README for acedb source code.
--
The code is GPL
If you use the acedb_ncbi code
please quote

AceView: a comprehensive cDNA-supported gene and transcripts annotation, 
Danielle Thierry-Mieg and Jean Thierry-Mieg
Genome Biology 2006, 7(Suppl 1):S12
http://genomebiology.com/2006/7/S1/S12

LINUX:
To compile acedb, you must first install the development packages (with header files) 
for libXaw, libXt, libXmu, libXext and libX11. For example on Fedora, RHEL, CentOS and 
friends these are named libXaw-devel etc... 
On Debian based systems (including Ubuntu) they are named eg libxaw-headers.

There is a tar file wh/x11.include.tar.gz that you could use if you cannot obtain the
headers, but these canned headers may not be exactly in suynch with your X11 libraries

--
The documentation is available at
   https://github.com/jtmieg/AceView/blob/master/acedb_query_language_documentation.pdf
--

wdoc 
	contains many documentation files

whelp 
	contains help files used by the compiled programs.

idoc
	internal documentation written by Mark S 

Quick guide to building the system
--

	% ln -s wmake/makefile .
	% make
		it will show you the possible machine configurations

    in sh or bash (linux default shell):
        % export ACEDB_MACHINE=LINUX_X86_64_4_OPT
    alternatively in csh or tcsh:
	% setenv ACEDB_MACHINE SOLARIS_4

        Use the right configuration for your machine.  
        frequent choices are:
		SOLARIS_4	any version of solaris
		SOLARIS_4_OPT	any version of solaris
		LINUX_4		any version of linux
                LINUX_4_OPT     optimized code for linux 32 bits 
                LINUX_X86_64_4_OPT optimized code linux 64 bit
	The 4 refers to Acebd version 4, there are many other machines
        predefined in directory wmake (ALPHA,IBM,SGI etc).

        If your machine is not listed
        please prepare a new file wmake/MACHINE_DEF and mail it to
          mieg@ncbi.nlm.nih.gov
        I will include it in the distrib,  but (in priciple) never edit 
        the machine independant makefile:  wmake/truemake
 
        On some machines, the optimized version mishandles the color table
        and the graphic program 'xace' 'xacembly' pops up in grey tones. If this
	happens, try the non-optimized graphic code. There is no known 
        optimization bug affecting the non graphic programs.

	% make -k all
                Notice that all object modules and all executable are created
                in the directory bin.$ACEDB_MACHINE, so you can compile for several
                platform in parallel.

		please use 'make -k all'
		the purpose of -k option is to continue compiling
		if one of the target fails. For example under my
		instalation of CYGWIN, i fail to compile the 
		rpc 'aceserver' program, because i cannot locate
		xdr_free in /usr/lib. But this is immaterial since
		the tcp 'taceserver' program, which has equivalent 
		functionalities compiles and runs.


	% cd demo 
	% sh test_note toto
		This will create a tiny database in directory toto
	% ../bin*/xace toto
		This should open the X11 graphic xacembly code
		click on the sequence class, then on one of the
		sequences in the main-keyset window, then on the
		DNA button in the sequence window
		The database is quasi empty, but this is a test
		that the whole code runs ok
		Click Exit in the main window
	% cd ../wac
		Look at the README in this directory, it contains the
		test suite for the client server system
		Notice that acedb supports 3 protocols, 
		rpc/sanger-tcp/ncbi-tcp
		AceView uses ncbi-tcp which is way faster, AcePerl
		supports rpc and sanger-tcp
		some machines, in particular windows do not support
		rpc
		To use AcePerl on LINUX ise the rpc method

What is here
--

demo
	a script to create a small demo database - useful to developers
	working on the database system, not necessarily useful for
	anyone else

idoc
	Mark Sienkiewicz wrote this documentation while learning the system.

w1	
	tools - basic libraries
	[ ace 9 has different message passing (eg. messout, fn names) ]

w2	
	graphics libraries - ps, gif, x11, mac
	[ different in ace 9 - gtk ] 

w4,5	database kernel

w6	object layer 
	universal graphics - keyset display, tree display, few others
	dna, peptide

w7	biology graphics code
	[ quite out of sync with ace 9 - merge is difficult: both have
	new features ]

w8, wabi 
	acembly layer
	[ not synchronized with ace 9 - we have features they do not have ]

w9	high layer tools from sanger: dotter, other

wabi	Acembly code to analyse and display sequencing projects and Solexa data

wac	AceC : C language programmers interface to acedb
        The directory contains a test suite
	AceC code can run standalone or connect to a distant server
	which can be the taceserver or tgifacemblyserver which
	are part of this package, or the saceserver which is
	part of the sanger acedb code and runs at CSHL

wacext	Contains many application code written in AceC
	some are used frequently, some are one time shots
	and a few are broken, but are not used elesewhere.
	cd wacext ; make -k all	

wace	obsolete tools for importing data

wacec	obsolete vahan's ace c library
        kept for compatibility

waction	obsolete - export data, run ext program, reload data
	never worked on all platforms

wbql
	AQL (Acedb Query Language) code, documentation and demo
	Having compiled the program (make -k all)
	type the command
	  tcsh wbql/bqltest.tcsh
	the expected message is:
	  ALL TESTS ARE SUCCESSFUL
	otherwise please mail mieg@ncbi.nlm.nih.gov
	The documentation is available at
	  https://github.com/jtmieg/AceView/blob/master/acedb_query_language_documentation.pdf

wc	examples using ace c

wdce	windows RPC - DCE
	from Richard II

wdnasearch
	will be dna search someday

wdoc
	documentation

wext
	code that uses acelib
	acelib is client library for applications to use - works only
	from disk. some of this code used in production

wfiche
	vahan's biology code - linked to our schema

wgd	
	library that creates gif images

wgf	
	gene finder data tables
	gene finder does "a priori gene finding"

wgnbk	
	old program to index and re-export pieces of a large file

wh	
	most include files

whelp	
	online help (html)

whooks	
	schemas and classes that are known intrisicially by the c code

wjo	contributed biology graphic code

wmake	all makefiles live here

wmd5	MD5 hash

wnq	"new query" recent tools (library) should be in w1

wquery	place to store standard queries - distributed with system
	often out of sync with schema
	obsolete?

wrpc	rpc client and server code

wscripts
	external code that we use - see wtools

wsocket7
	new socket server client (2 versions)
	[ was copied from ace 9, but doesn't work for us. ]

wspec
	standard wspec for creating new database
	contains standard worm schema
	- should have a minimum schema, or schema with everything the
	code knows.

wstaden
	code borrowed from roger staden - library to read "abi traces"
	localized for acedb

wtools
	external code that we use - see wscripts
	schema checker in python
	genbank to ace translator

wvsim	vahan's general library - like w1
	do not use
	we keep it for back compatibility so some applications