Free descent software for linux

Parse::RecDescent is a Perl module to generate Recursive-Descent Parsers.
SYNOPSIS
use Parse::RecDescent;
# Generate a parser from the specification in $grammar:
$parser = new Parse::RecDescent ($grammar);
# Generate a parser from the specification in $othergrammar
$anotherparser = new Parse::RecDescent ($othergrammar);
# Parse $text using rule startrule (which must be
# defined in $grammar):
$parser->startrule($text);
# Parse $text using rule otherrule (which must also
# be defined in $grammar):
$parser->otherrule($text);
# Change the universal token prefix pattern
# (the default is: s*):
$Parse::RecDescent::skip = [ t]+;
# Replace productions of existing rules (or create new ones)
# with the productions defined in $newgrammar:
$parser->Replace($newgrammar);
# Extend existing rules (or create new ones)
# by adding extra productions defined in $moregrammar:
$parser->Extend($moregrammar);
# Global flags (useful as command line arguments under -s):
$::RD_ERRORS # unless undefined, report fatal errors
$::RD_WARN # unless undefined, also report non-fatal problems
$::RD_HINT # if defined, also suggestion remedies
$::RD_TRACE # if defined, also trace parsers behaviour
$::RD_AUTOSTUB # if defined, generates "stubs" for undefined rules
$::RD_AUTOACTION # if defined, appends specified action to productions
Parse::RecDescent incrementally generates top-down recursive-descent text parsers from simple yacc-like grammar specifications.
Main features:
- Regular expressions or literal strings as terminals (tokens),
- Multiple (non-contiguous) productions for any rule,
- Repeated and optional subrules within productions,
- Full access to Perl within actions specified as part of the grammar,
- Simple automated error reporting during parser generation and parsing,
- The ability to commit to, uncommit to, or reject particular productions during a parse,
- The ability to pass data up and down the parse tree ("down" via subrule argument lists, "up" via subrule return values)
- Incremental extension of the parsing grammar (even during a parse),
- Precompilation of parser objects,
- User-definable reduce-reduce conflict resolution via "scoring" of matching productions.

GD::Simple module is a simplified interface to GD library.

SYNOPSIS

use GD::Simple;

# create a new image
$img = GD::Simple->new(400,250);

# draw a red rectangle with blue borders
$img->bgcolor(red);
$img->fgcolor(blue);
$img->rectangle(10,10,50,50);

# draw an empty rectangle with green borders
$img->bgcolor(undef);
$img->fgcolor(green);
$img->rectangle(30,30,100,100);

# move to (80,80) and draw a green line to (100,190)
$img->moveTo(80,80);
$img->lineTo(100,190);

# draw a solid orange ellipse
$img->moveTo(110,100);
$img->bgcolor(orange);
$img->fgcolor(orange);
$img->ellipse(40,40);

# draw a black filled arc
$img->moveTo(150,150);
$img->fgcolor(black);
$img->arc(50,50,0,100,gdNoFill|gdEdged);

# draw a string at (10,180) using the default
# built-in font
$img->moveTo(10,180);
$img->string(This is very simple);

# draw a string at (280,210) using 20 point
# times italic, angled upward 90 degrees
$img->moveTo(280,210);
$img->font(Times:italic);
$img->fontsize(20);
$img->angle(-90);
$img->string(This is very fancy);

# some turtle graphics
$img->moveTo(300,100);
$img->penSize(3,3);
$img->angle(0);
$img->line(20); # 20 pixels going to the right
$img->turn(30); # set turning angle to 30 degrees
$img->line(20); # 20 pixel line
$img->line(20);
$img->line(20);
$img->turn(-90); # set turning angle to -90 degrees
$img->line(50); # 50 pixel line

# draw a cyan polygon edged in blue
my $poly = new GD::Polygon;
$poly->addPt(150,100);
$poly->addPt(199,199);
$poly->addPt(100,199);
$img->bgcolor(cyan);
$img->fgcolor(blue);
$img->penSize(1,1);
$img->polygon($poly);

# convert into png data
print $img->png;

GD::Simple is a subclass of the GD library that shortens many of the long GD method calls by storing information about the pen color, size and position in the GD object itself. It also adds a small number of "turtle graphics" style calls for those who prefer to work in polar coordinates. In addition, the library allows you to use symbolic names for colors, such as "chartreuse", and will manage the colors for you.

The Pen

GD::Simple maintains a "pen" whose settings are used for line- and shape-drawing operations. The pen has the following properties:

fgcolor

The pen foreground color is the color of lines and the borders of filled and unfilled shapes.

bgcolor

The pen background color is the color of the contents of filled shapes.

pensize

The pen size is the width of the pen. Larger sizes draw thicker lines.

position

The pen position is its current position on the canvas in (X,Y) coordinates.

angle

When drawing in turtle mode, the pen angle determines the current direction of lines of relative length.

turn

When drawing in turtle mode, the turn determines the clockwise or counterclockwise angle that the pen will turn before drawing the next line.

font

The font to use when drawing text. Both built-in bitmapped fonts and TrueType fonts are supported.

fontsize

The size of the font to use when drawing with TrueType fonts.

One sets the position and properties of the pen and then draws. As the drawing progresses, the position of the pen is updated.

Methods

GD::Simple introduces a number of new methods, a few of which have the same name as GD::Image methods, and hence change their behavior. In addition to these new methods, GD::Simple objects support all of the GD::Image methods. If you make a method call that isnt directly supported by GD::Simple, it refers the request to the underlying GD::Image object. Hence one can load a JPEG image into GD::Simple and declare it to be TrueColor by using this call, which is effectively inherited from GD::Image:

my $img = GD::Simple->newFromJpeg(./myimage.jpg,1);

The rest of this section describes GD::Simple-specific methods.

$img->moveTo($x,$y)

This call changes the position of the pen without drawing. It moves the pen to position ($x,$y) on the drawing canvas.

$img->move($dx,$dy)
$img->move($dr)

This call changes the position of the pen without drawing. When called with two arguments it moves the pen $dx pixels to the right and $dy pixels downward. When called with one argument it moves the pen $dr pixels along the vector described by the current pen angle.

$img->lineTo($x,$y)

The lineTo() call simultaneously draws and moves the pen. It draws a line from the current pen position to the position defined by ($x,$y) using the current pen size and color. After drawing, the position of the pen is updated to the new position.

$img->line($dx,$dy)
$img->line($dr)

The line() call simultaneously draws and moves the pen. When called with two arguments it draws a line from the current position of the pen to the position $dx pixels to the right and $dy pixels down. When called with one argument, it draws a line $dr pixels long along the angle defined by the current pen angle.

$img->clear

This method clears the canvas by painting over it with the current background color.

$img->rectangle($x1,$y1,$x2,$y2)

This method draws the rectangle defined by corners ($x1,$y1), ($x2,$y2). The rectangles edges are drawn in the foreground color and its contents are filled with the background color. To draw a solid rectangle set bgcolor equal to fgcolor. To draw an unfilled rectangle (transparent inside), set bgcolor to undef.

$img->ellipse($width,$height)

This method draws the ellipse centered at the current location with width $width and height $height. The ellipses border is drawn in the foreground color and its contents are filled with the background color. To draw a solid ellipse set bgcolor equal to fgcolor. To draw an unfilled ellipse (transparent inside), set bgcolor to undef.

$img->arc($cx,$cy,$width,$height,$start,$end [,$style])

This method draws filled and unfilled arcs. See GD for a description of the arguments. To draw a solid arc (such as a pie wedge) set bgcolor equal to fgcolor. To draw an unfilled arc, set bgcolor to undef.

$img->polygon($poly)

This method draws filled and unfilled polygon using the current settings of fgcolor for the polygon border and bgcolor for the polygon fill color. See GD for a description of creating polygons. To draw a solid polygon set bgcolor equal to fgcolor. To draw an unfilled polygon, set bgcolor to undef.

$img->polyline($poly)

This method draws polygons without closing the first and last vertices (similar to GD::Image->unclosedPolygon()). It uses the fgcolor to draw the line.

$img->string($string)

This method draws the indicated string starting at the current position of the pen. The pen is moved to the end of the drawn string. Depending on the font selected with the font() method, this will use either a bitmapped GD font or a TrueType font. The angle of the pen will be consulted when drawing the text. For TrueType fonts, any angle is accepted. For GD bitmapped fonts, the angle can be either 0 (draw horizontal) or -90 (draw upwards).

For consistency between the TrueType and GD font behavior, the string is always drawn so that the current position of the pen corresponds to the bottom left of the first character of the text. This is different from the GD behavior, in which the first character of bitmapped fonts hangs down from the pen point.
This method returns a polygon indicating the bounding box of the rendered text. If an error occurred (such as invalid font specification) it returns undef and an error message in $@.

$metrics = $img->fontMetrics

($metrics,$width,$height) = GD::Simple->fontMetrics($font,$fontsize,$string)

This method returns information about the current font, most commonly a TrueType font. It can be invoked as an instance method (on a previously-created GD::Simple object) or as a class method (on the GD::Simple class).

When called as an instance method, fontMetrics() takes no arguments and returns a single hash reference containing the metrics that describe the currently selected font and size. The hash reference contains the following information:

xheight the base height of the font from the bottom to the top of
a lowercase m

ascent the length of the upper stem of the lowercase d

descent the length of the lower step of the lowercase j

lineheight the distance from the bottom of the j to the top of
the d

leading the distance between two adjacent lines

($delta_x,$delta_y)= $img->stringBounds($string)

This method indicates the X and Y offsets (which may be negative) that will occur when the given string is drawn using the current font, fontsize and angle. When the string is drawn horizontally, it gives the width and height of the strings bounding box.

$delta_x = $img->stringWidth($string)

This method indicates the width of the string given the current font, fontsize and angle. It is the same as ($img->stringBounds($string))[0]

($x,$y) = $img->curPos

Return the current position of the pen. Set the current position using moveTo().

$font = $img->font([$newfont] [,$newsize])

Get or set the current font. Fonts can be GD::Font objects, TrueType font file paths, or fontconfig font patterns like "Times:italic" (see fontconfig). The latter feature requires that you have the fontconfig library installed and are using libgd version 2.0.33 or higher.

As a shortcut, you may pass two arguments to set the font and the fontsize simultaneously. The fontsize is only valid when drawing with TrueType fonts.

$size = $img->fontsize([$newfontsize])

Get or set the current font size. This is only valid for TrueType fonts.

$size = $img->penSize([$newpensize])

Get or set the current pen width for use during line drawing operations.

$angle = $img->angle([$newangle])

Set the current angle for use when calling line() or move() with a single argument.

Here is an example of using turn() and angle() together to draw an octagon. The first line drawn is the downward-slanting top right edge. The last line drawn is the horizontal top of the octagon.

$img->moveTo(200,50);
$img->angle(0);
$img->turn(360/8);
for (1..8) { $img->line(50) }

$angle = $img->turn([$newangle])

Get or set the current angle to turn prior to drawing lines. This value is only used when calling line() or move() with a single argument. The turning angle will be applied to each call to line() or move() just before the actual drawing occurs.
Angles are in degrees. Positive values turn the angle clockwise.

$color = $img->fgcolor([$newcolor])

Get or set the pens foreground color. The current pen color can be set by (1) using an (r,g,b) triple; (2) using a previously-allocated color from the GD palette; or (3) by using a symbolic color name such as "chartreuse." The list of color names can be obtained using color_names().

$color = $img->bgcolor([$newcolor])

Get or set the pens background color. The current pen color can be set by (1) using an (r,g,b) triple; (2) using a previously-allocated color from the GD palette; or (3) by using a symbolic color name such as "chartreuse." The list of color names can be obtained using color_names().

$index = $img->translate_color(@args)

Translates a color into a GD palette or TrueColor index. You may pass either an (r,g,b) triple or a symbolic color name. If you pass a previously-allocated index, the method will return it unchanged.

$index = $img->alphaColor(@args,$alpha)

Creates an alpha color. You may pass either an (r,g,b) triple or a symbolic color name, followed by an integer indicating its opacity. The opacity value ranges from 0 (fully opaque) to 127 (fully transparent).
@names = GD::Simple->color_names

$translate_table = GD::Simple->color_names

Called in a list context, color_names() returns the list of symbolic color names recognized by this module. Called in a scalar context, the method returns a hash reference in which the keys are the color names and the values are array references containing [r,g,b] triples.

$gd = $img->gd

Return the internal GD::Image object. Usually you will not need to call this since all GD methods are automatically referred to this object.

($red,$green,$blue) = GD::Simple->HSVtoRGB($hue,$saturation,$value)

Convert a Hue/Saturation/Value (HSV) color into an RGB triple. The hue, saturation and value are integers from 0 to 255.

($hue,$saturation,$value) = GD::Simple->RGBtoHSV($hue,$saturation,$value)

Convert a Red/Green/Blue (RGB) value into a Hue/Saturation/Value (HSV) triple. The hue, saturation and value are integers from 0 to 255.

COLORS

This script will create an image showing all the symbolic colors.

#!/usr/bin/perl

use strict;
use GD::Simple;

my @color_names = GD::Simple->color_names;
my $cols = int(sqrt(@color_names));
my $rows = int(@color_names/$cols)+1;

my $cell_width = 100;
my $cell_height = 50;
my $legend_height = 16;
my $width = $cols * $cell_width;
my $height = $rows * $cell_height;

my $img = GD::Simple->new($width,$height);
$img->font(gdSmallFont);

for (my $c=0; $cfgcolor($color);
$img->rectangle(@topleft,@botright);
$img->moveTo($topleft[0]+2,$botright[1]+$legend_height-2);
$img->fgcolor(black);
$img->string($color);
}
}

print $img->png;

StrBio is a set of Java classes and libraries useful for development of software for computational structural biology research.

They are licenced under the LGPL.

he strbio.org classes are the basis for several published research projects, including the Pred2ary secondary structure prediction program and the ASTRAL database of protein domain sequences.

The most interesting structural biology applications included are:

Pred2ary protein secondary structure prediction
JThread protein fold prediction
ConvertProtein for interconversion of protein file formats (FASTA, PDB, MSF, ALN, CASP, DSSP, HSSP, YAPF)
Filters to exchange data with commonly used molecular biology applications (e.g., BLAST, MinArea, MODELLER)
MakeRAF tool to create the Rapid Access Format sequence maps for the ASTRAL database.

Other more general-purpose functionality that is included:

Neural network library, including Scaled Conjugate Gradient or Steepest Descent optimization
Hooke and Jeeves derivative-free global optimization algorithm
Misc mathematical objects and algorithms (vectors, matrices, etc)
Efficient string formatting using Printf-based syntax (printf, atoi, atof, etc.)

JetPAG is full-LL(k) optimizing parser and lexical analyzer generator. It is focused on high usability, efficiency and readability of generated code. JetPAG performs full L(k) analysis and tails is with powerful optimizations resulting a grammatically powerfull, resource-efficient and fast recognizers.
JetPAG is suitable for a wide spectrum of applications ranging from simple stand-alone small interpreters to high-end full-featured parser interpreter kits suitable for integration with larger applications. Generated recognizers are guaranteed to be faster than most current recurisve-descent generated ones. Provided documentation and tutorials in the website allow acquiring skill in JetPAG to be a matter of minutes.
Enhancements:
- Many bugs were fixed.
- The analysis engines were vastly improved with smarter optimizations.
- Easier grammars and several new practical options were introduced.
- Importing and exporting token types for use among several grammars is supported.
- Improvements were made to the code generator.

Common Text Transformation Library, CTTL for short, is a set of C++ classes and functions to understand and modify text data. Common Text Transformation Library implementation is based on STL classes and algorithms.
Concept of a substring plays major role in design of the text transformation library. CTTL substring is an object that interacts with fragments of text encapsulated by STL std::basic_string template class.
Template classes cttl::const_edge and cttl::edge, designed for constant and mutable data access, respectively, represent CTTL substrings. Substrings may be compared, inserted, deleted, or replaced across multiple text inputs. If content of text mutates, the substrings adjust their positions accordingly to the change. CTTL guarantees that substrings remain stable with respect to a potentially mutable text.
Within CTTL framework, a substring may be parsed with EBNF-like grammar. CTTL lexical analysis engine generates a stream of substrings corresponding to the parsed symbols. BNF and EBNF grammars can be written directly in C++.
Template meta-programming and operator overloading offer features to write C++ expressions that describe grammar rules. No additional steps of parsing, compiling, or generating source code are required. Compiled CTTL program implements LL(INF)-parser, the recursive-descent parser with infinite lookahead.
Enhancements:
- This release focuses on documentation enhancements, which include multiple documentation improvements and revisions.
- An alphabetical index of all CTTL facilities was added: http://cttl.sourceforge.net/documentation_idx.html.

The P-UMLaut tool allows the user to transform UML 2.0 Sequence Diagrams to semantically equivalent Petri Nets.
These Petri Nets may then be simulated using the supplied PN simulator (of PEP descent) or operated on with any tool that can work with high level Petri Nets.
By plugging different Realms into the simulation by way of an event filter, the modeled world may then be displayed and interacted with in various fashions. A 3D animation module is supplied as well as two examples utilizing the complete toolchain.
Enhancements:
- A new Petrinet Simulator was implemented in Java which features Highlevel-PN to Lowlevel-PN unfolding and Timed-PN simulation.
- Filtering was enhanced. Irrlicht 0.12 is used.