Free uml analysis classes software for linux

Sequence Analysis project is a collage of coding projects which I have written over the past several years for various clients in my work as a bioinformatics consultant.

These clients have graciously allowed me to release these works into the public domain as freeware for Macintosh OS X in order to promote the platform and to encourage migration from Classic.

The upper window panel can hold several sequences, which are both editable and selectable. The tabs in the lower analysis panel try to keep up with the current sequence selection to provide immediate feedback. The selection is used in some modules as only the portion being analyzed for other modules i.e. Digest is used to determine if enzymes cut in the in or outside of the selection.

Most commonly available sequence formats have been reverse engineered. You can also access a sequences from the NCBI via its GID or UID. This currently cannot be done from behind a firewall.

Most of the analyses are simple enough that they are obvious to use, Composition, pI. Others could stand some documenation i.e. Pairwise and Primer Design. The Publish tab uses a string to control the layout. Click on the Legend button for some help.

Net::Analysis are modules for analysing network traffic.

SYNOPSIS

Using an existing analyser:

$ perl -MNet::Analysis -e main help
$ perl -MNet::Analysis -e main TCP,v=1 dump.tcp - basic TCP info
$ perl -MNet::Analysis -e main HTTP,v=1 dump.tcp - HTTP stuff
$ perl -MNet::Analysis -e main Example2,regex=img dump.tcp - run an example

Writing your own analyser:

package MyExample;
use base qw(Net::Analysis::Listener::Base);
# Listen to events from other modules
sub tcp_monologue {
my ($self, $args) = @_;
my ($mono) = $args->{monologue};
my $t = $mono->t_elapsed()->as_number();
my $l = $mono->length();
# Emit your own event
$self->emit(name => example_event,
args => { kb_sec => ($t) ? $l/($t*1024) : N/A }
);
}
# Process your own event
sub example_event {
my ($self, $args) = @_;
printf "Bandwidth: %10.2f KB/secn", $args->{kb_sec};
}
1;
__top

ABSTRACT

Net::Analysis is a suite of modules that parse tcpdump files, reconstruct TCP sessions from the packets, and provide a very lightweight framework for writing protocol anaylsers.
__top

I wanted a batch version of Ethereal in Perl, so I could:

- sift through parsed protocols with structured filters
- write custom reports that mixed events from multiple protocols

So here it is. Net::Analysis is a stack of protocol handlers that emit, and listen for, events.

Directory Analysis Tool is used to analyze LDAP directories and report on their contents.

Useful if you want to find inactive accounts, people who havent changed passwords, or who has administrator privileges.

Network Security Analysis Tool is a fast, stable bulk security scanner designed to audit remote network services and check for versions, security problems, gather information about the servers and the machine, and much more.

A manpage providing extensive information on NSAT has been included in the distribution. It is available after a make install, or just by typing man doc/nsat.8 from this dir. It is suggested that you inform yourself at least about the -v (scan verbosity) option and edit the configuration file. To learn about changes in this version, please consult doc/CHANGES.

New to this version is support for distributed scanning. The manpage describes how to do a distributed scan. Note that distributed scanning in this version is just a preliminary, proof-of-concept, implementation with no guarantees for its security, reliability, or performance.

Check for updated vulnerability lists, config files, etc. from
http://nsat.sourceforge.net

Currently, these are lists of vulnerabilities:

nsat.cgi (CGI scripts)
nsat.conf (configuration)
src/mod/snmp.h (SNMP community names)

Perl6::Classes project contains first class classes in Perl 5.

SYNOPSIS

use Perl6::Classes;

class Composer {
submethod BUILD { print "Giving birth to a new composern" }
method compose { print "Writing some music...n" }
}

class ClassicalComposer is Composer {
method compose { print "Writing some muzak...n" }
}

class ModernComposer is Composer {
submethod BUILD($) { $.length = shift }
method compose() { print((map { int rand 10 } 1..$.length), "n") }
has $.length;
}

my $beethoven = new ClassicalComposer;
my $barber = new ModernComposer 4;
my $mahler = ModernComposer->new(400);

$beethoven->compose; # Writing some muzak...
$barber->compose # 7214
compose $mahler; # 89275869347968374698756....

Perl6::Classes allows the creation of (somewhat) Perl 6-style classes in Perl 5. The following features are currently supported:

subs, methods, and submethods
And their respective scoping rules.

Attributes
Which are available through the has keyword, and look like $.this.

Inheritance
Both single and multiple inheritance are available through the is keyword.

Signatures
Signatures on methods, subs, and submethods are supported, but just the Perl 5 kind.

Data hiding
Using the public, protected, and private traits, you can enforce (run-time) data hiding. This is not supported on attributes, which are always private.

Anonymous classes
That respect closures. You can now nest them inside methods of other classes, even other anonymous ones!

The Perl6::Classes module augments Perls syntax with a new declarator: class. It offers the advantage over Perls standard OO mechanism that it is conceptually easier to see (especially for those from a C++/Java background). It offers the disadvantage, of course, of being less versatile.

classesfaq is a Perl module with frequently asked questions about the Perl classes pragma.
Main features:
- Compile-time classes, no base class required
- Dynamic classes, alter or create at run-time
- Attributes, class and object, private, read-only, public
- Mixins, methods by name or regx, attributes also
- Single and multiple inheritance
- Accessors, optimized, overridable with read-only
- Accessor dispatch methods set and get
- Method declaration, delegation, ABSTRACT and EMPTY
- Separate new and clone methods, overridable
- Optional initialize method, aggregation
- Utility methods: dump, load, CLASS, SUPER
- Dynamically preserved declaration and mixin tracking
- Simplified exceptions, one line exception classes with inheritance trees
- Base exception class, light, robust, traceable
- 8 reusable exception classes in X:: namespace
- Compatible standard internals, easy porting, no surprises
What is the classes pragma?
A simple, stable, fast, and flexible way to use Perl 5 classes. If you look at no other Perl OO module look at this one, really. If you have done OO in Perl you will find this comfortably familiar. If not you may save yourself time and pain learning the classes pragma first or as you learn Perl OO--many have already.
Why should I use the classes pragma?
- Relevant: fills real-world need for conventional Perl OO
- Lazy: 100+ conventional lines reduced to 1
- Simple: standard readable terms, UML friendly
- Stable: 1000+ unit test points, used reliably in large applications
- Portable: OS independent, single file, 100% pure perl
- Fast: benchmarks faster or equal to the long way
- Light: only standard deps, requires greater than 5.6.1
- Sustainable: tag model, clean, commented
- Open: Perl artistic license, multi-language friendly
- Supported: mailing list, site, documented, actively maintained
If for no other reason because it is a new approach.

Mantissa is a collection of various mathematical tools aimed towards for simulation.
Mantissa contains a collection of algorithms, among which:
a small set of linear algebra classes
a least squares estimator
some curve fitting classes
several ordinary differentials equations integrators, either with fixed steps or adaptive stepsize control (see below)
vectors and rotations in a three dimensional space
algebra-related classes like rational and double polynomials
various orthogonal polynomials:
Chebyshev
Hermite
Laguerre
Legendre
some random numbers and vectors generation classes:
Robert M. Ziff four tap shift register (contributed by Bill Maier)
Makoto Matsumoto and Takuji Nishimura Mersenne twister
generators for vectors with correlated components
some basic (min, max, mean, standard deviation) statistical analysis classes
some optimization algorithms using direct search methods:
the Nelder-Mead simplex method
Virginia Torczons multi-directional method
Enhancements:
- For many basic objects provided by Mantissa like Vector3D, Rotation, and the various Polynomial classes, instances are now guaranteed to be immutable.
- This greatly simplifies safe sharing of instances without forcing users to either put severe restrictions on their use of Mantissa classes or make numerous copies just to make sure everything is safe.
- Since the change is a semantic change on the contract of the classes, this version introduces some incompatibilities with respect to previous ones.
- Upgrading to this version is not difficult, though.