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.

cpanm AlignDB::Window

perl -MCPAN -e shell
install AlignDB::Window