diff variant_effect_predictor/Bio/EnsEMBL/DBFile/FileAdaptor.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/DBFile/FileAdaptor.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,220 @@
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::DBFile::FileAdaptor - Base Adaptor for direct file access
+
+=head1 DESCRIPTION
+
+Basic wrapper class to provide access to file based data.
+
+This is primarily aimed at indexed Collection(.col) files which are optimised for Slice 
+based queries. Collections store fixed width width/windowed data as BLOBS.  This makes 
+it possible to seek to the a required location given slice coordinate and read the only 
+the required amount of data covering the slice.
+
+Currently only works as hybrid DBAdaptor e.g. ResultFeatureAdaptor which inherits both from 
+here and BaseFeatureAdaptor.
+
+=cut
+
+
+
+package Bio::EnsEMBL::DBFile::FileAdaptor;
+
+use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
+use strict;
+use warnings;
+
+
+=head2 get_filehandle
+
+  Arg[1]     : string     - filepath
+  Arg[2]     : HASHREF    - Optional params, see open_file
+  Example    : my $fh     = $self->get_filehandle($filepath, 1);
+  Description: Gets and caches a simple file handle.
+  Returntype : GLOB/undef - filehandle
+  Exceptions : warns if cache entry exists but is not defined 
+  Caller     : general
+  Status     : at risk
+
+=cut
+
+sub get_filehandle{
+  my ($self, $filepath, $params_hash) = @_;
+
+  my $file_op = '<';
+
+  if(exists $params_hash->{-file_operator}){
+	$file_op = $params_hash->{-file_operator};
+  }else{
+	$params_hash->{-file_operator} = $file_op;
+  }
+
+  if(! exists $self->{file_cache}{$filepath}{filehandle}){
+	my $fh = $self->Bio::EnsEMBL::DBFile::FileAdaptor::open_file($filepath, $params_hash);
+
+	if(defined $fh){
+	  $self->{file_cache}{$filepath}{filehandle} = $fh;
+	  #$self->initialise_filehandle($filepath) if $self->can('initialise_filehandle');
+	  $self->initialise_filehandle($filepath) if($file_op eq '<');
+	}
+  }
+  elsif(! defined $self->{file_cache}{$filepath}{filehandle}){
+	#This maybe one of several read/seek errors which will have already been warned
+	warn "Encountered and error with file handle for $filepath\n";
+  }
+  #else
+  # check against cache file op
+  # to make sure we aren't trying to open an already open fh with a different operator
+
+ 
+  return $self->{file_cache}{$filepath}{filehandle};
+}
+
+
+=head2 open_file
+
+  Arg[1]     : string     - filepath
+  Arg[2]     : HASHREF    - Optional params:
+                          -binmode       => 0|1,   # Boolean i.e. treat file as binary
+                          -file_operator => '>'    # Default is '<'
+                         #-perms_octal   =>  # Requires FileHandle
+  Example    : my $fh     = $self->open_file($filepath, {-binmode = > 1, -file_operator => '>'});
+  Description: Opens a file for reading or writing.
+  Returntype : GLOB/undef - filehandle
+  Exceptions : warns if file open fails
+               warns if file operator unsupported
+               warns if failed to set binmode
+  Caller     : general
+  Status     : at risk
+
+=cut
+
+sub open_file{
+  my ($self, $filepath, $params_hash) = @_;
+
+  #Validate params_hash? 
+  #rearrange? Will not warn/throw for invalid keys?
+  #perms octal, requires FileHandle? See EFGUtils::open_file
+
+
+
+  my $file_op = $params_hash->{-file_operator} || '<';
+
+  if(($file_op ne '<') &&
+	 ($file_op ne '>') &&
+	 ($file_op ne '>>')){
+	throw("Cannot perform open with unsupported operator:\t${file_op}${filepath}");
+  }
+
+  my $fh;
+  my $success = open($fh, "${file_op}${filepath}");
+  #$fh will be still be GLOB on fail
+  
+  #These warn instead of throw/die to allow
+  #open_file to be used to test a file
+  #this prevents throws/die when an attempting to access an absent file (good for webcode)
+  #could alternatively change to throw/die and eval where required
+  #prevents need to catch everywhere else and potential double reporting of error
+
+  if(! $success){
+	#undef $fh;
+	throw("Failed to open:\t$filepath\n$!\n");
+  }
+  elsif($params_hash->{-binmode}){
+	$success = binmode $fh;
+	  
+	if(! $success){
+	  throw("Failed to set binmode:\t$filepath\n$!");
+	  #undef $fh;
+	}
+  }
+
+  return $fh;
+}
+
+
+=head2 validate_file_length
+
+  Arg[1]     : string  - filepath
+  Arg[2]     : int     - expected length in bytes
+  Example    : $self->validate_file_length($filepath, $expected_length);
+  Description: Utility method which can be used during file creation
+  Returntype : None
+  Exceptions : warns if file open fails
+               throws if file is not expected length
+  Caller     : general
+  Status     : at risk - change to seek to accounts for 'logical characters'
+
+=cut
+
+sub validate_file_length{
+  my ($self, $filepath, $expected_length, $binmode) = @_;
+
+  #Currently not using cache as we rarely want to 
+  #use the file handle afterwards
+
+
+  #THIS WAS USING EFGUtils::open_file imported in the Collector::ResultFeature!!!!
+  #which is just a sub not a class method, and is in a parallel inheritance path
+  #No warnings about redefining method :(
+  #Force use of FileAdaptor::open_file
+
+  my $fh = $self->Bio::EnsEMBL::DBFile::FileAdaptor::open_file($filepath, {-binmode => $binmode});
+
+
+  #sysseek always returns length in bytes, change to seek which 
+  #uses logical characters i.e. actual encoding?
+  #Does seek use bytes in binmode and chars in non-binmode?
+
+  my $seeked_bytes = sysseek($fh, 0, 2);# 2 is SEEK_END
+  #There is no systell function. Use sysseek(FH, 0, 1) for that.
+
+  if($seeked_bytes < $expected_length){
+	throw("File is shorter($seeked_bytes) than expected($expected_length):\t$filepath\n");
+  }
+  elsif($seeked_bytes > $expected_length){
+	throw("File is longer($seeked_bytes) than expected($expected_length):\t$filepath\n");
+  }
+ 
+  return;
+}
+
+
+
+
+
+### STUBB/TEMPLATE METHODS ###
+#
+#   If required hese should be over-ridden in the 
+#   descendant FileAdaptor e.g. CollectionAdaptor
+#   Listed here rather for visibility (rather than 
+#   using 'can')
+
+
+sub initialise_filehandle{
+  return;
+}
+
+
+
+1;