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Bio::DB::GFF::Feature 1.4

Bio::DB::GFF::Feature 1.4


Bio::DB::GFF::Feature is a relative segment identified by a feature type. more>>
Bio::DB::GFF::Feature is a relative segment identified by a feature type.

Bio::DB::GFF::Feature is a stretch of sequence that corresponding to a single annotation in a GFF database. It inherits from Bio::DB::GFF::RelSegment, and so has all the support for relative addressing of this class and its ancestors. It also inherits from Bio::SeqFeatureI and so has the familiar start(), stop(), primary_tag() and location() methods (it implements Bio::LocationI too, if needed).

Bio::DB::GFF::Feature adds new methods to retrieve the annotations type, group, and other GFF attributes. Annotation types are represented by Bio::DB::GFF::Typename objects, a simple class that has two methods called method() and source(). These correspond to the method and source fields of a GFF file.

Annotation groups serve the dual purpose of giving the annotation a human-readable name, and providing higher-order groupings of subfeatures into features. The groups returned by this module are objects of the Bio::DB::GFF::Featname class.

Bio::DB::GFF::Feature inherits from and implements the abstract methods of Bio::SeqFeatureI, allowing it to interoperate with other Bioperl modules.
Generally, you will not create or manipulate Bio::DB::GFF::Feature objects directly, but use those that are returned by the Bio::DB::GFF::RelSegment->features() method.
Important note about start() vs end()

If features are derived from segments that use relative addressing (which is the default), then start() will be less than end() if the feature is on the opposite strand from the reference sequence. This breaks Bio::SeqI compliance, but is necessary to avoid having the real genomic locations designated by start() and end() swap places when changing reference points.

To avoid this behavior, call $segment->absolute(1) before fetching features from it. This will force everything into absolute coordinates.

For example:

my $segment = $db->segment(CHROMOSOME_I);
$segment->absolute(1);
my @features = $segment->features(transcript);

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Added: 2006-06-09 License: Perl Artistic License Price:
1232 downloads
Bio::Graphics::Feature 1.4

Bio::Graphics::Feature 1.4


Bio::Graphics::Feature is a simple feature object for use with Bio::Graphics::Panel. more>>
Bio::Graphics::Feature is a simple feature object for use with Bio::Graphics::Panel.

SYNOPSIS

use Bio::Graphics::Feature;

# create a simple feature with no internal structure
$f = Bio::Graphics::Feature->new(-start => 1000,
-stop => 2000,
-type => transcript,
-name => alpha-1 antitrypsin,
-desc => an enzyme inhibitor,
);

# create a feature composed of multiple segments, all of type "similarity"
$f = Bio::Graphics::Feature->new(-segments => [[1000,1100],[1500,1550],[1800,2000]],
-name => ABC-3,
-type => gapped_alignment,
-subtype => similarity);

# build up a gene exon by exon
$e1 = Bio::Graphics::Feature->new(-start=>1,-stop=>100,-type=>exon);
$e2 = Bio::Graphics::Feature->new(-start=>150,-stop=>200,-type=>exon);
$e3 = Bio::Graphics::Feature->new(-start=>300,-stop=>500,-type=>exon);
$f = Bio::Graphics::Feature->new(-segments=>[$e1,$e2,$e3],-type=>gene);

This is a simple Bio::SeqFeatureI-compliant object that is compatible with Bio::Graphics::Panel. With it you can create lightweight feature objects for drawing.

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Added: 2006-10-21 License: Perl Artistic License Price:
1098 downloads
Gimp::Feature 1.211

Gimp::Feature 1.211


Gimp::Feature is a Perl module that can check for specific features to be present before registering the script. more>>
Gimp::Feature is a Perl module that can check for specific features to be present before registering the script.

SYNOPSIS

use Gimp::Feature;
or
use Gimp::Feature qw(feature1 feature2 ...);

This module can be used to check for specific features to be present. This can be used to deny running the script when neccessary features are not present. While some features can be checked for at any time, the Gimp::Fu module offers a nicer way to check for them.

gtk

checks for the presence of the gtk interface module.

gtk-1.1, gtk-1.2

checks for the presence of gtk-1.1 (1.2) or higher.

perl-5.005

checks for perl version 5.005 or higher.

pdl

checks for the presence of a suitable version of PDL (>=1.9906).

gnome

checks for the presence of the Gnome-Perl module.

gtkxmhtl

checks for the presence of the Gtk::XmHTML module.

unix

checks wether the script runs on a unix-like operating system. At the moment, this is every system except windows, macos, os2 and vms.

persistency

checks wether the Gimp::Data module (Gimp::Data) can handle complex persistent data structures, i.e. perl references in addition to plain strings.

The following features can only be checked after Gimp-main> has been called (usually found in the form exit main). See Gimp::Fu on how to check for these.
gimp-1.1, gimp-1.2

checks for the presense of gimp in at least version 1.1 (1.2).

FUNCTIONS

present(feature)

Checks for the presense of the single feature given as the argument. Returns true if the feature is present, false otherwise.

need(feature,[function-name])

Require a specific feature. If the required feature is not present the program will exit gracefully, logging an appropriate message. You can optionally supply a function name to further specify the place where this feature was missing.

This is the function used when importing symbols from the module.

missing(feature-description,[function-name])

Indicates that a generic feature (described by the first argument) is missing. A function name can further be specified. This function will log the given message and exit gracefully.

describe(feature)

Returns a string describing the given feature in more detail, or undef if there is no description for this feature.

list()

Returns a list of features that can be checked for. This list might not be complete.

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Added: 2006-07-13 License: Perl Artistic License Price:
1201 downloads
RIFE 1.4

RIFE 1.4


RIFE offers an alternative approach to web application development and design. more>>
RIFE project is a full-stack web application framework with tools and APIs to implement most common web features. Each of its toolkits is usable by itself and together they offer powerful integrated features that boost your productivity.
RIFE ensures that every declaration and definition is handled in one place in the code. This simplifies the developers task by reducing code replication, enforcing consistency, and easing maintenance.
RIFEs design provides the best of request-based and component-based approaches and blends them together in a consistent component object model. The web engine provides a solution that values maintainability without compromising on productivity.
Through a centralized site structure, an application can be split up into easily reusable binary modules that can be seamlessly integrated into other projects.
There are currently two major schools of web application development frameworks: request-based and component-based.
Request-based frameworks are very close to the original CGI specification. They use controllers and actions that directly handle incoming requests. Each request is fundamentally stateless.
With the introduction of server-side sessions, a certain degree of statefulness has been achieved. The different frameworks basically differentiate themselves by the way they map logic to URLs and how data is structured and provided to the developer.
Component-based frameworks abstract the developer away from the internals of the request handling and encapsulate the logic into reusable components, often independent from the web medium.
The state is automatically handled by the framework, based on the data that is present in each component instance. Together with some form of event handling, this development model is very similar to the features offered by desktop GUI toolkits. The different frameworks basically differentiate themselves by the provided component API and how components are combined together.
RIFE combines both by taking control of the entire data and logic flow in a request-based model. Developers remain close to the architecture of CGI applications and have full control over URLs, forms, parameters, cookies and pathinfos.
However, instead of mapping actions and controllers directly to the request, RIFE provides a component object model that behaves identically in many different situations such as individual pages, intercepted requests, portal-like page fragments and integratable widgets.
Components can be wired together and be packaged as groups that are components in their own right. They can be distributed separately and be seamlessly integrated into any other RIFE project. This provides the same form of reusability as component-based frameworks, but with the raw control of the request-based approach.
Enhancements:
- Transparent meta data merging has been implemented, which is a creative solution to keeping POJOs pure and still make it possible to declare dynamic meta data in plain Java.
- Other highlights of this release are: new (X)HTML template tag syntaxes, experimental Ajax support with DWR integration, embedded element priorities, strict pathinfo mapping, deprecated CmfProperty and CmfValidation, flowlink-specific datalinks, mail queue support for authentication and SSL, support for setting reflexive outputs and globalvars across submissions, and several bugfixes.
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Added: 2006-03-06 License: LGPL (GNU Lesser General Public License) Price:
1329 downloads
Polar 1.4

Polar 1.4


Polar provides a smooth and simple cursor set created primarily in Inkscape. more>>
Polar provides a smooth and simple cursor set created primarily in Inkscape.
Polar Cursor Theme is a smooth and simple cursor set created primarily in Inkscape.
Installation
There are three cursor sets included in this package. The default with the orange busy cursors is called PolarCursorTheme and the blue and green variants have -Blue and -Green added to the end of their theme name. To make sure that all themes are installed (or only the one you want) extract to /.icons/ in your home folder.
Note
KDE users please note that installing the cursors through the control center can cause some cursors to use the default X cursors. To fix this simply extract the theme directly to /.icons/ in your home folder.
Finally a special thanks to all the authors of various cursor themes here on gnome-look.org for ideas.
Enhancements:
- Added Zoom cursors
- Fixes to cursor mappings
- Highlight added to clean up outlines
- Added Blue and Green busy cursors as an option
- Changed move cursor
- Small changes to other cursors
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Added: 2007-03-02 License: GPL (GNU General Public License) Price:
975 downloads
KeyPlayer 1.4

KeyPlayer 1.4


Java Keystroke and Mouse Event Tutor. Application to let you experiment to learn how mouse and keystroke events work. Output appears on the console. Just click the mouse or hit keystrokes and watch what details of the events generated. more>>

KeyPlayer - Java Keystroke and Mouse Event Tutor. Application to let you

experiment to learn how mouse and keystroke events work.

Output appears on the console. Just click the mouse or hit

keystrokes and watch what details of the events generated.

To install, Extract the zip download with Winzip, available from

http://www.winzip.com (or similar unzip utility) into any

directory you please, often C: -- ticking off the (user

folder names) option. To run as an application, type:

java -jar C:commindprodkeyplayerkeyplayer.jar

adjusting as necessary to account for where the jar file is.

Version 1.1 avoids dumping control chars to the console.

Version 1.3 adds a PAD and icon. renamed from keyplay to keyplayer.


Enhancements:
Version 1.4

add hex displays


System Requirements:Requires a Java 1.1 or later JRE
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Added: 2007-12-19 License: Free Price: Free
12 downloads
Murdoc 1.4

Murdoc 1.4


Murdoc is a system for documenting system management departments. more>>
Murdoc project is a system for documenting system management departments.
All documents of a system management department can be put in Murdoc for convenient browsing and searching.
It comes with several tools for creating content, like a Unix documenter (for automatically documenting Unix servers on a daily basis), a Windows documenter (for automatically documenting Microsoft Windows servers on a daily basis), and a Logbook writer (for entering logbook entries by the system administrators). A searching feature is included.
Main features:
- UNIX documenter (for automatically documenting UNIX servers on a daily basis)
- Windows documenter (for automatically documenting Microsoft Windows servers on a daily basis)
- Logbook writer (for entering logbook entries by the system administrators)
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Added: 2006-10-05 License: GPL (GNU General Public License) Price:
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FLAC 1.1.4

FLAC 1.1.4


FLAC stands for Free Lossless Audio Codec. more>>
FLAC is Free Lossless Audio Codec. Grossly oversimplified, FLAC is similar to MP3, but lossless, meaning that audio is compressed in FLAC without any loss in quality.
This is similar to how Zip works, except with FLAC you will get much better compression because it is designed specifically for audio, and you can play back compressed FLAC files in your favorite player (or your car or home stereo, see supported devices) just like you would an MP3 file.
FLAC is freely available and supported on most operating systems, including Windows, "unix" (Linux, *BSD, Solaris, OS X, IRIX), BeOS, OS/2, and Amiga. There are build systems for autotools, MSVC, Watcom C, and Project Builder.
The FLAC project consists of:
the stream format
reference encoders and decoders in library form
flac, a command-line program to encode and decode FLAC files
metaflac, a command-line metadata editor for FLAC files
input plugins for various music players
When we say that FLAC is "Free" it means more than just that it is available at no cost. It means that the specification of the format is fully open to the public to be used for any purpose (the FLAC project reserves the right to set the FLAC specification and certify compliance), and that neither the FLAC format nor any of the implemented encoding/decoding methods are covered by any known patent. It also means that all the source code is available under open-source licenses. It is the first truly open and free lossless audio format.
Main features:
- Lossless: The encoding of audio (PCM) data incurs no loss of information, and the decoded audio is bit-for-bit identical to what went into the encoder. Each frame contains a 16-bit CRC of the frame data for detecting transmission errors. The integrity of the audio data is further insured by storing an MD5 signature of the original unencoded audio data in the file header, which can be compared against later during decoding or testing.
- Fast: FLAC is asymmetric in favor of decode speed. Decoding requires only integer arithmetic, and is much less compute-intensive than for most perceptual codecs. Real-time decode performance is easily achievable on even modest hardware.
- Hardware support: Because of FLACs free reference implementation and low decoding complexity, FLAC is currently the only lossless codec that has any kind of hardware support.
- Streamable: Each FLAC frame contains enough data to decode that frame. FLAC does not even rely on previous or following frames. FLAC uses sync codes and CRCs (similar to MPEG and other formats), which, along with framing, allow decoders to pick up in the middle of a stream with a minimum of delay.
- Seekable: FLAC supports fast sample-accurate seeking. Not only is this useful for playback, it makes FLAC files suitable for use in editing applications.
- Flexible metadata: New metadata blocks can be defined and implemented in future versions of FLAC without breaking older streams or decoders. Currently there are metadata types for tags, cue sheets, and seek tables. Applications can write their own APPLICATION metadata once they register an ID
- Suitable for archiving: FLAC is an open format, and there is no generation loss if you need to convert your data to another format in the future. In addition to the frame CRCs and MD5 signature, flac has a verify option that decodes the encoded stream in parallel with the encoding process and compares the result to the original, aborting with an error if there is a mismatch.
- Convenient CD archiving: FLAC has a "cue sheet" metadata block for storing a CD table of contents and all track and index points. For instance, you can rip a CD to a single file, then import the CDs extracted cue sheet while encoding to yield a single file representation of the entire CD. If your original CD is damaged, the cue sheet can be exported later in order to burn an exact copy.
- Error resistant: Because of FLACs framing, stream errors limit the damage to the frame in which the error occurred, typically a small fraction of a second worth of data. Contrast this with some other lossless codecs, in which a single error destroys the remainder of the stream.
What FLAC is not:
- Lossy. FLAC is intended for lossless compression only, as there are many good lossy formats already, such as Vorbis, MPC, and MP3 (see LAME for an excellent open-source implementation).
- SDMI compliant, et cetera. There is no intention to support any methods of copy protection, which are, for all practical purposes, a complete waste of bits. (Another way to look at it is that since copy protection is futile, it really carries no information, so you might say FLAC already losslessly compresses all possible copy protection information down to zero bits!) Of course, we cant stop what some misguided person does with proprietary metadata blocks, but then again, non-proprietary decoders will skip them anyway.
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Added: 2007-02-14 License: GPL (GNU General Public License) Price:
994 downloads
Primes 1.4

Primes 1.4


calculates the prime numbers 1..N, tells you if N is prime etc. Prints tables of primes. Computes the prime just below or above N. calculates the prime numbers 1..N, tells you if N is prime etc. It is useful in computing optimal Hashtable sizes. Java source included. more>>

Primes - calculates the prime numbers 1..N, tells you if N is prime etc.

Prints tables of primes.

Computes the prime just below or above N.

It is useful in computing optimal Hashtable sizes.

Java source included.


Enhancements:
Version 1.4

mostly cosmetic, more documentation, tidy source.


System Requirements:
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Added: 2006-03-06 License: Free Price: Free
15 downloads
SeoQuake 1.4.1

SeoQuake 1.4.1


SeoQuake is a Firefox extension that allows a quick view of site parameters in the Search Engine Results Pages. more>>
SeoQuake is a Firefox extension that allows a quick view of site parameters in the Search Engine Results Pages.

(Google, Yahoo, MSN, Yandex, Rambler are supported)

SEObar indicate some SE-dependent parameters

Warning! Extension is using the advertisement block in results of search engines.

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Added: 2007-03-30 License: MPL (Mozilla Public License) Price:
969 downloads
athenaCL 1.4.5

athenaCL 1.4.5


athenaCL is a music analysis and algorithmic composition program. more>>
athenaCL is a music analysis and algorithmic composition program. The system can be scripted and embedded, and includes integrated instrument libraries, post-tonal and microtonal pitch modeling tools, multiple-format graphical outputs, and musical output in Csound, MIDI, audio file, XML, and text formats.

Musical parts are deployed as Textures, layered surface-defining objects containing numerous independent ParameterObjects to control pitch, tempo, rhythm, amplitude, panning, and instrument (Csound) parameters. The system includes an integrated library of Csound instruments, and supports output for external Csound instruments, MIDI, and a variety of alternative formats. Over sixty specialized Generator, Rhythm, and Filter ParameterObjects provide tools for stochastic, chaotic, cellular automata based, markov based, wave-form, fractional noise (1/f), genetic, Xenakis sieve, linear and exponential break-point segments, masks, and various other algorithmic models. ParameterObjects can be embedded in other ParameterObjects to provide powerful dynamic and masked value generation. Textures can be combined and edited, and tuned with algorithmic Temperament objects. Texture Clones allow the filtering and processing of Texture events, performing transformations not possible with parameter generation alone.

The analytic and algorithmic systems use Path objects for organizing and sharing pitch groups. Paths provide simultaneous representations of ordered content groups in set-class, pitch-class space, and pitch space. Paths may contain numerous PathVoices (voice leadings) and may be analyzed with both set-class similarity measures and voice leading rankings. As a reference utility, pitch groups can be searched, analyzed, and compared with a wide variety of tools

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Added: 2007-08-10 License: GPL (GNU General Public License) Price:
805 downloads
furious_tv 1.4

furious_tv 1.4


furious_tv is a set of tools to take XMLTV TV listings and enable a UNIX system to automatically record programs of a TV card. more>>
furious_tv is a set of tools to take XMLTV TV listings and enable a UNIX system to automatically record programs off of a TV card. It is written in C and uses a SAX parser for maximum speed and efficiency.
Enhancements:
- This version of furious_tv fixes a few miscellaneous bugs in the code and also adds support for non-US TV listings. Apparently in countries other than the US, the channel numbers vary a great deal (even in small areas), so non-US users needed a way to change channel numbers and have those changes persist when new listings were loaded into the database.
- Version 1.4 adds an option to ftv_listings ("-r") that instructs the parser to use the channel numbers in the listings to override the channel numbers in the database. This is really only a good idea if the listings probably have the correct channel numbers (e.g. US listings obtained using XMLTVs tv_grab_na grabber).
- One last point to keep in mind is that the channel numbers are preserved by looking at the channel names, so the channel names should not be changed manually because then ftv_listings will not recognize the channel as already in the database.
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Added: 2005-11-04 License: GPL (GNU General Public License) Price:
1449 downloads
FoxGame 1.4.14

FoxGame 1.4.14


FoxGame is an extension that can be used to enhance user experience with O-game. more>>
FoxGame is an extension that can be used to enhance user experience with O-game.
Enhance user experience with O-game (now works in every o-game version)
Adds a lot of features to the webgame O-game.
It also integrates Database features inside the game.
O-Game, is a real-time spacial browser game.
bs-BA/hr-HR/cs-SR can be downloaded as a separate version from http://foxgame.mozdev.org/ because there is no especific firefox version for those languages.
Main features:
- Automatic universe selector in login page.
- Reduced galaxy view: Planet column is not rendered and its functinality is moved to Name col., debris header reduced also.
- Extra delete options and spy report options: You can control messages from the top or the bottom.
- Fleet arrival and return time: In fleet destiny selection page you will see the time when you fleet will arrive and come back to your planet.
- Fleet retreat time: In fleet page you will see the time when your fleet will arrive if you order to come back.
- Multilanguage support: es-ES(spanish), en-US(english), de-DE(deutsch), pl-PL(polish), fr-FR(french), nl-NL/nl-BR (dutch), it-IT (italian), bs-BA/sr-CS/hr-HR (bosnian, serbian, croatian), pt-PT/pt-BR(portugese), tr-TR(Turkish), zh-CN/zh-TW (Simplified chinese and traditional chinese), ru-RU (russian), da-DK (danish), si-SL (slovenian) and sv-SE/sv-FI (swedish). If your language is not supported and you want to translate it, mail me.
- Almost all finishing hours: Research and buildings finishing hours, hangars qeue finishing time, you can see date/time in overview if you wish and even in phalanx.
- Highlight ally and private messages: Ally and private messages now have a diferent background to see them easily.
- Highlight big debris fields: Debris fields bigger than you fix min will have different background in galaxy view.
- Autochoose mision type: You can define mission priorities so FoxGame will select the mission according to that.
- Online DBs integration: Send reports to Milos (only ogame.com.es), EspRep and GalaxieTool directly within OGame (solar systems, stats and spy reports supported).
- In mines and power plants info screens (the ones you see when you click in the name) you will see the diferences between your actual level and the rest.
- Autoselect fleet destination: Select coord text anywhere go to fleet send screen and Voila! the destination is already selected. There is no need to take down numbers anymore.
- Private message signatures.
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Added: 2007-07-11 License: MPL (Mozilla Public License) Price:
611 downloads
PictureStories 1.4

PictureStories 1.4


PictureStories lets you make little webpages of stories you write where some of the words are replaced with images. more>>
PictureStories lets you make little webpages of stories you write where some of the words are replaced with images which is called rebus. What makes PictureStories cool is that the images are dynamically pulled from popular web-based image search engines (like Google).

Weve seen lots of cute little storybooks for kids that are like this, and we thought itd be neat to be able to do my own. Someone has probably had this idea before, but we couldnt find anything online anywhere, so we wrote it.
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Added: 2006-06-26 License: Freeware Price:
1215 downloads
gunzets 1.4

gunzets 1.4


gunzets is support software for Gunze touch screens. more>>
gunzets supports Gunze touch panels under Linux and XFree86. Supported panels are the serial, PS/2, and USB devices.
All devices are supported by means of an XFree86 module, and the USB device via a kernel module as well. Both XFree version 3.3.6 and 4.x are supported, as well as kernel 2.2 and 2.4. The driver is supported by Gunze USA.
Version restrictions:
- Debouncing is only supported for XFree 4.0 (not 3.3.6).
- A bounce event breaks smoothing processing
- Support for multi-screen operation is not supported.
Compiling
In order to successfully load the module you need to have the following facilities compiled in your kernel or loaded as modules:
- usb generic support (usbcore.o)
- a usb host controller driver (usb-ohci.o o usb-uhci.o)
- support for misc devices like the ps2 mouse (misc.o)
- the input mechanism (input.o)
To compile the driver just make. If your 2.4 or 2.2 kernel headers are not available from /usr/src/linux/include then specify KERNELDIR to point to your kernel source directory, either on the make command line or in the environment. For example:
make KERNELDIR=/usr/src/linux-2.4
To load the driver, use insmod:
insmod ./gunzets.o
To use the input mechanism, specify it on the command line:
insmod ./gunzets.o use_input=1
To automatically create the entry point in /dev (needed if you are not using the input mechanism) run the gunzets_load script instead:
./gunzets_load
Instllation
To install the module to the proper places you can run make install. You may also wish to copy gunzets_load from /usr/local/bin to /etc/rc.d/init.d or /etc/init.d and create a proper symbolic link for automatic load at boot.
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Added: 2005-04-26 License: GPL (GNU General Public License) Price:
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