;
      $obj->identifier ('123abc');
      $obj->first_page (23);
--- 14,23 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::Article->new(-identifier => '123abc',
                                       -first_page => 23,
                                       -last_page  => 68);
    #--- OR ---
  
!     $obj = Bio::Biblio::Article->new();
      $obj->identifier ('123abc');
      $obj->first_page (23);

Index: Journal.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/Journal.pm,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** Journal.pm	26 Sep 2006 22:03:05 -0000	1.15
--- Journal.pm	14 Jun 2007 14:16:10 -0000	1.16
***************
*** 14,22 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::Journal (-name => 'The Perl Journal',
                                       -issn  => '1087-903X');
    #--- OR ---
  
!     $obj = new Bio::Biblio::Journal;
      $obj->issn ('1087-903X');
  
--- 14,22 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::Journal->new(-name => 'The Perl Journal',
                                       -issn  => '1087-903X');
    #--- OR ---
  
!     $obj = Bio::Biblio::Journal->new();
      $obj->issn ('1087-903X');
  

Index: Patent.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/Patent.pm,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** Patent.pm	26 Sep 2006 22:03:05 -0000	1.15
--- Patent.pm	14 Jun 2007 14:16:10 -0000	1.16
***************
*** 14,22 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::Patent (-doc_number => '1-2-3-4-5');
  
    #--- OR ---
  
!     $obj = new Bio::Biblio::Patent;
      $obj->doc_number ('1-2-3-4-5');
  
--- 14,22 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::Patent->new(-doc_number => '1-2-3-4-5');
  
    #--- OR ---
  
!     $obj = Bio::Biblio::Patent->new();
      $obj->doc_number ('1-2-3-4-5');
  

Index: TechReport.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/TechReport.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** TechReport.pm	26 Sep 2006 22:03:05 -0000	1.14
--- TechReport.pm	14 Jun 2007 14:16:10 -0000	1.15
***************
*** 14,22 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::TechReport
                    (-authors => [
!                        new Bio::Biblio::Person (-lastname => 'Hasek'),
!                        new Bio::Biblio::Person (-lastname => 'Jagr'),
!                        new Bio::Biblio::Organisation (-name => 'NHL'),
                                 ]
                     -title => 'Pinned in the corner');
--- 14,22 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::TechReport->new
                    (-authors => [
!                        Bio::Biblio::Person->new(-lastname => 'Hasek'),
!                        Bio::Biblio::Person->new(-lastname => 'Jagr'),
!                        Bio::Biblio::Organisation->new(-name => 'NHL'),
                                 ]
                     -title => 'Pinned in the corner');

Index: PubmedBookArticle.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/PubmedBookArticle.pm,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** PubmedBookArticle.pm	26 Sep 2006 22:03:05 -0000	1.11
--- PubmedBookArticle.pm	14 Jun 2007 14:16:10 -0000	1.12
***************
*** 14,25 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::PubmedBookArticle
                    (-title => 'Still getting started'.
!                    -book => new Bio::Biblio::MedlineBook);
      # note that there is no specialised class PubmedBook
  
    #--- OR ---
  
!     $obj = new Bio::Biblio::PubmedBookArticle;
      $obj->title ('Still getting started');
  
--- 14,25 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::PubmedBookArticle->new
                    (-title => 'Still getting started'.
!                    -book => Bio::Biblio::MedlineBook->new());
      # note that there is no specialised class PubmedBook
  
    #--- OR ---
  
!     $obj = Bio::Biblio::PubmedBookArticle->new();
      $obj->title ('Still getting started');
  

Index: MedlineBookArticle.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/MedlineBookArticle.pm,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** MedlineBookArticle.pm	26 Sep 2006 22:03:05 -0000	1.12
--- MedlineBookArticle.pm	14 Jun 2007 14:16:10 -0000	1.13
***************
*** 14,23 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::MedlineBookArticle
                    (-title => 'Getting started'.
!                    -book => new Bio::Biblio::MedlineBook);
    #--- OR ---
  
!     $obj = new Bio::Biblio::MedlineBookArticle;
      $obj->title ('Getting started');
  
--- 14,23 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::MedlineBookArticle->new
                    (-title => 'Getting started'.
!                    -book => Bio::Biblio::MedlineBook->new());
    #--- OR ---
  
!     $obj = Bio::Biblio::MedlineBookArticle->new();
      $obj->title ('Getting started');
  

Index: Organisation.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/Organisation.pm,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** Organisation.pm	26 Sep 2006 22:03:05 -0000	1.15
--- Organisation.pm	14 Jun 2007 14:16:10 -0000	1.16
***************
*** 14,22 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::Organisation (-name => 'O\'Reilly');
  
    #--- OR ---
  
!     $obj = new Bio::Biblio::Organisation;
      $obj->name ('O\'Reilly');
  
--- 14,22 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::Organisation->new(-name => 'O\'Reilly');
  
    #--- OR ---
  
!     $obj = Bio::Biblio::Organisation->new();
      $obj->name ('O\'Reilly');
  

Index: Provider.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/Provider.pm,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** Provider.pm	26 Sep 2006 22:03:05 -0000	1.12
--- Provider.pm	14 Jun 2007 14:16:10 -0000	1.13
***************
*** 15,23 ****
  
      # usually this class is not instantiated but can be...
!     $obj = new Bio::Biblio::Provider (-type => 'Department');
  
    #--- OR ---
  
!     $obj = new Bio::Biblio::Provider;
      $obj->type ('Department');
  
--- 15,23 ----
  
      # usually this class is not instantiated but can be...
!     $obj = Bio::Biblio::Provider->new(-type => 'Department');
  
    #--- OR ---
  
!     $obj = Bio::Biblio::Provider->new();
      $obj->type ('Department');
  

Index: MedlineJournalArticle.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/MedlineJournalArticle.pm,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** MedlineJournalArticle.pm	26 Sep 2006 22:03:05 -0000	1.12
--- MedlineJournalArticle.pm	14 Jun 2007 14:16:10 -0000	1.13
***************
*** 14,27 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::MedlineJournalArticle (
                    -title => 'Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species.',
!                   -journal => new Bio::Biblio::MedlineJournal (-issn => '0027-8424'),
                    -volume => 96,
                    -issue => 7);
    #--- OR ---
  
!     $obj = new Bio::Biblio::MedlineJournalArticle;
      $obj->title ('...');
!     $obj->journal (new Bio::Biblio::MedlineJournal (-issn => '0027-8424'));
  
  =head1 DESCRIPTION
--- 14,27 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::MedlineJournalArticle->new(
                    -title => 'Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species.',
!                   -journal => Bio::Biblio::MedlineJournal->new(-issn => '0027-8424'),
                    -volume => 96,
                    -issue => 7);
    #--- OR ---
  
!     $obj = Bio::Biblio::MedlineJournalArticle->new();
      $obj->title ('...');
!     $obj->journal (Bio::Biblio::MedlineJournal->new(-issn => '0027-8424'));
  
  =head1 DESCRIPTION

Index: MedlineArticle.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/MedlineArticle.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** MedlineArticle.pm	26 Sep 2006 22:03:05 -0000	1.13
--- MedlineArticle.pm	14 Jun 2007 14:16:10 -0000	1.14
***************
*** 14,18 ****
  =head1 SYNOPSIS
  
!   $obj = new Bio::Biblio::MedlineArticle (-mesh_headings =>
                                              #array ref of hashes
                                           );
--- 14,18 ----
  =head1 SYNOPSIS
  
!   $obj = Bio::Biblio::MedlineArticle->new(-mesh_headings =>
                                              #array ref of hashes
                                           );

Index: JournalArticle.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/JournalArticle.pm,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** JournalArticle.pm	26 Sep 2006 22:03:05 -0000	1.16
--- JournalArticle.pm	14 Jun 2007 14:16:10 -0000	1.17
***************
*** 14,24 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::JournalArticle (-title => 'Come to grief',
!                                             -journal => new Bio::Biblio::Journal);
    #--- OR ---
  
!     $obj = new Bio::Biblio::JournalArticle;
      $obj->title ('Come to grief');
!     $obj->journal (new Bio::Biblio::Journal (-name => 'English Mysteries'));
  
  =head1 DESCRIPTION
--- 14,24 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::JournalArticle->new(-title => 'Come to grief',
!                                             -journal => Bio::Biblio::Journal->new());
    #--- OR ---
  
!     $obj = Bio::Biblio::JournalArticle->new();
      $obj->title ('Come to grief');
!     $obj->journal (Bio::Biblio::Journal->new(-name => 'English Mysteries'));
  
  =head1 DESCRIPTION

Index: Service.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/Service.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** Service.pm	26 Sep 2006 22:03:05 -0000	1.14
--- Service.pm	14 Jun 2007 14:16:10 -0000	1.15
***************
*** 14,22 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::Service (-name => 'Report generator');
  
    #--- OR ---
  
!     $obj = new Bio::Biblio::Service;
      $obj->name ('Report generator');
  
--- 14,22 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::Service->new(-name => 'Report generator');
  
    #--- OR ---
  
!     $obj = Bio::Biblio::Service->new();
      $obj->name ('Report generator');
  

Index: PubmedArticle.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/PubmedArticle.pm,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** PubmedArticle.pm	26 Sep 2006 22:03:05 -0000	1.11
--- PubmedArticle.pm	14 Jun 2007 14:16:10 -0000	1.12
***************
*** 14,18 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::PubmedArticle
                    (-pubmed_history_list =>
                         [ { 'pub_status' => 'pubmed',
--- 14,18 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::PubmedArticle->new
                    (-pubmed_history_list =>
                         [ { 'pub_status' => 'pubmed',
***************
*** 23,27 ****
    #--- OR ---
  
!     $obj = new Bio::Biblio::PubmedArticle;
      $obj->pubmed_status ('ppublish');
  
--- 23,27 ----
    #--- OR ---
  
!     $obj = Bio::Biblio::PubmedArticle->new();
      $obj->pubmed_status ('ppublish');
  

Index: Ref.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/Ref.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** Ref.pm	26 Sep 2006 22:03:05 -0000	1.14
--- Ref.pm	14 Jun 2007 14:16:10 -0000	1.15
***************
*** 14,22 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::Ref (-type  => 'Letter',
                                   -title => 'Onegin to Tatiana');
    #--- OR ---
  
!     $obj = new Bio::Biblio::Ref;
      $obj->type ('Letter');
  
--- 14,22 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::Ref->new(-type  => 'Letter',
                                   -title => 'Onegin to Tatiana');
    #--- OR ---
  
!     $obj = Bio::Biblio::Ref->new();
      $obj->type ('Letter');
  
***************
*** 187,191 ****
  
   Usage   : $self->add_cross_reference
!                (new Bio::Annotation::DBLink (-database   => 'EMBL',
  					     -primary_id => 'V00808');
   Function: adding a link to a database entry
--- 187,191 ----
  
   Usage   : $self->add_cross_reference
!                (Bio::Annotation::DBLink->new(-database   => 'EMBL',
  					     -primary_id => 'V00808');
   Function: adding a link to a database entry
***************
*** 208,212 ****
  =head2 add_author
  
!  Usage   : $self->add_author (new Bio::Biblio::Person (-lastname => 'Novak');
   Function: adding an author to a list of authors
   Returns : new value of 'authors' (a full list)
--- 208,212 ----
  =head2 add_author
  
!  Usage   : $self->add_author (Bio::Biblio::Person->new(-lastname => 'Novak');
   Function: adding an author to a list of authors
   Returns : new value of 'authors' (a full list)
***************
*** 228,232 ****
  =head2 add_contributor
  
!  Usage   : $self->add_contributor (new Bio::Biblio::Person (-lastname => 'Novak');
   Function: adding a contributor to a list of contributors
   Returns : new value of 'contributors' (a full list)
--- 228,232 ----
  =head2 add_contributor
  
!  Usage   : $self->add_contributor (Bio::Biblio::Person->new(-lastname => 'Novak');
   Function: adding a contributor to a list of contributors
   Returns : new value of 'contributors' (a full list)

Index: PubmedJournalArticle.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/PubmedJournalArticle.pm,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** PubmedJournalArticle.pm	26 Sep 2006 22:03:05 -0000	1.12
--- PubmedJournalArticle.pm	14 Jun 2007 14:16:10 -0000	1.13
***************
*** 14,22 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::PubmedJournalArticle (
  
                    # some attributes from MedlineJournalArticle
                    -title => 'Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species.',
!                   -journal => new Bio::Biblio::MedlineJournal (-issn => '0027-8424'),
                    -volume => 96,
                    -issue => 7,
--- 14,22 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::PubmedJournalArticle->new(
  
                    # some attributes from MedlineJournalArticle
                    -title => 'Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species.',
!                   -journal => Bio::Biblio::MedlineJournal->new(-issn => '0027-8424'),
                    -volume => 96,
                    -issue => 7,
***************
*** 31,37 ****
    #--- OR ---
  
!     $obj = new Bio::Biblio::PubmedJournalArticle;
      $obj->title ('...');
!     $obj->journal (new Bio::Biblio::MedlineJournal (-issn => '0027-8424'));
      $obj->pubmed_status ('ppublish');
  
--- 31,37 ----
    #--- OR ---
  
!     $obj = Bio::Biblio::PubmedJournalArticle->new();
      $obj->title ('...');
!     $obj->journal (Bio::Biblio::MedlineJournal->new(-issn => '0027-8424'));
      $obj->pubmed_status ('ppublish');
  

Index: WebResource.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/WebResource.pm,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** WebResource.pm	26 Sep 2006 22:03:05 -0000	1.15
--- WebResource.pm	14 Jun 2007 14:16:10 -0000	1.16
***************
*** 14,23 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::WebResource
                    (-url  => 'http://resources/best.html',
                     -estimated_size => 45000);
    # --- OR ---
  
!     $obj = new Bio::Biblio::WebResource;
      $obj->cost ('0.3 EURO');
  
--- 14,23 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::WebResource->new
                    (-url  => 'http://resources/best.html',
                     -estimated_size => 45000);
    # --- OR ---
  
!     $obj = Bio::Biblio::WebResource->new();
      $obj->cost ('0.3 EURO');
  

Index: Book.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/Book.pm,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** Book.pm	26 Sep 2006 22:03:05 -0000	1.16
--- Book.pm	14 Jun 2007 14:16:10 -0000	1.17
***************
*** 14,24 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::Book (-identifier => '123abc',
!                                   -editor => new Bio::Biblio::Person
                                              (-lastname => 'Loukides'),
                                    -isbn  => '0-596-00068-5');
    #--- OR ---
  
!     $obj = new Bio::Biblio::Book;
      $obj->isbn ('0-596-00068-5');
  
--- 14,24 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::Book->new(-identifier => '123abc',
!                                   -editor => Bio::Biblio::Person->new
                                              (-lastname => 'Loukides'),
                                    -isbn  => '0-596-00068-5');
    #--- OR ---
  
!     $obj = Bio::Biblio::Book->new();
      $obj->isbn ('0-596-00068-5');
  

Index: Thesis.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/Thesis.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** Thesis.pm	26 Sep 2006 22:03:05 -0000	1.13
--- Thesis.pm	14 Jun 2007 14:16:10 -0000	1.14
***************
*** 14,22 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::Thesis (-title => 'Perl on the edge');
  
   #--- OR ---
  
!     $obj = new Bio::Biblio::Thesis;
      $obj->title ('Perl on the edge');
  
--- 14,22 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::Thesis->new(-title => 'Perl on the edge');
  
   #--- OR ---
  
!     $obj = Bio::Biblio::Thesis->new();
      $obj->title ('Perl on the edge');
  

Index: MedlineJournal.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/MedlineJournal.pm,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** MedlineJournal.pm	26 Sep 2006 22:03:05 -0000	1.11
--- MedlineJournal.pm	14 Jun 2007 14:16:10 -0000	1.12
***************
*** 14,22 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::MedlineJournal
                 (-medline_ta => 'J Vasc Interv Radiol');
    #--- OR ---
  
!     $obj = new Bio::Biblio::MedlineJournal;
      $obj->medline_ta ('J Vasc Interv Radiol');
  
--- 14,22 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::MedlineJournal->new
                 (-medline_ta => 'J Vasc Interv Radiol');
    #--- OR ---
  
!     $obj = Bio::Biblio::MedlineJournal->new();
      $obj->medline_ta ('J Vasc Interv Radiol');
  

Index: MedlineBook.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/MedlineBook.pm,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** MedlineBook.pm	26 Sep 2006 22:03:05 -0000	1.12
--- MedlineBook.pm	14 Jun 2007 14:16:10 -0000	1.13
***************
*** 14,24 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::MedlineBook
!                   (-editor => new Bio::Biblio::Person
                               (-lastname => 'Loukides'),
                     -isbn  => '0-596-00068-5');
    #--- OR ---
  
!     $obj = new Bio::Biblio::MedlineBook;
      $obj->isbn ('0-596-00068-5');
  
--- 14,24 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::MedlineBook->new
!                   (-editor => Bio::Biblio::Person->new
                               (-lastname => 'Loukides'),
                     -isbn  => '0-596-00068-5');
    #--- OR ---
  
!     $obj = Bio::Biblio::MedlineBook->new();
      $obj->isbn ('0-596-00068-5');
  

Index: Person.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/Person.pm,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** Person.pm	26 Sep 2006 22:03:05 -0000	1.17
--- Person.pm	14 Jun 2007 14:16:10 -0000	1.18
***************
*** 14,22 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::Person (-lastname => 'Capek',
                                      -firstname => 'Karel');
    #--- OR ---
  
!     $obj = new Bio::Biblio::Person;
      $obj->firstname ('Karel');
      $obj->lastname ('Capek');
--- 14,22 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::Person->new(-lastname => 'Capek',
                                      -firstname => 'Karel');
    #--- OR ---
  
!     $obj = Bio::Biblio::Person->new();
      $obj->firstname ('Karel');
      $obj->lastname ('Capek');

Index: Proceeding.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/Proceeding.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** Proceeding.pm	26 Sep 2006 22:03:05 -0000	1.14
--- Proceeding.pm	14 Jun 2007 14:16:10 -0000	1.15
***************
*** 14,22 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::Proceeding (-title => 'JavaONE');
  
    #--- OR ---
  
!     $obj = new Bio::Biblio::Proceeding;
      $obj->title ('JavaONE');
  
--- 14,22 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::Proceeding->new(-title => 'JavaONE');
  
    #--- OR ---
  
!     $obj = Bio::Biblio::Proceeding->new();
      $obj->title ('JavaONE');
  

Index: IO.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/IO.pm,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** IO.pm	26 Sep 2006 22:03:05 -0000	1.19
--- IO.pm	14 Jun 2007 14:16:10 -0000	1.20
***************
*** 50,54 ****
      # code is used (note that the reading starts already when new()
      # is called)
!     $io = new Bio::Biblio::IO ('-format'   => 'medlinexml',
                                 '-file'     => $testfile,
                                 '-callback' => \&callback);
--- 50,54 ----
      # code is used (note that the reading starts already when new()
      # is called)
!     $io = Bio::Biblio::IO->new('-format'   => 'medlinexml',
                                 '-file'     => $testfile,
                                 '-callback' => \&callback);
***************
*** 63,67 ****
      use Bio::Biblio;
      use Bio::Biblio::IO;
!     my $xml = new Bio::Biblio->get_by_id ('12368254');
      my $reader = Bio::Biblio::IO->new ('-data' => $xml,
                                         '-format' => 'medlinexml');
--- 63,67 ----
      use Bio::Biblio;
      use Bio::Biblio::IO;
!     my $xml = Bio::Biblio->new->get_by_id ('12368254');
      my $reader = Bio::Biblio::IO->new ('-data' => $xml,
                                         '-format' => 'medlinexml');
***************
*** 74,87 ****
    #output formats:
  
!     $io = new Bio::Biblio::IO ('-format' => 'medlinexml',
                                 '-result' => 'raw');
    #--- OR ---
  
!     $io = new Bio::Biblio::IO ('-format' => 'medlinexml',
                                 '-result' => 'medline2ref');
  
    #--- OR ---
  
!     $io = new Bio::Biblio::IO ('-format' => 'pubmedxml',
                                 '-result' => 'pubmed2ref');
  
--- 74,87 ----
    #output formats:
  
!     $io = Bio::Biblio::IO->new('-format' => 'medlinexml',
                                 '-result' => 'raw');
    #--- OR ---
  
!     $io = Bio::Biblio::IO->new('-format' => 'medlinexml',
                                 '-result' => 'medline2ref');
  
    #--- OR ---
  
!     $io = Bio::Biblio::IO->new('-format' => 'pubmedxml',
                                 '-result' => 'pubmed2ref');
  
***************
*** 112,116 ****
  simple, not blessed hash table:
  
!     $io = new Bio::Biblio::IO ('-result' => 'raw');
  
  What other result formats are available depends on the module who
--- 112,116 ----
  simple, not blessed hash table:
  
!     $io = Bio::Biblio::IO->new('-result' => 'raw');
  
  What other result formats are available depends on the module who
***************
*** 118,122 ****
  ones are available:
  
!     $io = new Bio::Biblio::IO ('-result' => 'medline2ref');
  
  This is a default result format for reading citations by the
--- 118,122 ----
  ones are available:
  
!     $io = Bio::Biblio::IO->new('-result' => 'medline2ref');
  
  This is a default result format for reading citations by the
***************
*** 125,134 ****
  say where the citations come from):
  
!     $io = new Bio::Biblio::IO ('-file' => 'data/medline_data.xml');
  
  Another result format available is for PUBMED citations (which is a
  super-set of the MEDLINE citations having few more tags):
  
!     $io = new Bio::Biblio::IO ('-format' => 'pubmedxml',
                                 '-result' => 'pubmed2ref',
                                 '-data'   => $citation);
--- 125,134 ----
  say where the citations come from):
  
!     $io = Bio::Biblio::IO->new('-file' => 'data/medline_data.xml');
  
  Another result format available is for PUBMED citations (which is a
  super-set of the MEDLINE citations having few more tags):
  
!     $io = Bio::Biblio::IO->new('-format' => 'pubmedxml',
                                 '-result' => 'pubmed2ref',
                                 '-data'   => $citation);
***************
*** 136,140 ****
  Or, because C<pubmed2ref> is a default one for PUBMED citations, you can say just:
  
!     $io = new Bio::Biblio::IO ('-format' => 'pubmedxml',
                                 '-data'   => $citation);
  
--- 136,140 ----
  Or, because C<pubmed2ref> is a default one for PUBMED citations, you can say just:
  
!     $io = Bio::Biblio::IO->new('-format' => 'pubmedxml',
                                 '-data'   => $citation);
  

Index: BookArticle.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Biblio/BookArticle.pm,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** BookArticle.pm	26 Sep 2006 22:03:05 -0000	1.15
--- BookArticle.pm	14 Jun 2007 14:16:10 -0000	1.16
***************
*** 14,23 ****
  =head1 SYNOPSIS
  
!     $obj = new Bio::Biblio::BookArticle (-identifier => '123abc',
!                                          -book => new Bio::Biblio::Book);
    #--- OR ---
  
!     $obj = new Bio::Biblio::BookArticle;
!     $obj->book (new Bio::Biblio::Book);
  
  
--- 14,23 ----
  =head1 SYNOPSIS
  
!     $obj = Bio::Biblio::BookArticle->new(-identifier => '123abc',
!                                          -book => Bio::Biblio::Book->new());
    #--- OR ---
  
!     $obj = Bio::Biblio::BookArticle->new();
!     $obj->book (Bio::Biblio::Book->new());
  
  



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