/ 
Bio-Community-0.001008
River stage zero No dependents
/ Bio::Community::Role::Table

NAME

Bio::Community::Role::Table - Role to read/write data tables and provide random access to their cells

SYNOPSIS

package My::Package;

use Moose;
extends 'Bio::Root::IO';
with 'Bio::Community::Role::Table';

# Use the new(), _read_table(), _get_value(), _set_value(), _insert_line(),
# _delete_col() and _write_table()
# methods as needed
# ...

1;

DESCRIPTION

This role implements methods to read and write file structured as a table containing rows and columns. When reading a table from a file, an index is kept to provide random-access to any cell of the table. When writing a table to a file, cell data can also be given in any order. It is kept in memory until the file is written to disk.

Objects are constructed with the new() method. Since Table-consuming classes must inherit from Bio::Root::IO, all Bio::Root::IO options are accepted, e.g. -file, -fh, -string, -flush, etc. Other constructors are detailed in the APPENDIX.

AUTHOR

Florent Angly florent.angly@gmail.com

SUPPORT AND BUGS

User feedback is an integral part of the evolution of this and other Bioperl modules. Please direct usage questions or support issues to the mailing list, bioperl-l@bioperl.org, rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

If you have found a bug, please report it on the BioPerl bug tracking system to help us keep track the bugs and their resolution: https://redmine.open-bio.org/projects/bioperl/

COPYRIGHT

Copyright 2011-2014 by Florent Angly <florent.angly@gmail.com>

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.1 or, at your option, any later version of Perl 5 you may have available.

APPENDIX

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

delim

Usage   : my $delim = $in->delim;
Function: When reading or writing a table, get or set the delimiter, i.e. the
          characters that delimit the columns of the table. The default is the
          tab character "\t".
Args    : A string
Returns : A string

start_line

Usage   : my $line_num = $in->start_line;
Function: When reading a table, get or set the line number at which the table
          starts. The default is 1, i.e. the table starts at the first line of
          the file. This option is not used when writing a table, but see
          _write_table() for details.
Args    : A strictly positive number
Returns : A strictly positive number

end_line

Usage   : my $line_num = $in->end_line;
Function: When reading a table, get or set the line number at which the table
          ends. If undef (the default), the table ends at the last line of the
          file.
Args    : A strictly positive number or undef
Returns : A strictly positive number or undef

missing_string

Usage   : my $missing = $out->missing_string;
Function: When reading a table, get or set the line number at which the table
          ends. If undef (the default), the table ends at the last line of the
          file.
Args    : A string, e.g. '', '0', 'n/a', '-'
Returns : A string

_get_start_content

Usage   : my $txt = $in->_get_start_content;
Function: After the table has been parsed, this returns everything before -start_line
Args    : A strictly positive number
Returns : A strictly positive number

_get_max_line

Usage   : my $num_lines = $in->_get_max_line;
Function: Get the number of lines in the table
Args    : None
Returns : Positive integer

_get_max_col

Usage   : my $num_cols = $in->_get_max_col;
Function: Get the number of columns in the table
Args    : None
Returns : Positive integer

_read_table

Usage   : $in->_read_table;
Function: Read the table in the file and index the position of its cells.
Args    : None
Returns : 1 on success

_get_value

Usage   : my $value = $in->_get_value(1, 3);
Function: Get the value of the cell given its position in the table (line and
          column).
Args    : A strictly positive integer for the line
          A strictly positive integer for the column
Returns : A string for the value of the table at the given line and column
            or
          undef if line or column was out-of-bounds

_set_value

Usage   : $out->_set_value(1, 3, $value);
Function: Set the element at the given line and column of the table.
Args    : A strictly positive integer for the line
          A strictly positive integer for the column
          A string for the value of the table at the given line and column
Returns : 1 for success

_insert_line

Usage   : $out->_insert_line(3, ['sample1', 3, 10.9, 'Mus musculus']);
Function: Insert a line of values in the table, at the indicated line, shifting
          all other lines down. You can also append a line to the table by
          providing the maximum line number + 1.
Args    : A strictly positive integer for the line at which to insert
          An arrayref containing the values to insert (must match table width)
Returns : 1 for success

_delete_col

Usage   : $out->_delete_col(3);
Function: Delete a column of the table.
Args    : A strictly positive integer for the column to delete.
Returns : 1 for success

_write_table

Usage   : $out->_write_table;
Function: Write the content of the cells in the table to a file. It is
          generally called automatically when closing the object. However, if
          you want header lines before or after the table, you can write them
          to file using the _print() method of Bio::Root::IO prior and after
          calling _write_table().
Args    : None
Returns : 1 on success