NAME

RandomJungle::File::OOB - Low level access to the data in the RandomJungle OOB output file

VERSION

Version 0.05

SYNOPSIS

RandomJungle::File::OOB provides access to the data contained within RandomJungle's OOB output file. See RandomJungle::Jungle for higher-level methods.

        use RandomJungle::File::OOB;

        my $oob = RandomJungle::File::OOB->new( filename => $oobfile ) || die $RandomJungle::File::OOB::ERROR;
        $oob->parse || die $oob->err_str;

        my $file = $oob->get_filename; # returns the filename of the OOB file
        my $aref = $oob->get_matrix; # returns an aref to the entire matrix (all lines, in file order)

        # Note $i is the index (row num) of the sample, not the IID
        my $line = $oob->get_data_for_sample_index( $i ) || die $oob->err_str; # $line is unsplit

        my $href = $oob->get_data; # for debugging only; returns raw data structs

        # Error handling
        $oob->set_err( 'Something went boom' );
        my $msg = $oob->err_str;
        my $trace = $oob->err_trace;

METHODS

new()

Creates and returns a new RandomJungle::File::OOB object:

        my $oob = RandomJungle::File::OOB->new( filename => $oobfile );

The 'filename' parameter is required. Returns undef and sets $ERROR on failure.

parse()

Parses the OOB file specified in new():

        my $retval = $oob->parse;

Returns a true value on success. Sets err_str and returns undef on failure.

get_data_for_sample_index()

Returns a line from the OOB file, specified by sample index (row number, not IID):

        my $line = $oob->get_data_for_sample_index( $i ) || die $oob->err_str;

get_matrix()

Returns a reference to an array that contains the lines in the OOB file:

        my $aref = $oob->get_matrix;

get_filename()

Returns the name of the OOB file specified in new():

        my $file = $oob->get_filename;

get_data()

Returns the data structures contained in $self:

        my $href = $oob->get_data;

This method is for debugging only and should not be used in production code.

set_err()

Sets the error message (provided as a parameter) and creates a stack trace:

        $oob->set_err( 'Something went boom' );

err_str()

Returns the last error message that was set:

        my $msg = $oob->err_str;

err_trace()

Returns a backtrace for the last error that was encountered:

        my $trace = $oob->err_trace;

SEE ALSO

RandomJungle::Jungle, RandomJungle::Tree, RandomJungle::Tree::Node, RandomJungle::XML, RandomJungle::OOB, RandomJungle::RAW, RandomJungle::DB, RandomJungle::Classification_DB

AUTHOR

Robert R. Freimuth

COPYRIGHT

Copyright (c) 2011 Mayo Foundation for Medical Education and Research. All rights reserved.

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

The full text of the license can be found in the LICENSE file included with this module.

cpanm RandomJungle::Tree

perl -MCPAN -e shell
install RandomJungle::Tree