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R-YapRI-0.06
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/ R::YapRI::Block

NAME

R::YapRI::Block.pm

A module to segment the R commands.

SYNOPSIS


            

              
              
use R::YapRI::Base;
## WORKING WITH COMMAND BLOCKS:
my $rbase = R::YapRI::Base->new();
## Create a file-block_1
my $rblock1 = $rbase->create_block('BLOCK1');
$rblock1->add_command('x <- c(10, 9, 8, 5)');
$rblock1->add_command('z <- c(12, 8, 8, 4)');
$rblock1->add_command('x + z')
## Get name or rbase
my $blockname = $rblock1->get_blockname();
my $rbase = $rblock1->get_rbase();  
## Create a file-block_2
my $rblock2 = $rbase->create_block('BLOCK2');   
$rblock2->add_command('bmp(filename="myfile.bmp", width=600, height=800)');
$rblock2->add_command('dev.list()');
$rblock2->add_command('plot(c(1, 5, 10), type = "l")');
## Run each block
$rblock1->run_block();
$rblock2->run_block();
## Get the results
my $resultfile1 = $rblock1->get_resultfile();
my $resultfile2 = $rblock2->get_resultfile();
## Combine block before run it
my $newblock = $rbase->combine_blocks(['BLOCK1', 'BLOCK2'], 'NEWBLOCK');
$newblock->run_block();

DESCRIPTION

A wrapper to use blocks with R::YapRI::Base.

Use blocks through rbase object.

AUTHOR

Aureliano Bombarely <ab782@cornell.edu>

CLASS METHODS

The following class methods are implemented:

(*) CONSTRUCTORS:

There are two ways to create a new block:

1) Through rbase object.

my $rblock = $rbase->new_block($blockname);

2) Through R::YapRI::Block class

my $rblock = R::YapRI::Block->new($rbase, $blockname);

Both methods will add the new block to the rbase object.

constructor new


            

              
              
Usage: my $rblock = R::YapRI::Block->new($rbase, $blockname);
Desc: Create a new R block object associated with a R::YapRI::Base object
Ret: a R::YapRI::Block object
Args: $rbase, a R::YapRI::Base object.
      $blockname, an scalar, a blockname
      $cmdfile, a filename with the command file (optional).
       
Side_Effects: Die if no arguments are used.
              Die if $rbase argument is not a R::YapRI::Base object.
              Create a new command file if no commandfile is supplied.
              Add the block created to rbase object.
Example: my $rblock = R::YapRI::Block->new($rbase, 'MyBlock');

(*) ACCESSORS:

No set accessors have been created for rbase or blockname. They are controlled by R::YapRI::Base object.

get_rbase


            

              
              
Usage: my $rbase = $rblock->get_rbase(); 
Desc: Get rbase object from rblock
Ret: $rbase, a R::YapRI::Base object
Args: None
Side_Effects: None
Example: my $rbase = $rblock->get_rbase();

get_blockname


            

              
              
Usage: my $blockname = $rblock->get_blockname(); 
Desc: Get blockname from rblock object
Ret: $blockname, name of the block, an alias for cmdfile.
Args: None
Side_Effects: None
Example: my $blockname = $rblock->get_blockname();

get_command_file


            

              
              
Usage: my $filename = $rblock->get_command_file(); 
Desc: Get filename of the block from rbase object
Ret: $filename, the command filename for the block associated to rbase.
Args: None
Side_Effects: None
Example: my $filename = $rblock->get_command_file();

set_command_file


            

              
              
Usage: $rblock->set_command_file($filename); 
Desc: Set filename for a block
Ret: None
Args: $filename
Side_Effects: Die if no argument is used.
Example: $rblock->set_command_file($filename);

delete_command_file


            

              
              
Usage: $rblock->delete_command_file(); 
Desc: Delete command filename for a block and set command file as empty
Ret: None
Args: None
Side_Effects: None
Example: $rblock->delete_command_file();

get_result_file


            

              
              
Usage: my $filename = $rblock->get_result_file(); 
Desc: Get result filename of the block
Ret: $filename, the result filename for the block associated to rbase.
Args: None
Side_Effects: None
Example: my $filename = $rblock->get_result_file();

set_result_file


            

              
              
Usage: $rblock->set_result_file($filename); 
Desc: Set result filename for a block
Ret: None
Args: $filename, the result filename for the block associated to rbase.
Side_Effects: Die if no argument is used or if the result file doesnt exist
Example: $rblock->set_result_file($filename);

delete_result_file


            

              
              
Usage: $rblock->delete_result_file(); 
Desc: Delete result filename for a block and set command file as empty
Ret: None
Args: None
Side_Effects: None
Example: $rblock->delete_result_file();

(*) COMMAND METHODS:

add_command


            

              
              
Usage: $rblock->add_command($r_command); 
Desc: Add a R command line to a block
Ret: None
Args: $r_command, a string or a hash ref. with the R commands.
      If hashref. is used, it will translated to R using r_var from
      R::YapRI::Interpreter::Perl
Side_Effects: Die if no argument is used.
              Die if argument is not an scalar or an hash reference.
              Translate a perl hashref. to R command if hashref is used.
Example: $rblock->add_command('x <- c(10, 9, 8, 5)')
         $rblock->add_command({ '' => { x => [10, 9, 8, 5] } })

read_commands


            

              
              
Usage: my @commands = $rblock->read_commands(); 
Desc: Read all the R command lines from a block and return them in an 
      array.
Ret: @commands, an array with the commands used in the block
Args: None
Side_Effects: None
Example: None

run_block


            

              
              
Usage: $rblock->run_block(); 
Desc: Run R commands for a specific block.
Ret: None
Args: None
Side_Effects: None
Example: $rblock->run_block();

read_results


            

              
              
Usage: my @results = $rblock->read_results(); 
Desc: Read all the results lines from a block and return them as an 
      array.
Ret: @results, an array with the produced by the block
Args: None
Side_Effects: None
Example: my @results = $rblock->read_results();

(*) DESTRUCTORS:

Destructor will delete the files associated with this block (command and result) if the rbase switch keepfiles is disabled.

DESTROY


            

              
              
Usage: $block->DESTROY(); 
Desc: Destructor for block object. It also delete the command file and
      the result files associated with that block if keepfiles from
      rbase is disabled
Ret: None
Args: None
Side_Effects: None
Example: $block->DESTROY();

ACKNOWLEDGEMENTS

Lukas Mueller

Robert Buels

Naama Menda

Jonathan "Duke" Leto

COPYRIGHT AND LICENCE

Copyright 2011 Boyce Thompson Institute for Plant Research

Copyright 2011 Sol Genomics Network (solgenomics.net)

This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.