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Author: Tatiana Malygina <merlettaia@gmail.com>
Last-Update: 2016-07-17
Description: fixes remaining spelling warnings in man pages
--- a/GO/Model/Evidence.pm
+++ b/GO/Model/Evidence.pm
@@ -246,7 +246,7 @@
Returns -
Args -
-deprected - sets first pub_xref_list
+deprecated - sets first pub_xref_list
=cut
--- a/GO/Model/GeneProduct.pm
+++ b/GO/Model/GeneProduct.pm
@@ -16,7 +16,7 @@
=head1 DESCRIPTION
represents a gene product in a particular species (this will
-effectively always be refered to implicitly by the gene symbol even
+effectively always be referred to implicitly by the gene symbol even
though a gene may have >1 product)
=cut
--- a/GO/Model/GraphIterator.pm
+++ b/GO/Model/GraphIterator.pm
@@ -86,7 +86,7 @@
Returns - bool
Args - bool
-set this if you dont want relationships to be traversed twice;
+set this if you don't want relationships to be traversed twice;
this gives a more compact tree representation of the graph
=cut
@@ -100,7 +100,7 @@
by default, all relationship types are treated as transitive, and will
be traversed by the iterator
-sometimes you dont want to traverse all relations, even if they are
+sometimes you don't want to traverse all relations, even if they are
transitive. For example, when answering the query "find all genes
expressed in the embryo" you way want subtypes of embryo and parts of
the embryo but not things that develop_from the embryo.
--- a/GO/Model/Root.pm
+++ b/GO/Model/Root.pm
@@ -315,7 +315,7 @@
$name =~ s/.*://; # strip fully-qualified portion
if ($name eq "DESTROY") {
- # we dont want to propagate this!!
+ # we don't want to propagate this!!
return;
}
--- a/GO/Model/Seq.pm
+++ b/GO/Model/Seq.pm
@@ -185,7 +185,7 @@
$name =~ s/.*://; # strip fully-qualified portion
if ($name eq "DESTROY") {
- # we dont want to propagate this!!
+ # we don't want to propagate this!!
return;
}
--- a/GO/Model/Species.pm
+++ b/GO/Model/Species.pm
@@ -16,7 +16,7 @@
=head1 DESCRIPTION
represents a gene product in a particular species (this will
-effectively always be refered to implicitly by the gene symbol even
+effectively always be referred to implicitly by the gene symbol even
though a gene may have >1 product)
=cut
@@ -51,4 +51,3 @@
my $self = shift;
return ($self->genus || "")." ".($self->species || "");
}
-
--- a/GO/Model/Term.pm
+++ b/GO/Model/Term.pm
@@ -685,10 +685,10 @@
$as2->gene_product->symbol;
}
elsif ($sortk eq "ev_code") {
- confess("cant sort on evcode yet");
+ confess("can't sort on ev_code yet");
}
else {
- confess("dont know $sortk");
+ confess("don't know $sortk");
}
}
$cmp;
--- a/GO/Model/Xref.pm
+++ b/GO/Model/Xref.pm
@@ -184,7 +184,7 @@
Returns - string
Args - indent [integer]
-XML representation; you probably shouldnt call this directly, this
+XML representation; you probably shouldn't call this directly, this
will be called by entities that own xrefs
=cut
--- a/GO/Parser.pm
+++ b/GO/Parser.pm
@@ -246,7 +246,7 @@
the advantage of an event based parsing architecture is that it is
easy to build lightweight parsers, and heavy weight object models can
-be bypassed if prefered.
+be bypassed if preferred.
=head2 EXAMPLES
--- a/go-perl.pod
+++ b/go-perl.pod
@@ -30,7 +30,7 @@
=head1 DESCRIPTION
go-perl is part of the go-dev code distribution. It is also available
-as a seperate library in its own right.
+as a separate library in its own right.
go-perl is a collection of perl modules for working with ontologies
and data, in particular the Gene Ontology and other Open
|
