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Bio::Tools::Run::WrapperBase.3pm
Langue: en
Version: 2008-06-24 (ubuntu - 08/07/09)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::Tools::Run::WrapperBase - A Base object for wrappers around executablesSYNOPSIS
# 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/wiki/Mailing_lists - 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 the web:
http://bugzilla.open-bio.org/
AUTHOR - Jason Stajich
Email jason-at-bioperl.orgAPPENDIX
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 analysis run is stored. Returns : value of error_string Args : newvalue (optional)
arguments
Title : arguments Usage : $obj->arguments($newval) Function: Commandline parameters Returns : value of arguments 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 Returns : none Args : none
io
Title : io Usage : $obj->io($newval) Function: Gets a Bio::Root::IO object Returns : 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
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre