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Patch file needed for bioperl 1.2.1 in connection with bioperl-db.

svn path=/bioperl-db/trunk/; revision=438
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commit c84a201ea09a4e4177d86226537cf519b89ae86d 1 parent 71b40ef
@hlapp hlapp authored
Showing with 109 additions and 0 deletions.
  1. +109 −0 onto-term.patch
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109 onto-term.patch
@@ -0,0 +1,109 @@
+Index: Bio/Annotation/OntologyTerm.pm
+*** Bio/Annotation/OntologyTerm.pm 28 Feb 2003 05:15:42 -0000 1.5
+--- Bio/Annotation/OntologyTerm.pm 4 Apr 2003 15:39:25 -0000
+***************
+*** 388,392 ****
+--- 388,490 ----
+ return shift->term()->remove_synonyms(@_);
+ } # remove_synonyms
+
++ =head2 get_dblinks
++
++ Title : get_dblinks()
++ Usage : @ds = $term->get_dblinks();
++ Function: Returns a list of each dblinks of this GO term.
++ Returns : A list of dblinks [array of [scalars]].
++ Args :
++
++ =cut
++
++ sub get_dblinks {
++ return shift->term->get_dblinks(@_);
++ } # get_dblinks
++
++
++ =head2 add_dblink
++
++ Title : add_dblink
++ Usage : $term->add_dblink( @dbls );
++ or
++ $term->add_dblink( $dbl );
++ Function: Pushes one or more dblinks
++ into the list of dblinks.
++ Returns :
++ Args : One dblink [scalar] or a list of
++ dblinks [array of [scalars]].
++
++ =cut
++
++ sub add_dblink {
++ return shift->term->add_dblink(@_);
++ } # add_dblink
++
++
++ =head2 remove_dblinks
++
++ Title : remove_dblinks()
++ Usage : $term->remove_dblinks();
++ Function: Deletes (and returns) the definition references of this GO term.
++ Returns : A list of definition references [array of [scalars]].
++ Args :
++
++ =cut
++
++ sub remove_dblinks {
++ return shift->term->remove_dblinks(@_);
++ } # remove_dblinks
++
++ =head2 get_secondary_ids
++
++ Title : get_secondary_ids
++ Usage : @ids = $term->get_secondary_ids();
++ Function: Returns a list of secondary identifiers of this Term.
++
++ Secondary identifiers mostly originate from merging terms,
++ or possibly also from splitting terms.
++
++ Returns : A list of secondary identifiers [array of [scalar]]
++ Args :
++
++ =cut
++
++ sub get_secondary_ids {
++ return shift->term->get_secondary_ids(@_);
++ } # get_secondary_ids
++
++
++ =head2 add_secondary_id
++
++ Title : add_secondary_id
++ Usage : $term->add_secondary_id( @ids );
++ or
++ $term->add_secondary_id( $id );
++ Function: Adds one or more secondary identifiers to this term.
++ Returns :
++ Args : One or more secondary identifiers [scalars]
++
++ =cut
++
++ sub add_secondary_id {
++ return shift->term->add_secondary_id(@_);
++ } # add_secondary_id
++
++
++ =head2 remove_secondary_ids
++
++ Title : remove_secondary_ids
++ Usage : $term->remove_secondary_ids();
++ Function: Deletes (and returns) the secondary identifiers of this Term.
++ Returns : The previous list of secondary identifiers [array of [scalars]]
++ Args :
++
++ =cut
++
++ sub remove_secondary_ids {
++ return shift->term->remove_secondary_ids(@_);
++ } # remove_secondary_ids
++
+
+ 1;

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