Free 1.02 software for linux

Unicode::Normalize Perl module contains Unicode Normalization Forms.

SYNOPSIS

(1) using function names exported by default:
use Unicode::Normalize;

$NFD_string = NFD($string); # Normalization Form D
$NFC_string = NFC($string); # Normalization Form C
$NFKD_string = NFKD($string); # Normalization Form KD
$NFKC_string = NFKC($string); # Normalization Form KC

(2) using function names exported on request:

use Unicode::Normalize normalize;

$NFD_string = normalize(D, $string); # Normalization Form D
$NFC_string = normalize(C, $string); # Normalization Form C
$NFKD_string = normalize(KD, $string); # Normalization Form KD
$NFKC_string = normalize(KC, $string); # Normalization Form KC

Parameters:

$string is used as a string under character semantics (see perlunicode).

$code_point should be an unsigned integer representing a Unicode code point.

Note: Between XSUB and pure Perl, there is an incompatibility about the interpretation of $code_point as a decimal number. XSUB converts $code_point to an unsigned integer, but pure Perl does not. Do not use a floating point nor a negative sign in $code_point.

Normalization Forms

$NFD_string = NFD($string)

It returns the Normalization Form D (formed by canonical decomposition).

$NFC_string = NFC($string)

It returns the Normalization Form C (formed by canonical decomposition followed by canonical composition).

$NFKD_string = NFKD($string)

It returns the Normalization Form KD (formed by compatibility decomposition).

$NFKC_string = NFKC($string)

It returns the Normalization Form KC (formed by compatibility decomposition followed by canonical composition).

$FCD_string = FCD($string)

If the given string is in FCD ("Fast C or D" form; cf. UTN #5), it returns the string without modification; otherwise it returns an FCD string.

Note: FCD is not always unique, then plural forms may be equivalent each other. FCD() will return one of these equivalent forms.

$FCC_string = FCC($string)

It returns the FCC form ("Fast C Contiguous"; cf. UTN #5).
Note: FCC is unique, as well as four normalization forms (NF*).

$normalized_string = normalize($form_name, $string)

It returns the normalization form of $form_name.

As $form_name, one of the following names must be given.

C or NFC for Normalization Form C (UAX #15)
D or NFD for Normalization Form D (UAX #15)
KC or NFKC for Normalization Form KC (UAX #15)
KD or NFKD for Normalization Form KD (UAX #15)

FCD for "Fast C or D" Form (UTN #5)
FCC for "Fast C Contiguous" (UTN #5)

Module::Reload::Selective can reload Perl modules during development.

SYNOPSIS

Instead of:

use Foobar::MyModule;

Do this:

use Module::Reload::Selective;
&Module::Reload::Selective->reload(qw(Foobar::MyModule));
Or, if you need the "import" semantics of "use", do this:

use Foobar::MyModule (@ImportArgs);

Do this:

use Module::Reload::Selective;
Module::Reload::Selective->reload(qw(Foobar::MyModule));

import Foobar::MyModule (@ImportArgs);

... then configure your server or other runtime environment settings to trigger Module::Reload::Selective to only kick in when you need.

For example: you could have it kick in only when the web server is running on a particular port number or particular (development) host.

Peptide::Pubmed is a Perl module that can extract peptide sequences from MEDLINE article abstracts.

SYNOPSIS

use Peptide::Pubmed;
$parser = Peptide::Pubmed->new;
$in = {
PMID => q[15527327],
Author => q[Doe JJ, Smith Q],
Journal => q[J Biological Foo. 2004;8(2):123-30.],
Title => q[Foo, bar and its significance in phage display.],
Abstract =>
q[Peptide sequences EYHHYNK and Arg-Gly-Asp, but not ACCCGTNA or VEGFRI.],
Mesh => q[Genes, p53/genetics; Humans; Bar],
Chemical => q[Multienzyme Complexes; Peptide Library; Foo],
};
$parser->parse_abstract($in);

# get the peptide sequences in 1 letter symbols (select all words where the
# combined word/abstract score is above threshold:
# WordAbstScore >= WordAbstScoreMin):
@seqs = $parser->get_seqs;
print "@seqsn"; # prints: EYHHYNK RGD

EXAMPLES

# same as above, set threshold explicitly:
$parser->WordAbstScoreMin(0.4);
@seqs = $parser->get_seqs;

# set low threshold to get more peptide sequences (but at a cost of getting
# more false positives)
$parser->WordAbstScoreMin(-1);
@seqs = $parser->get_seqs;
print "@seqsn"; # prints: EYHHYNK RGD ACCCGTNA VEGFRI

# reset threshold back:
$parser->WordAbstScoreMin(0.4);

# get more data for the abstract:
$abst = $parser->get_abst;
print "$abst->{AbstScore}n"; # abstract score, in the [0,1] interval
print "$abst->{AbstMtext}n"; # abstract with sequences marked up:
# Peptide sequences EYHHYNK and Arg-Gly-Asp,
# but not ACCCGTNA or VEGFRI.

# get more data for the words, in addition to peptide sequences:
@words = $parser->get_words;
for my $word (@words) {
# combined word/abstract score, in the [0,1] interval
print "$word->{WordAbstScore}n";
# word as found in the abstract, eg Arg-Gly-Asp,
print "$word->{WordOrig}n";
# peptide sequence in 1 letter symbols, eg RGD
print "$word->{WordSequence}n";
}

# There are no mandatory input fields. This will work too, but may give lower score.
$in = {
Abstract =>
q[Peptide sequences EYHHYNK and Arg-Gly-Asp, but not ACCCGTNA or VEGFRI.],
};
$parser->parse_abstract($in);
@words = $parser->get_words;

# No peptide sequences are found in empty input:
$in = undef;
$parser->parse_abstract($in);
@words = $parser->get_words;

WWW::BBSWatch can send, via email, messages posted to a WWW bulletin board.

SYNOPSIS

use WWW::BBSWatch; # should really be a subclass

sub WWW::BBSWatch::article_list { # generates warning (rightly so)
my $self = shift;
my $content = shift;
return ($$content =~ m%($self->{bbs_url}?read=d*)%gs);
}
BBSWatch->new(-MAIL => me,
-BBS_URL => http://www.foo.org/cgi-bin/bbs.pl)->retrieve;
There are many interesting discussions that take place on World Wide Web Bulletin Boards, but I do not have the patience to browse to each article. I can process email and newsgroups many times faster than a WWW bulletin board because of the lag inherent in the web. Instead of ignoring this wealth of information, WWW::BBSWatch was created. It will monitor a World Wide Web Bulletin Board and email new postings to you. The email headers are as correct as possible, including reasonable From, Subject, Date, Message-Id and References entries.
This module requires LWP::UserAgent and MIME::Lite.
INTERFACE
$b = WWW::BBSWatch->new
Arguments are:
-BBS_URL: The URL of the bulletin boards index page. This field is required.
-MAIL: The email address to send mail to
-MDA: Sets the mail delivery agent by calling MIME::Lite::send(HOW, HOWARGS). If a scalar value is passed in, it is passed as send(" sendmail?, $mda_value). If an array ref is provided, send(@$mda_value) is called.
-DB: Basename of the database that keeps track of visited articles
-WARN_TIMEOUT: Number of seconds before warning message is sent proclaiming inability to contact BBS_URL page. Default is 10,800 (3 hours).
-MAX_ARTICLES: Maximum number of articles to send in one batch. Default is essentially all articles.
-VERBOSE: Controls the amount of informative output. Useful values are 0, 1, 2. Default is 0 (completely silent).

$b->retrieve([$catchup])

This method emails new bulletin board messages. If the optional parameter catchup is true, messages will be marked as read without being emailed. Nothing useful will happen unless the article_list method is defined to return the list of articles from the BBSs index page.

WWW::BBSWatch uses the LWP::UserAgent module to retrieve the index and articles. It honors firewall proxies by calling the LWP::UserAgent::env_proxy method. So if you are behind a firewall, define the environment variable http_proxy and your firewall will be handled correctly.

Test::Resub is a lexically scoped subroutine replacement for testing.

SYNOPSIS

#!/usr/bin/perl

use Test::More tests => 4;
use Test::Resub qw(resub);

{
package Somewhere;
sub show {
my ($class, $message) = @_;
return "$class, $message";
}
}

# sanity
is( Somewhere->show(beyond the sea), Somewhere, beyond the sea );

# scoped replacement of subroutine with argument capturing
{
my $rs = resub Somewhere::show, sub { hi }, capture => 1;
is( Somewhere->show(over the rainbow), hi );
is_deeply( $rs->method_args, [[over the rainbow]] );
}

# scope ends, resub goes away, original code returns
is( Somewhere->show(waiting for me), Somewhere, waiting for me );

This module allows you to temporarily replace a subroutine/method with arbitrary code. Later, you can tell how many times was it called and with what arguments each time. You can also specify that the subroutine/method must get called, must not get called, or may be optionally called.

UMMF::UML::MetaMetaModel is an implementation of the UML Meta-Meta-Model (M3).

SYNOPSIS

use UMMF::UML::MetaMetaModel;
my $factory = UMMF::UML::MetaMetaModel->factory;
my $model = $factory->create(Model);
$factory->create(Class, name => Foo, namespace => $model);
...

This package implements a meta-meta-model (M3) for generating the UML metamodel (M2).

UMMF::UML::MetaMetaModel is not an implementation of the MOF; It is actually a subset of the 1.5 Meta-model, as described in UML Spec. 1.5., p.2-13, but with a flattened package namespace.

It is the "Backbone" for generating the meta-model.

The UML 1.5 Meta-model is described in UMMF::UML::MetaModel package, in the ad-hoc language imported by UMMF::UML::Import::MetaMetaModel.

This meta-model is then used to generate the Perl (or Java) code for the classes in UMMF::UML::MetaModel::*.

The same exporters and importers can be used to process M* layers.

Thus, one description of the meta-model can generate multiple implementations.

ummf Perl module contains a driver for UMMF.

SYNOPSIS

ummf [-I dir] [-M MetaModel] [-m Main::Module] [-o {dir|-}] [-e exporter] input ...

This is a driver for the UMMF toolkit. It translates UML input documents into the export targets specified by the -e option. If -o - is specified the output is generated to STDOUT, otherwise the output is multiplexed into files underneath the directory specified by the -o option, using files2dirs.

If input is UML-1.5, then the internal UML 1.5 meta-model (from UMMF::UML::MetaModel) is used as input.

Input files can be .zargo (ArgoUML and Poseidon for UML 1.x), .zuml (Poseidon for UML 2.x) or XMI 1.0 or 1.2 documents.

USAGE

ummf -e java -e perl -o gen test/test1.xmi

Generates Java and Perl code in directory gen from test/test1.xmi.

ummf -e perl::hibernate -o gen test/test2.zargo

Generates Java Hibernate hbn.xml file in directory gen from test/test2.zargo.

ummf -e XMI -o - UML-1.5

Generates XMI for the UML 1.5 meta-model on the standard output stream.

ummf --perl5lib

Print the PERL5LIB path needed for Perl code generated by UMMF.

ummf -L Some::Package

Loads Some::Package.

ummf -m Some::Package @args ...

Loads Some::Package and executes >.

ummf -I dir/with/perl/modules

Executes use lib dir/with/perl/modules; including modules from the specified directory in the search path.

ummf -M UMMF::Boot::MetaModel

Uses UMMF::Boot::MetaModel for the meta-model, defaults to UMMF::UML_1_5.

ummf -profile MyMagicProfile -e Perl UML-1.5

Applies MyMagicProfile during export of Perl code on the UML 1.5 meta-model. This overides the default lib/ummf/profile/UML-1.5.ummfprofile file.