HARPER@finuh.bitnet ("ROBERT HARPER, FINLAND") (04/24/89)
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No 6
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<< EDITED BY ROBERT HARPER >>
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THE MYSTERIES OF ARC AND UUDECODE REVEALED
This issue of BIOBIT deals with the use of two sets of programmes,
namely programmes for ARCING/UNARCING and UUENCODING/UUDECODING. But
first a bit imagery. Lets imagine a jack-in-the-box. The basic
mechanism is a spring which has been compressed, and when you open the
box the puppet pops out. Well that is what the ARC programme does. It
allows you to take a file and compress it to a much smaller size than
the original, and ship it from one place to another and then uncompress
it so that it pops out to its original size. The obvious applications
are large documents, or spreadsheets. Some ARCing programmes can
compress text files (.DOC or .TXT) to 50% of their original size.
Whereas the best compression for programmes (.EXE or .COM) is generally
about 30-40% depending on the type of ARCing programme that you use.
Archiving is a very "hot" topic at the moment. On EARN/BITNET the
standard is the ARC format. On USENET there is a debate going on at the
moment whether or not to change from ARC to ZOO because ZOO is
available for a variety of different operating systems (MSDOS, UNIX,
VMS) and it would be nice to have an archiving system that is
compatible on many different systems. And then there is a new archiver
called PKZIP which gives very good compression percentages as well as
being very fast at extracting files from .ZIP files. The two main
things that people look for when they use a ARCing programme are
percentage compression and speed of extraction. PKZIP performs these
two activities very well and this is why it has an enthusiastic
following.
It is hard to think of an analogy for UUENCODING. Anyway here goes.
Let's compare a computer programme to an enzyme. The enzyme usually
performs a specific task. So does a programme. An enzyme has a certain
optimal temperature and pH before it works. If you don't handle it
properly it could become inactive and useless. Well that is what
happens when you try and send programmes over the network. They get
trashed at the various gateways and when they arrive, due to the rough
handling they have had they "loose all their activity", and they do
not work. (EBCDIC->ASCII translation ;-) )
Now an enzyme is only a certain arrangement of amino acids, and the
original code for them is to be found in a particular DNA sequence. So
in theory if you know the original DNA sequence you should be able to
make the enzyme from it... basic protein engineering. Well UUENCODE
takes a programme (.EXE or COM) and translates it into a code. This
code is pure ASCII and it can be safely transfered over the network.
When it arrives at its destination it is UUDECODED to produce the
original programme once again... a sort of reverse engineering.
It takes a series of three neucleotides to code for one amino acid, so
the DNA code sequence is larger than the code sequence for the enzyme.
The same is true for UUENCODED files. They are always larger than the
original programme. This is the reason that UUENCODE and ARC are
employed in conjunction with each other. ARC is used to make the file
as small as possible before the UUENCODING takes place. So now you know
why this archiving and uuencoding are taking place. Simple isn't it?
So lets now examine the steps involved getting a programme from BIONET
to Helsinki. At BIONET the programmes are ARCed to make them as small
as possible and then UUENCODED. When I get them to Helsinki and I
reverse the process.
For historical reasons we will be looking at ARC v5.12 which was the
first popular archiver. It has many different options but the three
most often used options used with ARC are A for ADD and V for verbose
and X for extract. At BIONET two files are added into the archive
PLASMIDC.ARC by giving the following commands
1) a) ARC A PLASMIDC.ARC PLASMID.EXE
b) ARC A PLASMIDC.ARC PAINT.BAT
The resulting PLASMIDC.ARC file is then UUENCODED with the following
command.
2 ) UUENCODE PLASMIDC.ARC PLASMIDC.UUE
The files are then brought to Helsinki by FTP and downloaded to a PC
using the KERMIT protocol. Once the file are on the micro, the
procedure is reversed. The UUDECODE programme looks at the the header
of the .UUE file and decodes it to give the .ARC file.
1) C:\>uudecode plasmidc.uue
Decoding plasmidc.uue
Destination is plasmidc.arc
The PLASMIDC.ARC file is then examined with the VERBOSE option just to
see what it contains. As you can see it contains the 2 files and the
EXE file has been compressed by 16%
C:\>arc v plasmidc.arc
Name Length Stowage SF Size now Date Time CRC
============ ======== ======== ==== ======== ========= ====== ====
PAINT.BAT 21 -- 0% 21 15 Aug 87 6:55p 8674
PLASMIDC.EXE 62754 Crunched 16% 52951 15 Aug 87 6:49p 8250
==== ======== ==== ========
Total 2 62775 16% 52972
The remaining step is now to EXTRACT the files with the X option
and then boot the programme on the micro, and after that you
should be able to draw simple plasmids.
2) C:\>arc x plasmidc.arc
Extracting file: PAINT.BAT
Extracting file: PLASMIDC.EXE
There are many different UUDECODE/UUENCODE programmes to be had, and
ARC comes in many different flavours as well. Find a set of programmes
that work well for your system and then stick to them. One STARTER KIT
which I can recommend is called UseNET CBIP Starter kit. For anyone
interested you can get it by FTP from swan.ulowell.edu (129.63.224.1),
file ibmpc/General/starter.kit
The file is too large to put into BIOBIT for it is about 800 lines, but
here is a short summary of the contents.
%%%%%%%%%%%%%%%%%%%%%%%%%%% EXTRACT %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
UseNet CBIP Starter's Kit
The files contained herein are public domain, with the exception of
ARC-E, (c) Copyrighted by Wayne Chin and Vernon D. Buerg. ALL RIGHTS
RESERVED.
This kit contains what you will need to begin downloading files from
comp.binaries.ibm.pc, or from various archive sites. This kit contains:
1) Instructions
2) BASIC source for UUDECODE
3) Pascal source for UUDECODE
4) C source for UUDECODE
5) ARC-E 3.1C, in uuencoded form
You will need:
1) Pascal or C compiler or BASIC Interpreter
2) File editor
What to do:
You will need to split this file into 5 parts. Each part is separated
by a line stating "---CUT HERE---" and a short description. Using a
text editor, separate the parts for the Pascal source, the C source,
and the UUEncoded ARC-E program. Then compile one of the sources to
create an executable version of uudecode, and then run it on the ARC-E
file. If you called the ARC-E file arce.uue, then type:
uudecode arce.uue
This will give you ARC-E.COM, an executable ARC file extractor. Type
'arc-e' for options. This file will allow you to extract all other ARC
files.
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Rob "that wasn't too painful was it?" HarperMT04@liverpool.ac.uk (Barry Moody) (04/24/89)
info ?