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

[Chris Fields]

Adam,

I'll patch these, however the best way to send patches is by following  
this:

http://www.bioperl.org/wiki/HOWTO:SubmitPatch

chris

On Jul 16, 2009, at 7:47 AM, Adam Sjøgren wrote:

> 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
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l