Free graphical representation software for linux

General Graphics User Interface is an effort to produce a common graphical user interface for any command-line program.

It uses a wizard-like input front end to collect the information needed. It then calls the desired program automatically with all the necessary options.

The user is able to point&click on various options and select them in a convenient way. In order to create a new user-interface, a user doesnt need to know a programming language, since there is a graphical editor for new GGUI "scripts".

Bio::Graphics::Panel is a Perl module to generate GD images of Bio::Seq objects.

SYNOPSIS

# This script parses a GenBank or EMBL file named on the command
# line and produces a PNG rendering of it. Call it like this:
# render.pl my_file.embl | display -

use strict;
use Bio::Graphics;
use Bio::SeqIO;

my $file = shift or die "provide a sequence file as the argument";
my $io = Bio::SeqIO->new(-file=>$file) or die "could not create Bio::SeqIO";
my $seq = $io->next_seq or die "could not find a sequence in the file";

my @features = $seq->all_SeqFeatures;

# sort features by their primary tags
my %sorted_features;
for my $f (@features) {
my $tag = $f->primary_tag;
push @{$sorted_features{$tag}},$f;
}

my $panel = Bio::Graphics::Panel->new(
-length => $seq->length,
-key_style => between,
-width => 800,
-pad_left => 10,
-pad_right => 10,
);
$panel->add_track( arrow => Bio::SeqFeature::Generic->new(-start=>1,
-end=>$seq->length),
-bump => 0,
-double=>1,
-tick => 2);
$panel->add_track(generic => Bio::SeqFeature::Generic->new(-start=>1,
-end=>$seq->length),
-glyph => generic,
-bgcolor => blue,
-label => 1,
);

# general case
my @colors = qw(cyan orange blue purple green chartreuse magenta yellow aqua);
my $idx = 0;
for my $tag (sort keys %sorted_features) {
my $features = $sorted_features{$tag};
$panel->add_track($features,
-glyph => generic,
-bgcolor => $colors[$idx++ % @colors],
-fgcolor => black,
-font2color => red,
-key => "${tag}s",
-bump => +1,
-height => 8,
-label => 1,
-description => 1,
);
}

print $panel->png;
$panel->finished;

exit 0;

The Bio::Graphics::Panel class provides drawing and formatting services for any object that implements the Bio::SeqFeatureI interface, including Ace::Sequence::Feature and Das::Segment::Feature objects. It can be used to draw sequence annotations, physical (contig) maps, or any other type of map in which a set of discrete ranges need to be laid out on the number line.

The module supports a drawing style in which each type of feature occupies a discrete "track" that spans the width of the display. Each track will have its own distinctive "glyph", a configurable graphical representation of the feature.
The module also supports a more flexible style in which several different feature types and their associated glyphs can occupy the same track. The choice of glyph is under run-time control.

Semantic zooming (for instance, changing the type of glyph depending on the density of features) is supported by a callback system for configuration variables. The module has built-in support for Bio::Das stylesheets, and stylesheet-driven configuration can be intermixed with semantic zooming, if desired.

You can add a key to the generated image using either of two key styles. One style places the key captions at the top of each track. The other style generates a graphical key at the bottom of the image.

Note that this module depends on GD. The optional SVG output depends on GD::SVG and SVG.

File::Stat::ModeString - conversion file stat mode to/from string representation.

SYNOPSIS

use File::Stat::ModeString;

$string = mode_to_string ( $st_mode );
$st_mode = string_to_mode ( $string );
$type = mode_to_typechar( $st_mode );

$record = < IN >; chomp $record;
$record =~ m/^some_prefixs+$MODE_STRING_REs+some_suffix$/o
or die "invalid record format";

die "Invalid mode in $string"
if is_mode_string_valid( $string );

This module provides a few functions for conversion between binary and literal representations of file mode bits, including file type.

All of them use only symbolic constants for mode bits from File::Stat::Bits.

CONSTANTS

$MODE_STRING_RE

Regular expression to match mode string (without ^$).

FUNCTIONS

is_mode_string_valid( $string )

Returns true if argument matches mode string pattern.

$type = mode_to_typechar( $mode )

Returns file type character of binary mode, ? on unknown file type.

$string = mode_to_string( $mode )

Converts binary mode value to string representation. ? in file type field on unknown file type.

$mode = string_to_mode( $string )

Converts string representation of file mode to binary one.

Linux graphical bootsplash allows you to use custom graphics during early system startup. It makes it possible to place a nice graphic behind or above the kernel boot messages.
Linux graphical bootsplash hooks into the fbcon layer and, if activated, searches the initial ramdisk for a JPEG picture to show.
On any output operations to the console, it takes care of painting a margin around your text and a background picture behind the text with a set of special cfb functions.
Main features:
- Nice graphics (JPEG)
- Antialiased text rendering (TrueType)
- Animations (MNG)
- Progress Bar
- Display of boot messages above or below a graphic. ("verbose" and "silent" modes)
- Fully themeable
Enhancements:
- The bootsplash patch was updated to apply cleanly against Linux kernel 2.6.21.

CvsGraph is a utility to make a graphical representation of all revisions and branches of a file in a CVS/RCS repository.
CvsGraph project has been inspired by the graph option in WinCVS, but I could not find a stand-alone version of this graph code. So, it was time to write one.
Enhancements:
- Merge lines between branches with the same parent were drawn cross-over.
- These were made easier to see by forcing them to originate on one side of the revision boxes.

Squid Graph is a free, simple, yet powerful Squid v2 native logfile analysis tool that generates reports with graphical representation of the proxy servers traffic.
Squid Graph is distributed under the GNU General Public Licence (GPL), which means it is FREE FOR USE AND DISTRIBUTION.
Squid Graph was developed using the Linux operating system running kernel versions ranging from 2.2.x to 2.4.x with PERL 5.6.0. It should work on all other similar operating systems with PERL 5.6 and above installed.
Some platforms which have been reported to run Squid Graph successfully are FreeBSD, OpenBSD, Sun Solaris and most Linux kernel versions and distributions.
Enhancements:
- No algorithm changes, mostly changes to contact information etc. due to hand-over of project to SecurLogic.
Installation:
Extracting the Tarball
- Extract the Squid Graph tarball file after you have downloaded it. Those with Redhat Linux (or other similar distributions) can do this: -
$ tar -zxvf squid-graph-x.x.tar.gz
- Alternatively, those with UNIX-like operating systems can do this: -
$ zcat squid-graph-x.x.tar.gz | tar -xvf -
Gathering the Pre-requisites
- As of version 3.0, Squid Graph requires the GD perl module. You can download it from http://stein.cshl.org/WWW/software/GD/ or you can use the included GD-1.3.3.tar.gz file in the extras/ directory.
- Follow the intructions in the GD perl module to get it installed correctly before you proceed.
Compiling
- Squid Graph runs out of the box. You dont have to compile it.
Putting it in the Right Place
- You might not prefer to have Squid Graph lying around in your current directory, so you should just move it to a directory which makes sense, such as /usr/local/squid-graph. e.g.
$ mv squid-graph-x.x /usr/local/squid-graph
Runing Squid Graph:
Quickstart
First, get yourself into the bin/ directory, for example: -
$ cd /usr/local/squid-graph/bin
Next, you run Squid Graph with the default options. The bare minimum for Squid Graph to run is the --output-dir option. The output directory is where the generated HTML reports and image files would be written.
$ ./squid-graph --output-dir=/var/www/html/reports < /usr/local/squid/logs/access.log
NOTE: Please check your directory permissions of your output directory!
Usually you would want the output to be generated into a directory which your web server is configured with access to. In the above example, /usr/local/squid/logs/access.log is your Squid logfile.
Where you store your Squid logfile differs from system to system. For default Redhat Linux installations, it should be in /log/squid/access.log. For those who compiled and installed Squid with the default options, it should be in /usr/local/squid/logs/access.log.
Removing the TCP or UDP Graphs
Most of you wont use cache ICP or log cache ICP, so there wont be any UDP messages in your logfiles. Disabling UDP is a good idea. You can do this by specifying the --tcp-only command line option.
$ ./squid-graph --tcp-only --output-dir=/var/www/re...
Likewise, if you only want to see UDP statistics, you can specify the --udp-only option.
$ ./squid-graph --udp-only --output-dir=/var/www/re...
Generating Cumulative Graphs
As of version 3.0, Squid Graph comes with a new feature to generage cumulative curves instead of the normal graphs. This can be done by specifying the --cumulative option.
$ ./squid-graph --cumulative --tcp-only --output-dir=/var/www/re...
To have a better understanding of what cumulative curves are, take a look at the output examples. Do note that enabling cumulative graphs disables the Average Transfer Duration graph automatically.
Disabling Average Transfer Duration Graphs
You can disable the Average Transfer Duration Graph by specifying the --no-transfer-duration option.
$ ./squid-graph --no-transfer-duration --output-dir=/var/www/re...
Specifying the Start/End Time
By default, Squid Graph generates reports based on the current time. It starts analyzing from 24 hours before the current time until the current time. Sometimes we cycle logfiles so it is necessary to specify when you want Squid Graph to start looking at your log files. This is done by specifying the --start option.
$ ./squid-graph --start=991353612 --output-dir=/var/www/re...
Likewise, you can specify the end time and Squid will automatically calculate the start time for you. This is done by specifying the --end command line option.
$ ./squid-graph --end=991352122 --output-dir=/var/www/re...
To get the last line of the Squid logfile, simply use tail -n1 logfile.log
Note that the start value is a numerical value which represents the number of seconds since 1970, NOT the conventional hh:mm:ss dd/mm/yyyy format. The reason why we did this is because Squid logs its time in this format, and we can easily use head -n1 logfile.log to view the first line of the log file to determine the start time.
Enhancements:
- Updated links after moving project to Sourceforge
- Updated links to incorrect GPL license in documentation
- Updated links to outdated GD Perl module
- Simplified package directory structure and removed old files
- No algorithm / logic changes

PyReverse is a set of tools for reverse engineering Python code. So far, it features dependency analysis tools, documentation generation, and XMI generation for importation in a UML modeling tool. A special module can be used to generate files readable by Argo UML.
currently PyReverse build a representation of the source tree with:
- docstring for modules, classes, functions
- exceptions raised in functions
- modules attributes, functions, classes
- classs attributes defined in the class scope, inheritance links
- class instances attributes defined in the __init__ method. If possible, get the default value
- functions parameters name and optional default value
- detection of interface/abstract classes and visibility using regular expressions
- detection of links between classes using attributes default value
PyReverse provides modules which use this representation for:
- producing a XMI 1.0 UML 1.3 DOM representation
- creating PGML diagrams definitions according to the project representation, the XMI definition and a XML file which describes briefly the content of the diagrams (see ???). Those diagrams can be readen/edited with Argo UML
- generating UML diagrams readable by VCG (see ???).
- analyzing dependencies (see ???).
- generate skeleton for unit tests, using the unit testing framework for the standard library.