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Consistent indentation

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1 parent a09f77f commit 6a001cd70553d1657ce1f6d46aa96d2fa651241d @fangly fangly committed Oct 18, 2012
Showing with 52 additions and 33 deletions.
  1. +52 −33 lib/Bio/Tools/Run/Alignment/Blat.pm
@@ -85,6 +85,7 @@ methods. Internal methods are usually preceded with a _
=cut
+
package Bio::Tools::Run::Alignment::Blat;
use strict;
@@ -138,6 +139,7 @@ sub new {
return $self;
}
+
=head2 program_name
Title : program_name
@@ -149,9 +151,10 @@ sub new {
=cut
sub program_name {
- return 'blat';
+ return 'blat';
}
+
=head2 program_dir
Title : program_dir
@@ -163,9 +166,10 @@ sub program_name {
=cut
sub program_dir {
- return Bio::Root::IO->catfile($ENV{BLATDIR}) if $ENV{BLATDIR};
+ return Bio::Root::IO->catfile($ENV{BLATDIR}) if $ENV{BLATDIR};
}
+
=head2 run
Title : run()
@@ -177,20 +181,21 @@ sub program_dir {
=cut
sub run {
- my ($self,$query) = @_;
- my @feats;
-
- if (ref($query) ) { # it is an object
- if (ref($query) =~ /GLOB/) {
- $self->throw("Cannot use filehandle as argument to run()");
- }
- my $infile = $self->_writeSeqFile($query);
+ my ($self,$query) = @_;
+ my @feats;
+
+ if (ref($query) ) { # it is an object
+ if (ref($query) =~ /GLOB/) {
+ $self->throw("Cannot use filehandle as argument to run()");
+ }
+ my $infile = $self->_writeSeqFile($query);
return $self->_run($infile);
- } else {
- return $self->_run($query);
- }
+ } else {
+ return $self->_run($query);
+ }
}
+
=head2 align
Title : align
@@ -200,13 +205,15 @@ sub run {
=cut
sub align {
- return shift->run(@_);
+ return shift->run(@_);
}
+
=head2 db
=cut
+
sub db {
my $self = shift;
return $self->{blat_db} = shift if @_;
@@ -218,6 +225,7 @@ sub db {
*DB = \&db;
+
=head2 qsegment
Title : qsegment
@@ -242,6 +250,7 @@ sub qsegment {
return $self->{blat_qsegment};
}
+
=head2 tsegment
Title : tsegment
@@ -266,13 +275,15 @@ sub tsegment {
return $self->{blat_tsegment};
}
+
# override this, otherwise one gets a default of 'mlc'
sub outfile_name {
my $self = shift;
return $self->{blat_outfile} = shift if @_;
return $self->{blat_outfile};
}
+
=head2 searchio
Title : searchio
@@ -298,12 +309,11 @@ sub searchio {
return $self->{blat_searchio} || {};
}
+
=head1 Bio::ParameterBaseI-specific methods
These methods are part of the Bio::ParameterBaseI interface
-=cut
-
=head2 set_parameters
Title : set_parameters
@@ -313,6 +323,7 @@ These methods are part of the Bio::ParameterBaseI interface
Args : [optional] hash or array of parameter/values. These can optionally
be hash or array references
Note : This only sets parameters; to set methods use the method name
+
=cut
sub set_parameters {
@@ -338,6 +349,7 @@ sub set_parameters {
}
}
+
=head2 reset_parameters
Title : reset_parameters
@@ -356,6 +368,7 @@ sub reset_parameters {
}
}
+
=head2 validate_parameters
Title : validate_parameters
@@ -370,6 +383,7 @@ sub reset_parameters {
sub validate_parameters { 0 }
+
=head2 parameters_changed
Title : parameters_changed
@@ -383,6 +397,7 @@ sub validate_parameters { 0 }
sub parameters_changed { 1 }
+
=head2 available_parameters
Title : available_parameters
@@ -400,6 +415,7 @@ sub available_parameters {
return @params;
}
+
=head2 get_parameters
Title : get_parameters
@@ -422,12 +438,11 @@ sub get_parameters {
return %params;
}
+
=head1 to_* methods
All to_* methods are implementation-specific
-=cut
-
=head2 to_exe_string
Title : to_exe_string
@@ -484,6 +499,7 @@ sub to_exe_string {
$string;
}
+
#=head2 _input
#
# Title : _input
@@ -496,12 +512,13 @@ sub to_exe_string {
sub _input() {
my ($self,$infile1) = @_;
- if(defined $infile1){
- $self->{'input'}=$infile1;
- }
- return $self->{'input'};
+ if (defined $infile1) {
+ $self->{'input'} = $infile1;
+ }
+ return $self->{'input'};
}
+
#=head2 _database
#
# Title : _database
@@ -530,31 +547,31 @@ sub _database() {
#=cut
sub _run {
- my ($self)= shift;
- my $str = $self->to_exe_string(-seq_file => shift);
+ my ($self)= shift;
+ my $str = $self->to_exe_string(-seq_file => shift);
my $out = $self->outfile_name || $self->_tempfile;
$str .= " $out".$self->_quiet;
- $self->debug($str."\n") if( $self->verbose > 0 );
+ $self->debug($str."\n") if( $self->verbose > 0 );
my %params = $self->get_parameters;
- my $status = system($str);
- $self->throw( "Blat call ($str) crashed: $? \n") unless $status==0;
-
+ my $status = system($str);
+ $self->throw( "Blat call ($str) crashed: $? \n") unless $status==0;
+
my $format = exists($params{out}) ?
$searchio_map{$params{out}} : 'psl';
- my @io = ref ($out) !~ /GLOB/ ? (-file => $out,) : (-fh => $out,);
- my $blat_obj = Bio::SearchIO->new(%{$self->searchio},
+ my @io = ref ($out) !~ /GLOB/ ? (-file => $out,) : (-fh => $out,);
+ my $blat_obj = Bio::SearchIO->new(%{$self->searchio},
@io,
-query_type => $params{prot} ? 'protein' :
$params{q} || 'dna',
-hit_type => $params{prot} ? 'protein' :
$params{t} || 'dna',
-format => $format);
- return $blat_obj;
+ return $blat_obj;
}
@@ -577,14 +594,16 @@ sub _writeSeqFile {
return $inputfile;
}
+
sub _tempfile {
my $self = shift;
my ($tfh,$outfile) = $self->io->tempfile(-dir=>$Bio::Root::IO::TEMPDIR);
- # this is because we only want a unique filename
- close($tfh);
+ # this is because we only want a unique filename
+ close($tfh);
return $outfile;
}
+
sub _quiet {
my $self = shift;
my $q = '';

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