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  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-03-10 07:19:11 UTC
  • mfrom: (1.2.3 upstream)
  • Revision ID: james.westby@ubuntu.com-20090310071911-fukqzw54pyb1f0bd
Tags: 1.6.0-2
https://launchpad.net/bugs/324001
* Removed patch system (not used):
  - removed instuctions in debian/rules;
  - removed quilt from Build-Depends in debian/control.
* Re-enabled tests:
  - uncommented test command in debian/rules;
  - uncommented previously missing build-dependencies in debian/control.
  - Re-enabled tests and uncommented build-dependencies accordingly.
* Removed libmodule-build-perl and libtest-harness-perl from
  Build-Depends-Indep (provided by perl-modules).
* Better cleaning of empty directories using find -type d -empty -delete
  instead of rmdir in debian/rules (LP: #324001).

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Bio/Index/Abstract.pm
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#
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# $Id: Abstract.pm,v 1.49.4.1 2006/10/02 23:10:20 sendu Exp $
 
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# $Id: Abstract.pm 15257 2008-12-24 05:27:05Z cjfields $
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#
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# BioPerl module for Bio::Index::Abstract
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#
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use Bio::Root::IO;
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use Symbol();
 
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use Symbol;
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use base qw(Bio::Root::Root);
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sub new {
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    my($class, @args) = @_;
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    my $self = $class->SUPER::new(@args);
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    my( $filename, $write_flag, $dbm_package, $cachesize, $ffactor ) =
 
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    my( $filename, $write_flag, $dbm_package, $cachesize, $ffactor, $pathtype ) =
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        $self->_rearrange([qw(FILENAME 
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                                             WRITE_FLAG
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                                             DBM_PACKAGE
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                                             CACHESIZE
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                                             FFACTOR
 
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                              WRITE_FLAG
 
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                              DBM_PACKAGE
 
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                              CACHESIZE
 
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                              FFACTOR
 
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                              PATHTYPE
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                              )], @args);
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    # Store any parameters passed
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    $self->write_flag($write_flag)   if $write_flag;
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    $self->dbm_package($dbm_package) if $dbm_package;
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    #If user doesn't give a path, we default it to absolute
 
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    $pathtype ? $self->pathtype($pathtype) : $self->pathtype('absolute');
 
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    $self->{'_filehandle'} = []; # Array in which to cache SeqIO objects
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    $self->{'_DB'}         = {}; # Gets tied to the DBM file
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        # We're really fussy/lazy, expecting all file names to be fully qualified
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        $self->throw("No files to index provided") unless @files;
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        for(my $i=0;$i<scalar @files; $i++)  {
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                if( $Bio::Root::IO::FILESPECLOADED && File::Spec->can('rel2abs') ) {        
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                        if( ! File::Spec->file_name_is_absolute($files[$i]) ) {
 
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                if( $Bio::Root::IO::FILESPECLOADED && File::Spec->can('rel2abs') ) {
 
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                        if( ! File::Spec->file_name_is_absolute($files[$i])
 
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                            && $self->pathtype() ne 'relative') {
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                                $files[$i] = File::Spec->rel2abs($files[$i]);
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                        }
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                } else {
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                                 # if it is the same size - fine. Otherwise die 
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                                 if( -s $file == $size ) {
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                                         warn "File $file already indexed. Skipping...\n" 
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                                                if $self->verbose >= 0;
 
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                                         $self->warn("File $file already indexed. Skipping..."); 
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                                         next FILE;
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                                 } else {
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                                         $self->throw("In index, $file has changed size ($size). Indicates that the index is out of date");
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                         }
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                         # index this file
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                         warn "Indexing file $file\n" if( $self->verbose > 0);
 
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                         $self->debug("Indexing file $file\n");
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                         # this is supplied by the subclass and does the serious work
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                         $recs += $self->_index_file( $file, $i ); # Specific method for each type of index
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        return ($count, $recs);
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}
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=head2 pathtype
 
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  Title   : pathtype
 
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  Usage   : $index->pathtype($pathtype)
 
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  Function: Set the type of the file path
 
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            Only two values are supported, 'relative' or 'absolute'.
 
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            If the user does not give any value, it is set to
 
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            absolute by default. Thus it mimics the default
 
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            behavior of Bio::Index::Abstract module.
 
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  Example : my $index = Bio::Index::Abstract->(-pathtype => 'relative',
 
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                                               -file     => $file.inx,
 
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                                              );
 
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            or
 
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            $index->pathtype('relative');
 
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  Returns : Type of the path.
 
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  Args    : String (relative|absolute)
 
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=cut
 
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sub pathtype {
 
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    my($self, $type) = @_;
 
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    if(defined($type)){
 
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        if($type ne 'absolute' && $type ne 'relative'){
 
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            $self->throw("Type of path can only be 'relative' or 'absolute', not [$type].");
 
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        }
 
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        $self->{'_filepathtype'} = $type;
 
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    }   
 
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    return $self->{'_filepathtype'};
 
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}
 
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=head2 _filename
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  Title   : _filename
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sub add_record {
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        my( $self, $id, @rec ) = @_;
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        $self->debug( "Adding key $id\n") if( $self->verbose > 0 );
 
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        $self->debug( "Adding key $id\n");
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        if( exists $self->db->{$id} ) {
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                $self->warn("overwriting a current value stored for $id\n");
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        }