/ 
bioperl-1.2.3
/ Bio::Tools::Run::WrapperBase

NAME

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

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.

FEEDBACK

Mailing Lists

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

Reporting Bugs

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/

AUTHOR - Jason Stajich

Email jason@bioperl.org

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

APPENDIX

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

run

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

error_string

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)

no_param_checks

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)

save_tempfiles

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

outfile_name

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

tempdir

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

cleanup

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

io

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

version

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

executable

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

program_path

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

program_dir

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

program_name

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