From 06b5d0db4c62821db55b45e193308ddaad8c1232 Mon Sep 17 00:00:00 2001
From: lapp <lapp@bioperl.org>
Date: Mon, 10 Mar 2003 21:53:56 +0000
Subject: [PATCH] Sync'ed RichSeqI with the implementation. RichSeq provides
 backward compatibility to the old API. Fixed doc bug in SimpleValue.

svn path=/bioperl-live/trunk/; revision=5736
---
 Bio/Annotation/SimpleValue.pm |  3 ++-
 Bio/Seq/RichSeq.pm            |  2 +-
 Bio/Seq/RichSeqI.pm           | 33 ++++++++++++++++++++++++---------
 t/Taxonomy.t                  |  1 +
 4 files changed, 28 insertions(+), 11 deletions(-)

diff --git a/Bio/Annotation/SimpleValue.pm b/Bio/Annotation/SimpleValue.pm
index fe54b3ff8..e2e3fd50f 100644
--- a/Bio/Annotation/SimpleValue.pm
+++ b/Bio/Annotation/SimpleValue.pm
@@ -221,7 +221,8 @@ sub value{
 
  Example : 
  Returns : a L<Bio::Ontology::TermI> compliant object, or undef
- Args    : on set, new value (a scalar or undef, optional)
+ Args    : on set, new value (a L<Bio::Ontology::TermI> compliant
+           object or undef, optional)
 
 
 =cut
diff --git a/Bio/Seq/RichSeq.pm b/Bio/Seq/RichSeq.pm
index 7e8ed6b8d..715bcb8f7 100644
--- a/Bio/Seq/RichSeq.pm
+++ b/Bio/Seq/RichSeq.pm
@@ -131,7 +131,7 @@ sub new {
     defined $division && $self->division($division);
     defined $mol && $self->molecule($mol);
     if(defined($keywords)) {
-	if(ref($keywords) eq "ARRAY") {
+	if(ref($keywords) && (ref($keywords) eq "ARRAY")) {
 	    $self->add_keyword(@$keywords);
 	} else {
 	    # got a string - use the old API
diff --git a/Bio/Seq/RichSeqI.pm b/Bio/Seq/RichSeqI.pm
index b3a9ca9ff..b7a93ddcb 100644
--- a/Bio/Seq/RichSeqI.pm
+++ b/Bio/Seq/RichSeqI.pm
@@ -12,7 +12,7 @@
 
 =head1 NAME
 
-Bio::Seq::RichSeqI - RichSeq interface, mainly for database orientated sequences
+Bio::Seq::RichSeqI - interface for sequences from rich data sources, mostly databases
 
 =head1 SYNOPSIS
 
@@ -22,7 +22,7 @@ Bio::Seq::RichSeqI - RichSeq interface, mainly for database orientated sequences
     @dates       = $richseq->get_dates; 
     $seq_version = $richseq->seq_version;  
     $pid         = $richseq->pid;
-    $keywords    = $richseq->keywords;
+    @keywords    = $richseq->get_keywords;
 
 =head1 DESCRIPTION
 
@@ -80,6 +80,11 @@ use Bio::SeqI;
  Title   : get_secondary_accessions
  Usage   : 
  Function: Get the secondary accessions for a sequence.
+
+           An implementation that allows modification of this array
+           property should provide the methods add_secondary_accession
+           and remove_secondary_accessions, with obvious purpose.
+
  Example :
  Returns : an array of strings
  Args    : none
@@ -165,6 +170,11 @@ sub pid {
  Usage   :
  Function: Get (and set, depending on the implementation) the dates the
            databank entry specified for the sequence
+
+           An implementation that allows modification of this array
+           property should provide the methods add_date and
+           remove_dates, with obvious purpose.
+
  Example :
  Returns : an array of strings
  Args    :
@@ -200,18 +210,23 @@ sub seq_version{
 
 }
 
-=head2 keywords
+=head2 get_keywords
 
- Title   : keywords
- Usage   : $obj->keywords($newval)
- Function: 
- Returns : value of keywords (a string)
- Args    : newvalue (optional) (a string)
+ Title   : get_keywords
+ Usage   : $obj->get_keywords()
+ Function: Get the keywords for this sequence object.
+
+           An implementation that allows modification of this array
+           property should provide the methods add_keyword and
+           remove_keywords, with obvious purpose.
+
+ Returns : an array of strings
+ Args    : 
 
 
 =cut
 
-sub keywords {
+sub get_keywords {
    my ($self) = @_;
    $self->throw("hit keywords in interface definition - error");
 }
diff --git a/t/Taxonomy.t b/t/Taxonomy.t
index 1f8549fce..5eb51ef61 100644
--- a/t/Taxonomy.t
+++ b/t/Taxonomy.t
@@ -31,6 +31,7 @@ unless( $n ) {
     ok($n->ncbi_taxid, 9606);
     ok($n->division, 'mammals');
 }
+sleep(3);
 my $yeastid = $db->get_taxaid('Saccharomyces cerevisiae');
 ok($yeastid, 4932);
 
-- 
2.11.4.GIT