[Bioperl-l] Fwd: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/Microarray/Tools: use superclasses initialization and argument processing/ attribute setting as suggested in styleguide

[Jason Stajich]

Since we've started discussing the idea of starting to move things out  
into smaller packages, does it make sense to move this Bio::Microarray  
into its own package before it gets bigger? What about the old bioperl- 
microarray stuff from Allen Day?

I also know that as we haven't branched for 1.6 Chris we'll have to  
make some decisions about new code going in before then?

Not trying to stifle any of the development with extra work but trying  
to see if we should start to make some logical slices of packages?

-jason

Begin forwarded message:

> From: Marian Thieme <thm09830 at dev.open-bio.org>
> Date: December 10, 2008 6:10:21 AM PST
> To: bioperl-guts-l at bioperl.org
> Subject: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/Microarray/ 
> Tools: use superclasses initialization and argument processing/  
> attribute setting as suggested in styleguide
>
> Revision: 15134
> Author:   thm09830
> Date:     2008-12-10 09:10:21 -0500 (Wed, 10 Dec 2008)
>
> Log Message:
> -----------
> use superclasses initialization and argument processing/attribute  
> setting as suggested in styleguide
>
> Modified Paths:
> --------------
>    bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm
>    bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm
>
> Modified: bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm
> ===================================================================
> --- bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm	 
> 2008-12-10 12:51:47 UTC (rev 15133)
> +++ bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm	 
> 2008-12-10 14:10:21 UTC (rev 15134)
> @@ -78,12 +78,13 @@
>
> sub new {
>
> -  my ($class, $file_name) = @_;
> -  my $self = $class->SUPER::new();
> +  my ($class, @args) = @_;
> +  my $self = $class->SUPER::new(@args);
> +  my ($file_name)=$self->_rearrange([qw(AFFY_DESIGN_FILENAME)],  
> @args);
> +
>   $self->{_frags_hash}=undef;
>   $self->{_oligos2calc_hash}=undef;
>   $self->throw("Must provide filename as first argument !") unless  
> $file_name;
> -
>
>   my %max_ins_hash=();
>   $self->{_frags_hash}=$self- 
> >_parse_Affy_mtDNA_design_annotation_file($file_name);
>
> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm
> ===================================================================
> --- bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm	2008-12-10  
> 12:51:47 UTC (rev 15133)
> +++ bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm	2008-12-10  
> 14:10:21 UTC (rev 15134)
> @@ -194,8 +194,11 @@
>
> sub new {
>
> -  my ($class, $design_file_name, $format, $refseq_max_ins_hash,  
> $refseq) = @_;
> -  my $self = $class->SUPER::new();
> +  #my ($class, $design_file_name, $format, $refseq_max_ins_hash,  
> $refseq) = @_;
> +  my ($class, @args) = @_;
> +  my $self = $class->SUPER::new(@args);
> +  my ($design_file_name, $format, $refseq_max_ins_hash, $refseq)= 
> $self->_rearrange([qw(AFFY_DESIGN_FILENAME FORMAT_OF_DESIGN_FILE  
> MAX_INSERTION_HASH_REFERENCE REFERENCE_SEQUENCE)], @args);
> +
>   $self->{_frags_hash}=undef;
>   $self->{_max_ins_hash}=undef;
>   $self->{_refseq}=undef;
>
>
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Jason Stajich
jason at bioperl.org