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Bio::NEXUS::WeightSet is a Perl module that represents column weights in alignment ( for each character).

SYNOPSIS

new Bio::NEXUS::WeightSet($name, @weights, $iswt);

A module representing column weights in alignment (for each character)

METHODS

new

Title : new
Usage : $node = new Bio::NEXUS::WeightSet($name, @weights);
Function: Creates a new Bio::NEXUS::WeightSet object
Returns : Bio::NEXUS::WeightSet object
Args : none

set_weights

Title : set_weights
Usage : $weight->set_weights(@weights);
Function: stores it in the list weights
Returns : none
Args : list of weights

get_weights

Title : get_weights
Usage : @wts=@{$weightset->get_weights()};
Function: Returns the weights array
Returns : reference to array containing weights
Args : none

select_weights

Title : select_weights
Usage : $set->select_weights($columns);
Function: select a subset of characters
Returns : new self with subset of weights
Args : column numbers

is_wt

Title : is_wt
Usage : croak unless $weight->is_wt();
Function: Returns if object has weights (1 yes, 0 no)
Returns : weight existence (integer)
Args : none

set_name

Title : set_name
Usage : $weight->set_name($name);
Function: Sets the name of the weightset
Returns : none
Args : name (string)

get_name

Title : get_name
Usage : $name=$weight->get_name();
Function: Returns the name of the weightset
Returns : name (string)
Args : none

equals

Name : equals
Usage : $set->equals($another);
Function: compare if two WeightSet objects are equal
Returns : boolean
Args : an WeightSet object

Graph::Weighted is an abstract, weighted graph implementation.

SYNOPSIS

use Graph::Weighted;

$g = Graph::Weighted->new(
data => [
[ 0, 1, 2, 0, 0 ], # A vertex with two edges.
[ 1, 0, 3, 0, 0 ], # "
[ 2, 3, 0, 0, 0 ], # "
[ 0, 0, 1, 0, 0 ], # A vertex with one edge.
[ 0, 0, 0, 0, 0 ] # A vertex with no edges.
]
);

$g = Graph::Weighted->new(
data => {
weight => {
a => { b => 1, c => 2 }, # A vertex with two edges.
b => { a => 1, c => 3 }, # "
c => { a => 2, b => 3 }, # "
d => { c => 1 }, # A vertex with one edge.
e => {} # A vertex with no edges.
}
foo => [
[ 1, 2, 3 ],
[ 4, 5, 6 ],
[ 7, 8, 9 ]
],
}
);

$g = Graph::Weighted->new(
data => $Math_Matrix_object,
retrieve_as => ARRAY,
);

$data = $g->weight_data;

$w = $g->graph_weight;

$w = $g->vertex_weight($v1);
$w = $g->vertex_weight($v1, $w + 1);

$w = $g->edge_weight($v1, $v2);
$w = $g->edge_weight($v1, $v2, $w + 1);

$vertices = $g->heaviest_vertices;
$vertices = $g->lightest_vertices;

$w = $g->max_weight; # Weight of the largest vertices.
$w = $g->min_weight; # Weight of the smallest vertices.

# Call the weight methods of the inherited Graph module.
$x = $g->MST_Kruskal;
$x = $g->APSP_Floyd_Warshall;
$x = $g->MST_Prim($p);

PDL::Tips is a Perl module with small tidbits of useful arcana. Programming tidbits and such.

SYNOPSIS
use PDL;

# Whatever happens here.

This page documents useful idioms, helpful hints and tips for using Perl Data Language v2.0.

Help

Use help help within perldl or the pdldoc program from the command line for access to the PerlDL documentation. HTML versions of the pages should also be present, in the HtmlDocs/PDL directory of the PDL distribution. To find this directory, try the following

perldl> foreach ( map{"$_/PDL/HtmlDocs"}@INC ) { p "$_n" if -d $_ }

Indexing idioms

The following code normalizes a bunch of vectors in $a. This works regardless of the dimensionality of $a.

$a /= $a->sumover->dummy(0);

What is actually happening?

If you want to see what the code is actually doing, try the command

PDL::Core::set_debugging(1);

somewhere. This spews out a huge amount of debug info for PDL into STDOUT. It is planned to eventually make this redirectable and the messages selectable more accurately.

Many of the messages come from Basic/Core/pdlapi.c and you can look at the source to see what is going on.

If you have any extra time to work on these mechanisms, infrom the pdl-porters mailing list.

Content Area Focus is an extension used to solve the content area focus loss.

Target audience: those who are mostly using the keyboard to navigate around and switch between tabs; frequently they encounter situations in which the content area doesnt have focus.

Method: just giving focus to the content area for any "regular" keystrokes made when the main-window is in focus.

bitmask project is a light-weight and fast 2D collision detection library.
The bitmask library provides pixel-perfect collision detection for use in games and other applications. Functions are provided for building bitmasks and testing them for intersection.
The routines can optionally provide a point of intersection and the number of overlapping pixels. The library aims for high performance and portability; it is written in ANSI C and is completely independent of the underlying graphics implementation.
Enhancements:
- Bugfix for bitmask_draw.
- Better testcases.
- Small performance improvements.