[Bioperl-l] Bio::SeqIO::abi - [PATCH] Update pod and make get_trace_data() return the current value.

Adam Sjøgren asjo at koldfront.dk
Thu Jul 16 08:47:44 EDT 2009

The pod references the option -read_graph_data and the method
read_graph_data(), but neither are handled by the code; the code
uses "get_trace_data".

The method get_trace_data() is used as an accessor in the code:
called without an argument to read the value - but the method
overwrites the current value with 0 if called without any arguments;
so calling get_trace_data() without arguments returns 0 always,
making it impossible to reach the read_trace_with_graph() call.
 Bio/SeqIO/abi.pm |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Bio/SeqIO/abi.pm b/Bio/SeqIO/abi.pm
index d6bc2da..2638b38 100644
--- a/Bio/SeqIO/abi.pm
+++ b/Bio/SeqIO/abi.pm
@@ -24,7 +24,7 @@ Do not use this module directly.  Use it via the Bio::SeqIO class.
 This object can transform Bio::Seq objects to and from abi trace
 files.  To optionally read the trace graph data (which can be used
 to draw chromatographs, for instance), set the optional
-'-read_graph_data' flag or the read_graph_data method to a value
+'-get_trace_data' flag or the get_trace_data method to a value
 evaluating to TRUE.
 =head1 FEEDBACK
@@ -182,7 +182,7 @@ sub write_seq {
 sub get_trace_data {
 	my ($self, $val) = @_;
-	$self->{_get_trace_data} = $val ? 1 : 0;
+	$self->{_get_trace_data} = $val ? 1 : 0 if (defined $val);

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