NAME
AlignDB::Window - Split integer spans into a series of windows
DESCRIPTION
AlignDB::Window provides methods to split integer spans, including interval, inside area and outside area, into a series of windows.
ATTRIBUTES
sw_size - sliding windows' size, default is 100
min_interval - mininal indel interval length, default is 11
max_out_distance - maximal outside distance, default is 10
max_in_distance - maximal inside distance, default is 5
METHODS
common parameters
$comparable_set - AlignDB::IntSpan object
$interval_start - start point of the interval
$interval_end - end point in the interval
$internal_start - start position in the internal region
$internal_end - end position in the internal region
$sw_size - size of windows
$min_interval - minimal size of intervals
$maximal_distance - maximal distance
$strand - '+' or '-'
interval_window
my @interval_windows = $self->interval_window(
$comparable_set, $interval_start, $interval_end,
$sw_size, $min_interval,
);Split an interval to windows.
Length of windows are variable, but all positions of the interval are counted.
outside_window
my @outside_windows = $self->outside_window(
$comparable_set, $internal_start, $internal_end,
$sw_size, $maximal_distance,
);Draw outside windows from a internal region.
All windows are 100 bp length. Start from 1 and end to $maximal_distance.
outside_window_2
my @outside_windows = $self->outside_window_2(
$comparable_set, $internal_start, $internal_end,
$sw_size, $maximal_distance,
);Draw outside windows from a internal region.
The first window is 50 bp and all others are 100 bp length. Start from 0 and end to $maximal_distance.
inside_window
my @inside_windows = $self->inside_window(
$comparable_set, $interval_start, $interval_end,
$sw_size, $maximal_distance,
);Draw inside windows from a internal region.
All windows are 100 bp length. Start counting from the edges.
inside_window_2
my @inside_windows = $self->inside_window_2(
$comparable_set, $interval_start, $interval_end,
$sw_size, $maximal_distance,
);Draw inside windows from a internal region.
All windows are 100 bp length. Start counting from the center.
center_window
my @center_windows = $self->center_window(
$comparable_set, $internal_start, $internal_end,
$sw_size, $maximal_distance,
);Draw windows for a certain region.
Center is 0, and the first window is 50 bp and all others are 100 bp length. Start from 0 and end to $maximal_distance.
center_intact_window
my @center_intact_windows = $self->center_intact_window(
$comparable_set, $internal_start, $internal_end,
$sw_size, $maximal_distance,
);Draw windows for a certain region.
Center is 0, and the first window is 50 bp and all others are 100 bp length. Start from 0 and end to $maximal_distance.
strand_window
my @windows = $self->strand_window(
$comparable_set, $interval_start, $interval_end,
$sw_size, $strand,
);Draw windows for a certain region
AUTHOR
Qiang Wang <wang-q@outlook.com>
COPYRIGHT AND LICENSE
This software is copyright (c) 2008 by Qiang Wang.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.