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Books

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Introducing Atari ST Machine Code
This book aims to teach the practical fundamentals of using MC 68000 assembly language on the ATARI ST range of personal computers. No knowledge or assembly language is assumed, through is is expected that the reader has the use of an ATARI ST and has the ability to copy, move and delete files, format disks, etc from the GEM desktop, and use the GEM interface. Scan by uicr0Bee.

First Edition: December 1990
Revised: September 1991
Programmer's Guide To GEM
Book is an in-depth introduction to GEM for programmers. Prior programming knowledge is assumed
and basic C prioficiency to be able to read samples. Scan by uicr0Bee.
Compute!'s ST Applications Programming In C
COMPUTE!'s ST Applications Guide: Programming in C is written for C programmers. It does not teach C programming, but rather includes a library of functions that makes using GEM routines easier to access from your own C programs. Scan by uicr0Bee.
Atari ST GEM's Programmer Reference By Abacus/Data Becker
The complete guide to programming the ST using the Graphics Environment Manager. Second printing, March 1986. Scan by uicr0Bee.
Atari ST Internals
3rd ed. by K. Gerits L. Englisch R. Bruckmann
If you're Atari ST coder, this is absolutely must read. Every Atari ST subsystem is described on hardware and software level. Book contains also BIOS/GEMDOS/XBIOS/Line A/AES/VDI reference which is great help while coding, m68k processor architecture and operation, m68k instruction set/addressing modes, listing of important system vectors. Nearly everything you should know. With Atari Compendium and ST/TT Profibuch (which was never translated from german) ST Internals is one of the best hardware/software references for Atari ST range of computers.
At the end of the book there is disassembled system startup sequence. This is updated revision, contains information about blitter which was missing in previous editions.
Learning C on The Atari ST
Introductory Atari ST C course. Author uses Megamax C compiler.
Atari ST Machine Language
Complete Atari ST m68k assembly course, Abacus, Fourth Printing, March 1989. Scan by uicr0Bee.
Atari ST Basic to C
For everyone who would like to make transition from ST basic to C language. Abacus, Second Printing, May 1988. Scan by uicr0Bee.
68000-68010-68020-Primer
Overview of Motorola 16/32 bit processors: 68000, 68010 and 68020. First edition, second printing 1987.
Modern Atari System Software - A Programmers Guide
by HiSoft 1993. Very nice reference manual for newer Atari machines like Falcon030. It covers all the major subsystems found in m68k Atari machines, object file formats (DRI/GST), guidelines for developing GEM applications, SpeedoGDOS informations, overview of MiNT os(this info can be outdated, because MiNT had alot of changes since then) several handy lookup tables with system calls, system errors and many more. It contains additional info and bindings for HiSoft products like Devpac assembler, Lattice C and HiSoft basic. Scan by uicr0Bee.
Atari ST 3D Graphics Programming Concepts and Techniques
For programmers interested in 3D graphics. 2D/3D transformations, hidden lines and surfaces, data structures for 3D objects, object animation, spatial projection, screen manipulation, rotation of objects, light and shadows. Examples are in m68k assembly with use of GEM and mono resolution. Scan by uicr0Bee.
Atari Compendium 1st revision (HTML format)
Definitive Atari 16/32 bit computers documentation (besides Profibuch). It's in english. Every subsystem found in Atari computers is well explained, some things are little outdated, about MiNT for example. It covers Falcon which is omitted in Profibuch. Package contains also system bindings for Lattice C and Pure C and example source codes from the book in txt files.
This version is in html format so you can view it offline in any web browser. You can also view it online:
https://bus-error.nokturnal.pl/atari_compendium/html/toc.htm
Highly recommended!
The Concise Atari ST 68000 Programmers Reference Guide
Glentop Publishing 1986, book title is little misguiding. In general it's contains general overview of Atari ST architecture, ports, interfaces/subsystems(graphics/sound/input), TOS/GEM system calls, describes essential things about M68000(architecture, instruction set, adressing modes, but very briefly). It contains also little overview/comparison of coding tools / m68k assemblers (very outdated though). It could be good for it's time, if not unreadable layout. Browsing and finding any information in this book is quite difficult. Newer editions of this book contained informations about blitter (this version contains no info about it).
Atari Profibuch ST-STE-TT
Definitive guide to Atari computers, 1500 pages describing TOS operating system calls (BIOS/XBIOS/GEM/AES), how internal systems work. Many illustrations. The only disadvantage is that it is in german and doesn't cover Falcon030 at all. Book was released recently for free by it's authors.
Beside of Atari Compedium it's a must read.