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Summary

Bio::Tools::Run::WrapperBase - A Base object for wrappers around executables

Package variables

Included modules

Inherit

Bio::Root::RootI

Synopsis

  # do not use this object directly, it provides the following methods
  # for its subclasses

  my $errstr = $obj->error_string();
  my $exe    = $obj->executable();
  $obj->save_tempfiles($booleanflag)
  my $outfile= $obj->outfile_name();
  my $tempdir= $obj->tempdir(); # get a temporary dir for executing
  my $io     = $obj->io;  # Bio::Root::IO object
  my $cleanup= $obj->cleanup(); # remove tempfiles

  $obj->run({-arg1 => $value});

Description

This is a basic module from which to build executable wrapper modules.
It has some basic methods to help when implementing new modules.

Methods

Methods description

 Title   : cleanup
 Usage   : $wrapper->cleanup();
 Function: Will cleanup the tempdir directory after a PAML run
 Returns : none
 Args    : none

 Title   : error_string
 Usage   : $obj->error_string($newval)
 Function: Where the output from the last analysus run is stored.
 Returns : value of error_string
 Args    : newvalue (optional)

 Title   : executable
 Usage   : my $exe = $factory->executable();
 Function: Finds the full path to the executable
 Returns : string representing the full path to the exe
 Args    : [optional] name of executable to set path to
           [optional] boolean flag whether or not warn when exe is not found

 Title   : io
 Usage   : $obj->io($newval)
 Function: Gets a Bio::Root::IO object
 Returns : Bio::Root::IO object
 Args    : none

 Title   : no_param_checks
 Usage   : $obj->no_param_checks($newval)
 Function: Boolean flag as to whether or not we should
           trust the sanity checks for parameter values  
 Returns : value of no_param_checks
 Args    : newvalue (optional)

 Title   : outfile_name
 Usage   : my $outfile = $wrapper->outfile_name();
 Function: Get/Set the name of the output file for this run
           (if you wanted to do something special)
 Returns : string
 Args    : [optional] string to set value to

 Title   : program_dir
 Usage   : my $dir = $factory->program_dir();
 Function: Abstract get method for dir of program. To be implemented
           by wrapper.
 Returns : string representing program directory 
 Args    : none

 Title   : program_name
 Usage   : my $name = $factory->program_name();
 Function: Abstract get method for name of program. To be implemented
           by wrapper.
 Returns : string representing program name
 Args    : none

 Title   : program_path
 Usage   : my $path = $factory->program_path();
 Function: Builds path for executable 
 Returns : string representing the full path to the exe
 Args    : none

 Title   : run
 Usage   : $wrapper->run({ARGS HERE});
 Function: Support generic running with args passed in
           as a hashref
 Returns : Depends on the implementation, status OR data
 Args    : hashref of named arguments

 Title   : save_tempfiles
 Usage   : $obj->save_tempfiles($newval)
 Function: 
 Returns : value of save_tempfiles
 Args    : newvalue (optional)

 Title   : tempdir
 Usage   : my $tmpdir = $self->tempdir();
 Function: Retrieve a temporary directory name (which is created)
 Returns : string which is the name of the temporary directory
 Args    : none

 Title   : version
 Usage   : $version = $wrapper->version()
 Function: Returns the program version (if available)
 Returns : string representing version of the program 
 Args    : [Optional] value to (re)set version string

Methods code

sub cleanup {

   my ($self) = @_;
   $self->io->_io_cleanup();
   if( defined $self->{'_tmpdir'} &&
       -d $self->{'_tmpdir'} ) {
       $self->io->rmtree($self->{'_tmpdir'});
   }

}

sub error_string {

   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'_error_string'} = $value;
    }
    return $self->{'_error_string'} || '';

}

sub executable {

   my ($self, $exe,$warn) = @_;

   if( defined $exe ) {
     $self->{'_pathtoexe'} = $exe;
   }
   unless( defined $self->{'_pathtoexe'} ) {
       my $prog_path = $self->program_path;
       if( $prog_path && -e $prog_path && -x $prog_path ) {
           $self->{'_pathtoexe'} = $prog_path;
       } else {
           my $exe;
           if( ( $exe = $self->io->exists_exe($self->program_name) ) &&
               -x $exe ) {
               $self->{'_pathtoexe'} = $exe;
           } else {
               $self->warn("Cannot find executable for ".$self->program_name) if $warn;
               $self->{'_pathtoexe'} = undef;
           }
       }
   }
   $self->{'_pathtoexe'};

}

sub io {

   my ($self) = @_;
   unless( defined $self->{'io'} ) {
       $self->{'io'} = new Bio::Root::IO(-verbose => $self->verbose());
   }
    return $self->{'io'};

}

sub no_param_checks {

   my ($self,$value) = @_;
   if( defined $value || ! defined $self->{'no_param_checks'} ) {
       $value = 0 unless defined $value;
      $self->{'no_param_checks'} = $value;
    }
    return $self->{'no_param_checks'};

}

sub outfile_name {

   my ($self,$nm) = @_;
   if( defined $nm || ! defined $self->{'_outfilename'} ) { 
       $nm = 'mlc' unless defined $nm;
       $self->{'_outfilename'} = $nm;
   }
   return $self->{'_outfilename'};

}

sub program_dir {

    my ($self) = @_;
    $self->throw_not_implemented();

}

sub program_name {

    my ($self) = @_;
    $self->throw_not_implemented();
}


1;

}

sub program_path {

    my ($self) = @_;
    my @path;
    push @path, $self->program_dir if $self->program_dir;
    push @path, $self->program_name.($^O =~ /mswin/i ?'.exe':'');

    return Bio::Root::IO->catfile(@path);

}

sub run {

   my ($self,@args) = @_;
   $self->throw_not_implemented();

}

sub save_tempfiles {

   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'save_tempfiles'} = $value;
    }
    return $self->{'save_tempfiles'};

}

sub tempdir {

   my ($self) = @_;
   
   unless( $self->{'_tmpdir'} ) {
       $self->{'_tmpdir'} = $self->io->tempdir(CLEANUP => ! $self->save_tempfiles );
   }
   unless( -d $self->{'_tmpdir'} ) { 
       mkdir($self->{'_tmpdir'},0777);
   }
   $self->{'_tmpdir'};

}

sub version {

   my ($self,@args) = @_;
   return undef;

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

Email jason@bioperl.org
Describe contact details here

Additional contributors names and emails here

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _