[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 12:47:44 UTC 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);
$self->{_get_trace_data};
}
--
1.6.0.4
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