g2_main.dox

RNA二级结构预测程序

/* this file is used mainly to hold some general g2 doxygen
documentation in the doxygen format */


/* define some main groups */

/**
 * \defgroup interface g2 User Interface
 */

/**
 * \ingroup interface
 * \defgroup physdev g2 Physical devices
 *
 * g2 physical devices are drivers for different output
 * formats.
 *
 */



/** \mainpage


\section licence License Notice

This library is free software; you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as
published by the Free Software Foundation; either version 2.1 of the
License, or (at your option) any later version.  This library is
distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
License for more details.  You should have received a copy of the GNU
Lesser General Public License along with this library; if not, write
to the Free Software Foundation, Inc., 59 Temple Place, Suite 330,
Boston, MA 02111-1307 USA *

Copyright (C) 1998-2004 Ljubomir Milanovic & Horst Wagner.


\section introduction Introduction

\subsection what What is g2 ?

\subsubsection short Short version (if you are in hurry)

    - 2D graphic library
    - Simple to use
    - Supports several types of output devices (currently X11,
      PostScript, devices supported by gd http://www.boutell.com/gd/
      (PNG, JPEG), FIG (http://www.xfig.org) and MS Windows windows)
    - Concept allows easy implementation of new device types
    - Virtual devices allow to send output simultaneously to several devices
    - User definable coordinate system
    - Written in ANSI-C
    - Tested under Digital Unix, AIX, Linux, VMS and Windows NT
    - Perl support
    - Fortran interface

\subsubsection long Long version

g2 is a simple to use graphics library for 2D graphical applications
written in Ansi-C. This library provides a comprehensive set of
functions for simultaneous generation of graphical output on different
types of devices. Presently, following devices are currently supported
by g2: X11, gd (PNG and JPEG), PostScript and FIG (xfig).
One major feature of the g2_library is the concept of virtual devices.
An arbitrary number of physical devices (such as PostScript, or X11) can
be grouped to create a so-called virtual device. Commands sent to such a
virtual devices will automatically issued to all attached physical
devices. This allows for example simultaneous output to a PNG file and a
Postscript file. A virtual device in turn can be attached to another
virtual device, allowing to construct trees of devices.
Virtual devices can also be useful when using different user-coordinate
systems. E.g. one X11 window showing an overview of a graphical output,
and a second window showing a zoom of a more detailed area of the
graphic. Drawing in both windows is performed by one single command to
the virtual device.

\code
                                   /-------> PNG:   g2_attach(id_PNG,..
            ----------------------- 
g2_plot---> | Virtual device: id  |--------> X11:   g2_attach(id_X11,...
            -----------------------
                                   \-------> PS:    g2_attach(id_PS,...
\endcode

If you don't need or like the concept of virtual devices, simply ignore it.



\section getting   Getting Started

\subsection preinstallation Preinstallation tasks:

    * PNG and JPEG support

    g2 uses the gd library by Thomas Boutell to generate PNG files. This
    package is freeware (however not GPL) and can be downloaded at
    http://www.boutell.com/gd/.
    Linux users might prefer to install a pre-compiled gd rpm package
    which should be available at your local RedHat mirrorsite.
    NT users should install the gd source package in a subdirectory
    named "gd" which should be located in the same directory as the g2
    subdirectory (but not in the g2 directory itself). Otherwise file
    locations for gd must be modified in the g2 project workspace.
    Unix and VMS users will have to build and install gd according to
    the instructions found in the gd distribution.


\subsection installation Installation


LINUX

    -# Either install RPM packet with binaries, or compile as described
      in the UNIX section

UNIX

    -# Extract package with gzip -dc g2-xxxx.tar.gz | tar xvf -
    -# Run './configure'
    -# Optionally run 'make depend'
    -# Run 'make'
    -# Run 'make install' or copy libg2.a and g2.h, g2_X11.h, g2_gd.h,
      anf g2_PS.h to the default locations for library and include files.
    -# Optional: cd to demo directory and run 'make demo' to compile demo applications

WINDOWS NT

    -# Extract package using either the .tar.gz or the .zip distribution
    -# MS Visual C++ users can build both library and demos with the
      supplied project file: g2.dsw (To obtain an icon and use menu
      functions you must also build the g2res project in g2.dsw)
    -# users of gcc or other commandline based compilers with make
      support continue as in Unix example
    -# It is also possible to compile g2 on winNT/95 using the free
      cygwin32 library and a X-windows library for windows.
      Theoretically it should be possible to support both X-windows and
      native NT/95 windows at the same time.

PERL (old instructions)

    -# Change to directory g2_perl
    -# Perform following steps
          -# perl Makefile.PL
          -# make
          -# make test
          -# make install
    -# See the \ref perl "Perl interface" section for more information
    -# swig is also supported, more details are comming ...

VMS

  -# Try to extract either the tar.gz or the zip distribution (whatever
    is easier for you)
  -# type mms to compile library (descrip.mms file is suplied)
  -# run mms in demo directory to compile demo applications


\subsection simple A simple example

The following example is a minimal application. It draws a rectangle in
a postscript file.

\code
#include <g2.h>
#include <g2_PS.h>

main()
{
    int id;
    id = g2_open_PS("rect.ps", g2_A4, g2_PS_land); 
    g2_rectangle(id, 20, 20, 150, 150); 
    g2_close(id);
}
\endcode

- Always include <g2.h>. Additionally include header files for all
types of devices you want to use.
- Open devices using g2_open_XY functions. The open function
returns a device id of type int, which you need to refer to the device.
- Call g2_close() to close device.
- Consider turning off auto flush (g2_set_auto_flush()) for improved performance.
 

You want to draw a PNG file instead of a PostScript file ?

replace the PS header file with

\code
#include <g2_gd.h>
\endcode

and replace the g2_open_PS function call with

\code
id = g2_open_gd("rect.png", 300, 200, g2_gd_png);
\endcode

You want to draw to a PNG file and a PostScript file with one plot
command ?

Here we use the concept of virtual devices. Open a PNG and PostScript
device, then open a virtual device and attach both the PNG and
PostScript device to the virtual device. Plot commands to the virtual
device will be issued to both PNG and PostScript device. You can attach
and detatch further devices at any time.

\code
#include <g2.h>
#include <g2_PS.h>
#include <g2_gd.h>

main()
{
    int id_PS,id_PNG,id;

    id_PS  = g2_open_PS("rect.ps", g2_A4, g2_PS_land);
    id_PNG = g2_open_gd("rect.png", 300, 200, g2_gd_png);
    id     = g2_open_vd();

    g2_attach(id, id_PS);
    g2_attach(id, id_PNG);

    g2_rectangle(id, 20, 20, 150, 150);
    g2_circle(id, 50, 60, 100);

    g2_close(id);
}
\endcode

Note: closing a virtual device automatically closes all attached devices.


\subsubsection more More examples

More examples showing the usage of different user coordinate systems,
multiple virtual devices, etc. can be found in the distribution (demo
directory).

    
\subsection fortran Fortran interface

The Fortran interface for g2 is currently tested for Linux and Digital
Unix/OSF. Function names for Fortran are the same as in C, however
following differences exist:

    * all variables including device IDs are of type REAL
    * void functions are implemented as subroutines and must be called
      with CALL
    * constants defined by #define in C (e.g. g2_A4) do not work. Get
      corresponding values from the apropriate header files.

A short Fortran example:

\code
        program demo
        real d,color
        d=g2_open_PS('demo_f.ps', 4.0, 1.0)
        call g2_plot(d, 50.0, 50.0)
        call g2_string(d, 25.0, 75.0, 'TEST ')
        color=g2_ink(d, 1.0, 0.0, 0.0)
        write (6,*) color
        call g2_pen(d, color)
        call g2_circle(d, 20.0, 20.0, 10.0)
        call g2_flush(d)
        call g2_close(d)
        stop
        end
\endcode

\subsection perl Perl interface (old info)

The perl interface for g2 is currently tested for Linux and Digital
Unix/OSF. Function names in perl are the same as in C, however the
device itself is implemented object orientated, i.e. the device argument
is ommited in all functions.
E.g., following simple perl script:

\code
use G2;

$d = newX11 G2::Device(100,100);
$d->circle(10, 10, 20);
$d->string(20, 40, "Hello World");

print "\nDone.\n[Enter]\n";
getc(STDIN);

$d->close()
\endcode

The creator functions are newX11, newGIF, newPS, etc. and accept the
same arguments as the open functions in the C version.
See the perl documentation (perldoc G2) for more details and the test.pl
script for a more extensive example.

\section Contact

You can contact the authors and contributors by e-mail (/ is @ and - is .):

- Ljubomir Milanovic: 			ljubo/users-sourceforge-net
- Horst Wagner:       			wagner/users-sourceforge-net
- Tijs Michels (spline implementation):	tijs/vimec-nl

or visit g2 home page on: http://g2.sourceforge.net/

*/



/** \page paper  PS paper sizes


\subsection paper PostScript paper sizes

\code
g2 Name                 Name                 Size(Pt)
--------------------------------------------------------
g2_A0                   A0                   2384 x 3370
g2_A1                   A1                   1684 x 2384
g2_A2                   A2                   1191 x 1684
g2_A3                   A3                    842 x 1191
g2_A4                   A4                    595 x 842
g2_A5                   A5                    420 x 595
g2_A6                   A6                    297 x 420
g2_A7                   A7                    210 x 297
g2_A8                   A8                    148 x 210
g2_A9                   A9                    105 x 148
g2_B0                   B0                   2920 x 4127
g2_B1                   B1                   2064 x 2920
g2_B2                   B2                   1460 x 2064
g2_B3                   B3                   1032 x 1460
g2_B4                   B4                    729 x 1032
g2_B5                   B5                    516 x 729
g2_B6                   B6                    363 x 516
g2_B7                   B7                    258 x 363
g2_B8                   B8                    181 x 258
g2_B9                   B9                    127 x 181
g2_B10                  B10                    91 x 127
g2_Comm_10_Envelope     Comm #10 Envelope     297 x 684
g2_C5_Envelope          C5 Envelope           461 x 648
g2_DL_Envelope          DL Envelope           312 x 624
g2_Folio                Folio                 595 x 935
g2_Executive            Executive             522 x 756
g2_Letter               Letter                612 x 792
g2_Legal                Legal                 612 x 1008
g2_Ledger               Ledger               1224 x 792
g2_Tabloid              Tabloid               792 x 1224
\endcode

    
*/