2 spacing not 4 spacing

modules/Bio/EnsEMBL/Utils/IO/FASTASerializer.pm

@@ -6,7 +6,7 @@
   This software is distributed under a modified Apache license.
   For license details, please see
 
-    http://www.ensembl.org/info/about/code_licence.html
+  http://www.ensembl.org/info/about/code_licence.html
 
 =head1 CONTACT
 
@@ -28,25 +28,25 @@ Bio::EnsEMBL::Utils::IO::FASTASerializer
   $serializer->chunk_factor(1000);
   $serializer->line_width(60);
   $serializer->print_Seq($slice);
-  
+
   $serializer = Bio::EnsEMBL::Utils::IO::FASTASerializer->new($filehandle,
-    sub {
-        my $slice = shift;
-        return "Custom header";
-    }
+  sub {
+    my $slice = shift;
+    return "Custom header";
+  }
   );
-  
+
 =head1 DESCRIPTION
 
   Replacement for SeqDumper, making better use of shared code. Outputs FASTA
   format with optional custom header and formatting parameters. Set line_width
   and chunk_factor to dictate buffer size depending on application. A 60kb
   buffer is used by default with a line width of 60 characters.
-  
+
   Custom headers are set by supplying an anonymous subroutine to new(). Custom
-  header code must accept a Slice or Bio::PrimarySeqI compliant object as 
+  header code must accept a Slice or Bio::PrimarySeqI compliant object as
   argument and return a string.
-  
+
   The custom header method can be overridden later through set_custom_header()
   but this is not normally necessary.
 
@@ -63,162 +63,162 @@ use base qw(Bio::EnsEMBL::Utils::IO::Serializer);
 
 =head2 new
 
-  Arg [1]    : Filehandle (optional) 
-  Arg [2]    : CODEREF subroutine for writing custom headers
-  Arg [3]    : [optional] Chunking size (integer)
-  Arg [4]    : [optional] Line width (integer)
-  Example    : $dumper = Bio::EnsEMBL::Utils::IO::FASTASerializer->new($filehandle,$header_function,1000,60);
+  Arg [1]  : Filehandle (optional)
+  Arg [2]  : CODEREF subroutine for writing custom headers
+  Arg [3]  : [optional] Chunking size (integer)
+  Arg [4]  : [optional] Line width (integer)
+  Example  : $dumper = Bio::EnsEMBL::Utils::IO::FASTASerializer->new($filehandle,$header_function,1000,60);
   Description: Constructor
-               Allows the specification of a custom function for rendering
-               header lines.
+         Allows the specification of a custom function for rendering
+         header lines.
   Returntype : Bio::EnsEMBL::Utils::IO::FASTASerializer;
   Exceptions : none
-  Caller     : general
+  Caller   : general
 
 =cut
 
 sub new {
-    my $caller = shift;
-    my $class = ref($caller) || $caller;
-    my $filehandle = shift;
-    my $header_function = shift;
-    my $chunk_factor = shift;
-    my $line_width = shift;
-    
-    my $self = $class->SUPER::new($filehandle);
-    
-    $self->{'header_function'} = $header_function;
-    $self->{'line_width'} = ($line_width)? $line_width : 60; 
-    $self->{'chunk_factor'} = ($chunk_factor)? $chunk_factor : 1000; 
-    # gives a 60kb buffer by default, increase for higher database and disk efficiency. 
-    
-    # TODO: Check this error trap works as intended
-    if ( defined($self->{'header_function'}) ) { 
-        if (ref($self->{'header_function'}) ne "CODE") { 
-            throw("Custom header function must be an anonymous subroutine when instantiating FASTASerializer");}
-    }
-    else {
-        $self->{'header_function'} = sub {
-            my $slice = shift;
-            
-            if(check_ref($slice, 'Bio::EnsEMBL::Slice')) {
-                my $id       = $slice->seq_region_name;
-                my $seqtype  = 'dna';
-                my $idtype   = $slice->coord_system->name;
-                my $location = $slice->name;
-                
-                return "$id $seqtype:$idtype $location";
-            }
-            else {
-                # must be a Bio::Seq , or we're doomed
-                
-                return $slice->display_id;
-            }
-        };
-        
-    }
-    
-    return $self;
+  my $caller = shift;
+  my $class = ref($caller) || $caller;
+  my $filehandle = shift;
+  my $header_function = shift;
+  my $chunk_factor = shift;
+  my $line_width = shift;
+
+  my $self = $class->SUPER::new($filehandle);
+
+  $self->{'header_function'} = $header_function;
+  $self->{'line_width'} = ($line_width)? $line_width : 60;
+  $self->{'chunk_factor'} = ($chunk_factor)? $chunk_factor : 1000;
+  # gives a 60kb buffer by default, increase for higher database and disk efficiency.
+
+  # TODO: Check this error trap works as intended
+  if ( defined($self->{'header_function'}) ) {
+    if (ref($self->{'header_function'}) ne "CODE") {
+      throw("Custom header function must be an anonymous subroutine when instantiating FASTASerializer");}
+  }
+  else {
+    $self->{'header_function'} = sub {
+      my $slice = shift;
+
+      if(check_ref($slice, 'Bio::EnsEMBL::Slice')) {
+        my $id     = $slice->seq_region_name;
+        my $seqtype  = 'dna';
+        my $idtype   = $slice->coord_system->name;
+        my $location = $slice->name;
+
+        return "$id $seqtype:$idtype $location";
+      }
+      else {
+        # must be a Bio::Seq , or we're doomed
+
+        return $slice->display_id;
+      }
+    };
+
+  }
+
+  return $self;
 }
 
 =head2 print_metadata
 
-    Arg [1]    : Bio::EnsEMBL::Slice
-    Description: Printing header lines into FASTA files. Usually handled
-                 internally to the serializer.                
-    Returntype : None
-    Caller     : print_Seq
+  Arg [1]  : Bio::EnsEMBL::Slice
+  Description: Printing header lines into FASTA files. Usually handled
+         internally to the serializer.
+  Returntype : None
+  Caller   : print_Seq
 =cut
 
 sub print_metadata {
-    my $self = shift;
-    my $slice = shift;
-    my $fh = $self->{'filehandle'};
-    my $function = $self->header_function();
-    my $metadata = $function->($slice);
-    print $fh '>'.$metadata."\n";
+  my $self = shift;
+  my $slice = shift;
+  my $fh = $self->{'filehandle'};
+  my $function = $self->header_function();
+  my $metadata = $function->($slice);
+  print $fh '>'.$metadata."\n";
 }
 
 =head2 print_Seq
 
-    Arg [1]    : Bio::EnsEMBL::Slice or other Bio::PrimarySeqI compliant object
-    
-    Description: Serializes the slice into FASTA format. Buffering is used
-                 While other Bioperl PrimarySeqI implementations can be used,
-                 a custom header function will be required to accommodate it.
-                 
-    Returntype : None
-    
+  Arg [1]  : Bio::EnsEMBL::Slice or other Bio::PrimarySeqI compliant object
+
+  Description: Serializes the slice into FASTA format. Buffering is used
+         While other Bioperl PrimarySeqI implementations can be used,
+         a custom header function will be required to accommodate it.
+
+  Returntype : None
+
 =cut
 
 sub print_Seq {
-    my $self = shift;
-    my $slice = shift;
-    my $fh = $self->{'filehandle'};
-    
-    $self->print_metadata($slice);
-    my $width = $self->{line_width};
-    
-    # set buffer size
-    my $chunk_size = $self->{'chunk_factor'} * $width;
-        
-    my $start = 1;
-    my $end = $slice->length();
+  my $self = shift;
+  my $slice = shift;
+  my $fh = $self->{'filehandle'};
+
+  $self->print_metadata($slice);
+  my $width = $self->{line_width};
+
+  # set buffer size
+  my $chunk_size = $self->{'chunk_factor'} * $width;
+
+  my $start = 1;
+  my $end = $slice->length();
 
   #chunk the sequence to conserve memory, and print
-  
+
   my $here = $start;
-  
+
   while($here <= $end) {
     my $there = $here + $chunk_size - 1;
-    $there = $end if($there > $end); 
+    $there = $end if($there > $end);
     my $seq = $slice->subseq($here, $there);
     $seq =~ s/(.{1,$width})/$1\n/g;
     print $fh $seq or die "Error writing to file handle";
     $here = $there + 1;
   }
-  
+
   if ($slice->length > 0) {$self->{'achieved_something'} = 1;}
-  
+
 }
 
 =head2 line_width
 
-    Arg [1]    : Integer e.g. 60 or 80
-    Description: Set and get FASTA format line width. Default is 60
-    Returntype : Integer
-    
+  Arg [1]  : Integer e.g. 60 or 80
+  Description: Set and get FASTA format line width. Default is 60
+  Returntype : Integer
+
 =cut
 
 sub line_width {
-    my $self = shift;
-    my $line_width = shift;
-    if ($line_width) { $self->{'line_width'} = $line_width };
-    return $self->{'line_width'} 
+  my $self = shift;
+  my $line_width = shift;
+  if ($line_width) { $self->{'line_width'} = $line_width };
+  return $self->{'line_width'}
 }
 
 =head2 chunk_factor
-    Arg [1]    : Integer e.g. 1000
-    Description: Set and get the multiplier used to dictate buffer size
-                 Chunk factor x line width = buffer size in bases.
-    Returntype : Integer
+  Arg [1]  : Integer e.g. 1000
+  Description: Set and get the multiplier used to dictate buffer size
+         Chunk factor x line width = buffer size in bases.
+  Returntype : Integer
 =cut
 
 sub chunk_factor {
-    my $self = shift;
-    my $chunk_factor = shift;
-    if ($chunk_factor) { $self->{'chunk_factor'} = $chunk_factor};
-    return $self->{'chunk_factor'}
+  my $self = shift;
+  my $chunk_factor = shift;
+  if ($chunk_factor) { $self->{'chunk_factor'} = $chunk_factor};
+  return $self->{'chunk_factor'}
 }
 
 =head2 set_custom_header
 
-    Arg [1]    : CODE reference
-    Description: Set the custom header function. Normally this is done at
-                 construction time, but can be overridden here.
-    Example    : $serializer->set_custom_header( sub { return 'New header'});
-    Returntype : 
-    
+  Arg [1]  : CODE reference
+  Description: Set the custom header function. Normally this is done at
+         construction time, but can be overridden here.
+  Example  : $serializer->set_custom_header( sub { return 'New header'});
+  Returntype :
+
 =cut
 
 sub set_custom_header {
@@ -229,11 +229,11 @@ sub set_custom_header {
 
 =head2 header_function
 
-    Arg [1]    : CODE reference (optional)
-    Description: Getter/setter for the custom header code
-    Example    : $serializer->header_function( sub { return 'New header'});
-    Returntype : CODE
-    
+  Arg [1]  : CODE reference (optional)
+  Description: Getter/setter for the custom header code
+  Example  : $serializer->header_function( sub { return 'New header'});
+  Returntype : CODE
+
 =cut
 
 sub header_function {
@@ -245,4 +245,4 @@ sub header_function {
   return $self->{header_function};
 }
 
-1;
\ No newline at end of file
+1;