}
puts $hfh "(Index) "
puts $hfh " (Help on Help)"
puts $hfh "$line
"
puts $hfh {}
}
} else {
#Normal line of text
if [string length $helpfile] {
set words [split $line " "]
foreach key $words {
if {-1 == [set myoffset [lsearch -exact $myindex $key]]} {
puts -nonewline $hfh "$key "
} else {
puts -nonewline $hfh "$key "
}
}
puts $hfh ""
}
}
}
puts $hfh {}
puts $hfh {}
close $hfh
--
Henry J. Cobb hcobb@fly2.berkeley.edu, Bad-Think Criminal
This is a fat cross platform .sig virus,
able to run on many different platforms.
From owner-acedb@net.bio.net Tue Jun 14 23:00:00 1994
Path: biosci!MENDEL.AGRON.IASTATE.EDU!lorenzen
From: lorenzen@MENDEL.AGRON.IASTATE.EDU (Lisa Lorenzen)
Newsgroups: bionet.software.acedb
Subject: SubClass
Date: 15 Jun 1994 05:01:10 -0700
Organization: BIOSCI International Newsgroups for Molecular Biology
Lines: 17
Sender: daemon@net.bio.net
Distribution: world
Message-ID: <9406151159.AA02868@mendel.agron.iastate.edu>
NNTP-Posting-Host: net.bio.net
Hi! Not meaning to beat a dead horse (I have seen remnants
of this before), but who out there has used the subclass
mechanism?? I would like to look at a database that has
(what it looks like, as well as models/wspecfile if possible)
and perhaps a reminder of how you invoke the subclass. I believe
it was Dave Matthews who asked if you could arrange subclasses
in the main window, or if they always appeared at the bottom,
I never caught the reply to that???
Thanks a lot -
Lisa :-)
From owner-acedb@net.bio.net Tue Jun 14 23:00:00 1994
Newsgroups: bionet.software.acedb
Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!cs.utexas.edu!convex!convex!constellation!rex!cpu1.omrf.uokhsc.edu!barsteadr
From: barsteadr@omrf.uokhsc.edu (Bob Barstead, Oklahoma Medical Research Foundation, 825 N.E. 13th Street, Oklahoma City, OK 73104 (barsteadr@omrf.uokhsc.edu))
Subject: solaris write access
Sender: news@rex.uokhsc.edu (News Admin)
Message-ID: <1994Jun15.160518.1@omrf.uokhsc.edu>
Date: Wed, 15 Jun 1994 22:05:18 GMT
Nntp-Posting-Host: cpu1.omrf.uokhsc.edu
Organization: Oklahoma Medical Research Foundation
Lines: 11
For the solaris version of acedb: As may have been
discussed already, adding users into the passwd.wrm file does not
seem to provide write access, even for the acedb administrator.
Can someone tell me which permissions on which files need to be
changed in order to get write access. Also, which files need to
be modified so that other users have read access.
Thanks
Bob Barstead
Oklahoma Medical Research Foundation
barsteadr@omrf.uokhsc.edu
From owner-acedb@net.bio.net Tue Jun 14 23:00:00 1994
Path: biosci!daresbury!not-for-mail
From: rd@mrc-lmb.cam.ac.uk (Richard Durbin)
Newsgroups: bionet.software.acedb
Subject: Re: Contig assembly?
Date: 15 Jun 1994 23:17:18 +0100
Lines: 34
Sender: daemon@mserv1.dl.ac.uk
Distribution: bionet
Message-ID: <2tnule$ku7@mserv1.dl.ac.uk>
Original-To: acedb@dl.ac.uk
eesnyder@sequana.com asks about contig assembly in ACEDB.
Unfortunately this has a messy history. The physical map display was
based on the program CONTIG9 written by John Sulston for the C.
elegans mapping project. Contig9 had full editing and fingerprint
based assembly functions, but the acedb pmap display was originally
only for display of a current state of the map. We intended to bring
all the editing functions across into acedb, but the person assigned
to do the task turned out to never complete it, and eventually left,
leaving a nearly working mess that nobody else wants to look at. This
is the code reffered to in the help pages, which is not linked into
the release, so you won't find it. Sorry for not removing the
references in the help pages.
Since then we have in fact completed a Unix/X port of the original
contig9 software, but outside ACEDB. In fact this was based on an
automated f2c translation of the VAX fortran, with ACEDB/X graphics
replacing all the terminal based graphics. This program is called
contigc, and is either now or very soon will be available from
Friedemann Wobus (fw@sanger.ac.uk). Since the "look and feel" is
still that of a textronix terminal system there is essentially no use
of the mouse, and it looks old-fashioned, but seems to work exactly as
the VAX code did.
More relevant to ACEDB, Jean Thierry-Mieg and Ulrich Sauvage have been
working on new physical map assembly functions linked into the modern
vertical map display of ACEDB. I gather they have some impressive
results and the interface is more intuitive and potentially much more
powerful. I suggest you contact them (mieg@crbm.cnrs-mop.fr or
ulrich@crbm.cnrs-mop.fr) to find out the current state of their
system, and whether they can support an active mapping project.
Richard Durbin
From owner-acedb@net.bio.net Tue Jun 14 23:00:00 1994
Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews
From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews")
Newsgroups: bionet.software.acedb
Subject: Re: solaris write access
Date: 15 Jun 1994 14:58:18 -0700
Organization: BIOSCI International Newsgroups for Molecular Biology
Lines: 20
Sender: daemon@net.bio.net
Distribution: world
Message-ID: <9406152203.AA00387@greengenes.cit.cornell.edu>
NNTP-Posting-Host: net.bio.net
Since I'm just now installing a copy of my database on a Solaris 2.3 machine, I
took note of all the steps I did that could be relevant:
The owner of the directory and all its files is 'dmatthew'.
I edited wspec/passwd.wrm to list 'dmatthew'.
I said "setenv ACEDB_SU".
I said "setenv ACEDB