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removed IO's mode() usage

svn path=/bioperl-microarray/trunk/; revision=11828
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commit 04f15d265140faac379d5a8b8d71499a232c47b7 1 parent ac5165a
allenday authored
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3  Bio/Expression/MicroarrayIO/affymetrix.pm
@@ -124,7 +124,8 @@ sub _initialize{
my %param = @args;
@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
- if($self->mode eq 'r'){
+ if($param{-file} or $param{-fh}){
+# if($self->mode eq 'r'){
print STDERR "loading array template and data...\n" if $self->verbose;
$self->datafile($param{-file});
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6 Bio/Expression/MicroarrayIO/dchipxls.pm
@@ -93,7 +93,6 @@ sub new {
my $class = ref($caller) || $caller;
my $self = bless {}, $class;
-
$self->_initialize(@args);
return $self;
}
@@ -125,7 +124,8 @@ sub _initialize{
my %param = @args;
@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
- if($self->mode eq 'r'){
+ if($param{-file} or $param{-fh}){
+# if($self->mode eq 'r'){
print STDERR "loading array template and data...\n" if $self->verbose;
$self->datafile($param{-file});
@@ -165,7 +165,7 @@ sub next_array {
print STDERR "loading data...\n" if $self->verbose;
#create an object for parsing the array data;
- my $array = new Bio::Expression::Microarray::Affymetrix::dChipXLS;
+ my $array = Bio::Expression::Microarray::Affymetrix::dChipArray->new;
while ( defined( $_ = $self->_readline(-raw=>1) ) ) {
#if we see the beginning of a new file
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