From touro at capoeirabrasil.com.au  Tue Jul  3 19:28:45 2001
From: touro at capoeirabrasil.com.au (Bill Shui)
Date: Wed, 4 Jul 2001 09:28:45 +1000
Subject: Question on EMBOSS libraries
Message-ID: <20010704092845.A5508@capoeira.sydney>

I am currently using EMBOSS for my thesis work.

My thesis project is to integrate key functionalities of emboss into
a XML database system, such that these functions could be activated by
invoking a function call in the XML query.


for example.

    this could be equivalent to SQL's function call.


    select multialign(sequence) from TableA where sequence_id = "blerg";


    the multialign function will be a modified emboss function which
    carries out the multiple sequence alignments.


what I do not need to used functions in the ajax/emboss/nucleus libraries
that loads data from acd files, etc. All I need are the core functions that
does the actual computation work.


I have started reading through the emboss source code, but I'm a bit unclear
as to which functions could be regarded as the core functions. (that exclude
all the acd file loading, codon table loading, etc...)


thanks in advance.

regards.
Bill
-- 
<Reed> It is important to note that the primary reason the
       Roman Empire fail is that they had no concept of
       zero... thus they could not test the success or
       failure of their C programs.
---------------------------------------------
Bill Shui           Email:	wshui at mail.usyd.edu.au
				touro at capoeirabrasil.com.au
				bill.shui at proteomesystems.com
Bioinformatics Programmer



From dmartin at bioinformatics.msiwtb.dundee.ac.uk  Wed Jul  4 06:45:17 2001
From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin)
Date: Wed, 4 Jul 2001 11:45:17 +0100 (BST)
Subject: changes to embprop.c, emowse and charge to cope with modified amino
 acids.
Message-ID: <Pine.LNX.4.33.0107041124440.10086-100000@bioinformatics.msiwtb.dundee.ac.uk>


Dear all,

I'm writing this generally so that you can comment (and point out good
reasons why I shouldn't do this) before I go ahead and make these changes.
I am happy to do the work, just give me the nod and I'll send amended
files.

Background:

I have had some discussion with PMR over the last few days about changing
the emowse program to reflect how mass spec is actually done. the major
thrust of what I wanted was to be able to use a different amino acid data
file to reflect different methods used in mass spec.

Problem:

Eamino.dat is hardcoded into the emboss libraries (and into charge.c) as
the source data file for the amino acid data. This is not readily
changeable at run time. Just modifying Eamino.dat and saving in
.embossdata is a kludge that is not universally applicable (ie it is
impossible from a web interface).

Solution:

Have the datafile name passed as an advanced parameter on the command
line.

Changes suggested:

embprop.c

embPropAminoRead(void) should change to embPropAminoRead( AjPFile fp ) and
the code adjusted to cope (delete two lines dealing with file opening).

embPropCalcMolwt

this should return an ajFatal at 'if (! propInit)'. Programs should call
embPropAminoRead with the AjPFile retrieved from the ACD parsing (defaults
to Eamino.dat of course).

See a related note about this method below.


emowse.c

EMOWSE needs to retrieve the file pointer from teh command line and pass
it to embPropAminoRead (AjPFile datafile = ajAcdGetInFile('aadata');
embPropAminoRead(datafile);)



charge.c

Charge has its own reading routines that should be modifed as above.


Further comemnts on molecular weight.
====================================

At the end of embPropCalcMolwt the program adds the molecular weight of
water to the peptide.

Stylistically this is ugly as it is as a float rather than as a defined
constant.

Scientifically it less useful as it eliminates the possibility of terminal
modifications.

I would suggest that this be amended as follows:

embPropCalcMolwt be retained with the same signature but call a new method

embPropCalcmolwtMod(char *s, ajint start, ajint end, double nmass, double
cmass);

using the constants PROPENZN_H and PROPENZC_OH (defined as 1.000 and
17.0153 respectively) so the default remains.

this new method has the content of the original Molwt method but with the
final sum being

return sum + nmass + cmass;

This then lets a program determine the N and C terminal groups.

Various could be defined and allowed as a list in an ACD file, eg
PROPENZN_ACETYL for acetylated N termini

Thoughts and comments?

..d



From peter.rice at uk.lionbioscience.com  Wed Jul  4 06:46:23 2001
From: peter.rice at uk.lionbioscience.com (Peter Rice)
Date: Wed, 04 Jul 2001 11:46:23 +0100
Subject: changes to embprop.c, emowse and charge to cope with modified 
 aminoacids.
References: <Pine.LNX.4.33.0107041124440.10086-100000@bioinformatics.msiwtb.dundee.ac.uk>
Message-ID: <3B42F3FF.41994DE1@uk.lionbioscience.com>

David Martin writes:

>EMOWSE needs to retrieve the file pointer from teh command line and pass
>it to embPropAminoRead (AjPFile datafile = ajAcdGetInFile('aadata');
>embPropAminoRead(datafile);)

I assume you mean ajAcdGetDataFile to read from a standard set of data
files. ajAcdGetInFile is an input file in the user's directory.

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723



From dmartin at bioinformatics.msiwtb.dundee.ac.uk  Wed Jul  4 09:00:43 2001
From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin)
Date: Wed, 4 Jul 2001 14:00:43 +0100 (BST)
Subject: Updated molecular weight determination 
Message-ID: <Pine.LNX.4.33.0107041341270.10086-100000@bioinformatics.msiwtb.dundee.ac.uk>


I haven't modified charge yet but have completed the library changes and
also generated some standard data files for monoisotopic masses (and
pyridylethylated cysteine)

It seems to work fine for me (so far).


modified files:

nucleus/embprop.h
nucleus/embprop.c
emboss/emowse.c
emboss/acd/emowse.acd
doc/programs/text/emowse.txt

How do you want me to send them and who to?

..d

----------------------------------
David Martin PhD
Bioinformatics Scientific Officer
Wellcome Trust Biocentre, Dundee
----------------------------------



From dmartin at bioinformatics.msiwtb.dundee.ac.uk  Wed Jul  4 12:21:20 2001
From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin)
Date: Wed, 4 Jul 2001 17:21:20 +0100 (BST)
Subject: Pyroglutamate formation and molecular weights.
Message-ID: <Pine.LNX.4.33.0107041713110.10086-100000@bioinformatics.msiwtb.dundee.ac.uk>


In certain instances, an N-terminal glutamate can form a ring structure
(pyroglutamate).

It would be nice to check for this by checking fragments (in
embMolGetFrags ) for both the modified and unmodified version. This can be
readily done by adding a function that takes as a parameter a flag value
to tell it to add pyroglutamate fragments to the list alongside the
ordinary fragments.

It would be nice also to add a field to the EmbSMolFrag to take a comment
about any modification, either a simple flag or an integer code for the
modification. This can then be used in the output to inform the user.

I'll change it and send the changed files (embmol.* and emowse.* )

..d


----------------------------------
David Martin PhD
Bioinformatics Scientific Officer
Wellcome Trust Biocentre, Dundee
----------------------------------



From bauer at genprofile.com  Thu Jul  5 08:11:34 2001
From: bauer at genprofile.com (David Bauer)
Date: Thu, 05 Jul 2001 14:11:34 +0200
Subject: showseq filtering displayed features?
Message-ID: <3B445976.58628E30@genprofile.com>

Hi,

I asked some time ago that I would like to have the filtering options
(matchsource, matchtype and matchtag) which are in showfeat also
available in showseq.
I got the response that it is a good idea, but I can't see it
implemented up to now (1.13.3). Is this still somewhere on your ToDo
lists ?

Many thanks,
David.
-- 
Dr. David Bauer
GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus 
Robert-Roessle-Str. 10, D-13125 Berlin, Germany
bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151



From touro at capoeirabrasil.com.au  Thu Jul  5 20:12:04 2001
From: touro at capoeirabrasil.com.au (Bill Shui)
Date: Fri, 6 Jul 2001 10:12:04 +1000
Subject: Question on EMBOSS libraries (fwd)
In-Reply-To: <Pine.LNX.4.21.0107051644590.896-100000@plum.lsc.pku.edu.cn>
References: <Pine.LNX.4.21.0107051644590.896-100000@plum.lsc.pku.edu.cn>
Message-ID: <20010706101204.A3357@capoeira.sydney>

Hi Alan,
    Bill here, I thought I should clarify my question.

    Basically, I didn't want to use emboss to write XML reports, it should
    be handled by the database system.

    I'm writing a bioinformatics plugin to a semi-structured database system.

    The the query would not be like SQL, but of the same essence.

    I had a look at the code, but I thought it really depends on lot of acd
    files, so everytime you want to run a program, you'll have to initialise
    pretty much all of the acd settings and loading matrices, etc.


    what I want to do is that all these settings, ie. matrices and codon
    tables will be loaded into the database management system's main kernel
    at the system start up.

    such that when a user later issue a command to run a certain program,
    it need not to reinitialize all the settings. Since I"m really breaking
    up all the emboss code to suit my need, I really need to know which
    routines in the ajax library are essential for the core computation, eg.
    routines that do the actual sequence alignments.


hope this clarified my previous question.

thanks in advance.

Bill

    

On Thu, Jul 05, 2001 at 04:46:11PM +0800, Jingchu Luo wrote:
> This is the feedback I got from Alan Bleasby, the EMBOSS head.
> 
> ---------- Forwarded message ----------
> Date: Thu, 5 Jul 2001 08:41:22 +0100 (BST)
> From: ableasby at hgmp.mrc.ac.uk
> To: luojc at plum.lsc.pku.edu.cn
> Subject: Re: Question on EMBOSS libraries (fwd)
> 
> Indeed. The question is so vague though I don't know precisely
> what he wants. If you read the minutes of the last EMBOSS
> meeting (:-) last Friday then you'll see I volunteered
> to have emboss write XML reports as an option.
> 
> Cheers old chum
> 
> Alan
> 

-- 
<Reed> It is important to note that the primary reason the
       Roman Empire fail is that they had no concept of
       zero... thus they could not test the success or
       failure of their C programs.
---------------------------------------------
Bill Shui           Email:	wshui at mail.usyd.edu.au
				touro at capoeirabrasil.com.au
				bill.shui at proteomesystems.com
Bioinformatics Programmer



From gbottu at ben.vub.ac.be  Tue Jul 10 06:33:01 2001
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Tue, 10 Jul 2001 12:33:01 +0200 (MET DST)
Subject: question about sequence weights
Message-ID: <200107101033.MAA11472@bigben.vub.ac.be>

from : BEN

	Dear colleagues,
	
I have a question. The programs pretty (GCG), prettybox (GCG+egcg) and 
prettyplot (egc) all allowed to use as input a List File with a "weight"
attribute. I think that EMBOSS prettyplot does not or does it ?

	Guy Bottu




From peter.rice at uk.lionbioscience.com  Tue Jul 10 06:33:24 2001
From: peter.rice at uk.lionbioscience.com (Peter Rice)
Date: Tue, 10 Jul 2001 11:33:24 +0100
Subject: question about sequence weights
References: <200107101033.MAA11472@bigben.vub.ac.be>
Message-ID: <3B4AD9F4.41F26BA3@uk.lionbioscience.com>

Dear Guy,

> I have a question. The programs pretty (GCG), prettybox (GCG+egcg) and
> prettyplot (egc) all allowed to use as input a List File with a "weight"
> attribute. I think that EMBOSS prettyplot does not or does it ?

Was this ever used outside of SeqLab?

EMBOSS does have weights internally. It should be relatively simple to add
them to list files somehow, and even to store them in other sequence
formats (apart from MSF).

At present, you need MSF input to get the weights into EMBOSS. That is the
only sequence format that explicitly has them (so you can use seqret to
convert your list to an MSF file, and edit the weights there)

regards,

Peter

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723



From bauer at genprofile.com  Thu Jul 12 03:50:01 2001
From: bauer at genprofile.com (David Bauer)
Date: Thu, 12 Jul 2001 09:50:01 +0200
Subject: abiview
Message-ID: <3B4D56A9.FA1F66E@genprofile.com>

Hi,

we are doing some tests with the MJGeneSys BaseStation.
This machine creates output files in SCF 3.00 format. The good old ted
does not understand these tracefiles.
Are there any plans to extend abiview so it can read and display not
only ABI traces but also SCF which would be usefull also for Licor users
?

Thanks !
David.
-- 
Dr. David Bauer
GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus 
Robert-Roessle-Str. 10, D-13125 Berlin, Germany
bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151



From jkb at mrc-lmb.cam.ac.uk  Thu Jul 12 04:31:51 2001
From: jkb at mrc-lmb.cam.ac.uk (James Bonfield)
Date: Thu, 12 Jul 2001 09:31:51 +0100
Subject: abiview
In-Reply-To: <3B4D56A9.FA1F66E@genprofile.com>; from bauer@genprofile.com on Thu, Jul 12, 2001 at 09:50:01AM +0200
References: <3B4D56A9.FA1F66E@genprofile.com>
Message-ID: <20010712093151.A27762@arran.mrc-lmb.cam.ac.uk>

On Thu, Jul 12, 2001 at 09:50:01AM +0200, David Bauer wrote:
> we are doing some tests with the MJGeneSys BaseStation.
> This machine creates output files in SCF 3.00 format. The good old ted
> does not understand these tracefiles.

Ted is _OLD_. I'm suprised anyone still uses it.

The "gap4 viewer" (free to everyone, including commercial users) is
distributed on our ftp site (ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/) and also
contains Trev, a modern replacement for ted. We plan to separate this out
sometime soon so that you don't need to obtain lots of other stuff just to get 
trev - we'll just stick Trev up as a separate download.

The main file reading code from Trev (and previously Ted) is called
io_lib. The source is freely available (under something approximately a BSD
licence) on the LMB ftp site too. This supports ABI, ALF, SCF (v2 and v3) as
well as the newer highly compressed formats CTF and ZTR. We have no issues
with the Emboss team making use of this code in abiview. Io_lib, although
mainly a library, also contains some example programs which includes one to
convert between formats and to convert between SCF versions. (It 
doesn't allow writing to ABI or ALF formats; as both are proprietory we do not 
wish to create code to further their use.)

James

-- 
James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/



From friends at openxxx.net  Sat Jul 14 21:17:32 2001
From: friends at openxxx.net (friends at openxxx.net)
Date: Sun, 15 Jul 2001 02:17:32 +0100 (BST)
Subject: Hello, your friend recommended openxxx to you
Message-ID: <20010715011732.5B62417B22@mercury.hgmp.mrc.ac.uk>



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From peter.rice at uk.lionbioscience.com  Mon Jul 16 05:34:58 2001
From: peter.rice at uk.lionbioscience.com (Peter Rice)
Date: Mon, 16 Jul 2001 10:34:58 +0100
Subject: New features in ACD files for 2.0.0
Message-ID: <3B52B542.A37BAB72@uk.lionbioscience.com>

New features in ACD files for 2.0.0

1. New ACD type
   ============

1.1 Report
    ------

Feature report, intended to replace the output file for applications
that write results which can be interpreted as 'features' (start and
end positions and score, with some possible annotation). These
applications will change to store their results internally as feature
tables, and will write reports using a default format (similar to
their present output), but can be given a command line option to write
the output in any other standard feature report format.

The initial report format is GFF, or any other feature format.

Attributes will be extended - for example to specify protein or DNA
features as this now affects the valid feature formats.

Further report types will be added to produce alignment output
(-aformat and so on for the qualifiers).


Attributes:

name           report file name
extension      file name extension

Qualifiers:

-rformat       report format
-ropenfile     report file name
-rextension    file name extension
-rname         base file name



2. GUI extensions
   ==============

As proposed on the emboss-dev mailing list by James Bonfield, we now
have groups of ACD options. The basic grouping uses a 'section' and
'endsection' pair, with names to ensure correct usage. THese sections
can be nested.

Section names are intended to use a limited vocabulary so that they
can be converted to standard names in GUI interfaces. SRS, for
example, groups options in this way (see the blast launch options on
the EBI's SRS server).


2.1 Section
    -------

specified as:

section: name [ attribute: value ]

Attributes:

info     text that EMBOSS could (in future) use as a prompt
         before the first option in the section
comment  general comment, in case of need
type     type name ("frame" or "page", or undefined)

side     side specification (top, bottom, left, right) (for type: frame)
border   width of border (for type: frame only)

folder   folder name (for type: page only)


Types:

In James Bonfield's original specification, there are two special
types of section which display differently in his interface. "frame"
was intended to be the default, although this is not strictly
implemented in ajacd.c yet.

James' original descriptions (from the emboss-dev mailings, with the
attribute names updated):

=========================================================================

type       A choice between "frame" and "page".
           Defaults to frame.
           This controls whether the section should be a labelled frame or
           a page in a notebook. The distinction only really matters for
           GUI or WWW based systems. In Tcl the choice is pretty clear. In
           WWW I'd expect a frame to be a table; a page is trickier to
           implement (and may require javascript), but I've seen such
things
           done regularly.

info       A heading for the frame or page. Defaults to ""
           A page without a heading would look rather odd, but a frame
           without a heading is OK - it's just a bordered block.

folder     Only needed for type:frame.
           The notebook to associate this page to. Defaults to "", which
           implies all pages are part of the same notebook. This is only
           needed if a program wishes to make use of more than one tabbed
           notebook, in which case this is used to determine which book a
           page is within.
           *Note* James originally called this 'book'

border     Only needed for type:frame. Defaults to 1.
           The border width of the frame.

side       Only needed for type:frame. Defaults to top.
           This is used for 'frame packing'. It is only needed if we wish
           to express complex layout designs. Eg:

           +----------------------------------+
           |            Section1              |
           |   blah                           |
           |   blah                           |
           | +-------------+ +--------------+ +
           | | Section2    | | Section3     | |
           | |   blah      | |   blah       | |
           | +-------------+ +--------------+ |
           +----------------------------------+

I think perhaps the border and side attributes are overkill, and I haven't
yet 
used them except in test ACD files. Naturally all of these are really just
"hints" to the interface, which may ultimately do whatever it prefers.

=========================================================================

Note that SRS can handle these attributes reasonably well, so they
could be widely useful even if James does not eventually use them.


2.2 Other GUI hints in EMBOSS
    -------------------------

(These were already in 1.0.0)

integers and floats (and arrays) have 'increment' to specify an
increment for GUIs which go beyond typing in a number.

lists and selects have 'button' and 'maximum' to specify whether to
use a pull down menu or selectin list, or a set of radio buttons or
checkboxes. 'Maximum' is so far always 1, but there is no reason why
multiple selections would not be used in future.

2.3 Command line interface
    ----------------------

The new 'section/endsection' groups can be implemented in the command
line interface, for example by starting a new line and issuing the
'info' prompt before prompting for a value in a section. An obvious
example would be gap penalties for an alignment program.

We can expect to change the order of options in many applications to
fit them into sections. This will change the order in which programs
prompt the user, and will help us to standardise on where to place
prompts for output file and graph type.

3. Other GUIs
   ==========

GUI authors are very welcome to help in this task. Has anyone tried
rearranging the ACD options for other interfaces?

It would be useful to have a status report from each of the EMBOSS GUIs.
The current list of known EMBOSS GUIs and otehr interfaces is at:

http://www.uk.embnet.org/Software/EMBOSS/Doc/interfaces.html

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723



From touro at capoeirabrasil.com.au  Thu Jul 19 21:01:57 2001
From: touro at capoeirabrasil.com.au (Bill Shui)
Date: Fri, 20 Jul 2001 11:01:57 +1000
Subject: No subject
Message-ID: <20010720110156.A28801@capoeira.sydney>

What kind of report writing features have been implemented in EMBOSS 2.0?

thanks in advance.

Bill
-- 
The mark of a good party is that you wake up the next morning
wanting to change your name and start a new life in different
city.
                -- Vance Bourjaily, "Esquire"
---------------------------------------------
Bill Shui           Email: wshui at bigpond.net.au
			   wshui at cse.unsw.edu.au
			   touro at capoeirabrasil.com.au
			   bill.shui at proteomesystems.com
Bioinformatics Programmer




From touro at capoeirabrasil.com.au  Tue Jul  3 23:28:45 2001
From: touro at capoeirabrasil.com.au (Bill Shui)
Date: Wed, 4 Jul 2001 09:28:45 +1000
Subject: Question on EMBOSS libraries
Message-ID: <20010704092845.A5508@capoeira.sydney>

I am currently using EMBOSS for my thesis work.

My thesis project is to integrate key functionalities of emboss into
a XML database system, such that these functions could be activated by
invoking a function call in the XML query.


for example.

    this could be equivalent to SQL's function call.


    select multialign(sequence) from TableA where sequence_id = "blerg";


    the multialign function will be a modified emboss function which
    carries out the multiple sequence alignments.


what I do not need to used functions in the ajax/emboss/nucleus libraries
that loads data from acd files, etc. All I need are the core functions that
does the actual computation work.


I have started reading through the emboss source code, but I'm a bit unclear
as to which functions could be regarded as the core functions. (that exclude
all the acd file loading, codon table loading, etc...)


thanks in advance.

regards.
Bill
-- 
<Reed> It is important to note that the primary reason the
       Roman Empire fail is that they had no concept of
       zero... thus they could not test the success or
       failure of their C programs.
---------------------------------------------
Bill Shui           Email:	wshui at mail.usyd.edu.au
				touro at capoeirabrasil.com.au
				bill.shui at proteomesystems.com
Bioinformatics Programmer



From dmartin at bioinformatics.msiwtb.dundee.ac.uk  Wed Jul  4 10:45:17 2001
From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin)
Date: Wed, 4 Jul 2001 11:45:17 +0100 (BST)
Subject: changes to embprop.c, emowse and charge to cope with modified amino
 acids.
Message-ID: <Pine.LNX.4.33.0107041124440.10086-100000@bioinformatics.msiwtb.dundee.ac.uk>


Dear all,

I'm writing this generally so that you can comment (and point out good
reasons why I shouldn't do this) before I go ahead and make these changes.
I am happy to do the work, just give me the nod and I'll send amended
files.

Background:

I have had some discussion with PMR over the last few days about changing
the emowse program to reflect how mass spec is actually done. the major
thrust of what I wanted was to be able to use a different amino acid data
file to reflect different methods used in mass spec.

Problem:

Eamino.dat is hardcoded into the emboss libraries (and into charge.c) as
the source data file for the amino acid data. This is not readily
changeable at run time. Just modifying Eamino.dat and saving in
.embossdata is a kludge that is not universally applicable (ie it is
impossible from a web interface).

Solution:

Have the datafile name passed as an advanced parameter on the command
line.

Changes suggested:

embprop.c

embPropAminoRead(void) should change to embPropAminoRead( AjPFile fp ) and
the code adjusted to cope (delete two lines dealing with file opening).

embPropCalcMolwt

this should return an ajFatal at 'if (! propInit)'. Programs should call
embPropAminoRead with the AjPFile retrieved from the ACD parsing (defaults
to Eamino.dat of course).

See a related note about this method below.


emowse.c

EMOWSE needs to retrieve the file pointer from teh command line and pass
it to embPropAminoRead (AjPFile datafile = ajAcdGetInFile('aadata');
embPropAminoRead(datafile);)



charge.c

Charge has its own reading routines that should be modifed as above.


Further comemnts on molecular weight.
====================================

At the end of embPropCalcMolwt the program adds the molecular weight of
water to the peptide.

Stylistically this is ugly as it is as a float rather than as a defined
constant.

Scientifically it less useful as it eliminates the possibility of terminal
modifications.

I would suggest that this be amended as follows:

embPropCalcMolwt be retained with the same signature but call a new method

embPropCalcmolwtMod(char *s, ajint start, ajint end, double nmass, double
cmass);

using the constants PROPENZN_H and PROPENZC_OH (defined as 1.000 and
17.0153 respectively) so the default remains.

this new method has the content of the original Molwt method but with the
final sum being

return sum + nmass + cmass;

This then lets a program determine the N and C terminal groups.

Various could be defined and allowed as a list in an ACD file, eg
PROPENZN_ACETYL for acetylated N termini

Thoughts and comments?

..d



From peter.rice at uk.lionbioscience.com  Wed Jul  4 10:46:23 2001
From: peter.rice at uk.lionbioscience.com (Peter Rice)
Date: Wed, 04 Jul 2001 11:46:23 +0100
Subject: changes to embprop.c, emowse and charge to cope with modified 
 aminoacids.
References: <Pine.LNX.4.33.0107041124440.10086-100000@bioinformatics.msiwtb.dundee.ac.uk>
Message-ID: <3B42F3FF.41994DE1@uk.lionbioscience.com>

David Martin writes:

>EMOWSE needs to retrieve the file pointer from teh command line and pass
>it to embPropAminoRead (AjPFile datafile = ajAcdGetInFile('aadata');
>embPropAminoRead(datafile);)

I assume you mean ajAcdGetDataFile to read from a standard set of data
files. ajAcdGetInFile is an input file in the user's directory.

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723



From dmartin at bioinformatics.msiwtb.dundee.ac.uk  Wed Jul  4 13:00:43 2001
From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin)
Date: Wed, 4 Jul 2001 14:00:43 +0100 (BST)
Subject: Updated molecular weight determination 
Message-ID: <Pine.LNX.4.33.0107041341270.10086-100000@bioinformatics.msiwtb.dundee.ac.uk>


I haven't modified charge yet but have completed the library changes and
also generated some standard data files for monoisotopic masses (and
pyridylethylated cysteine)

It seems to work fine for me (so far).


modified files:

nucleus/embprop.h
nucleus/embprop.c
emboss/emowse.c
emboss/acd/emowse.acd
doc/programs/text/emowse.txt

How do you want me to send them and who to?

..d

----------------------------------
David Martin PhD
Bioinformatics Scientific Officer
Wellcome Trust Biocentre, Dundee
----------------------------------



From dmartin at bioinformatics.msiwtb.dundee.ac.uk  Wed Jul  4 16:21:20 2001
From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin)
Date: Wed, 4 Jul 2001 17:21:20 +0100 (BST)
Subject: Pyroglutamate formation and molecular weights.
Message-ID: <Pine.LNX.4.33.0107041713110.10086-100000@bioinformatics.msiwtb.dundee.ac.uk>


In certain instances, an N-terminal glutamate can form a ring structure
(pyroglutamate).

It would be nice to check for this by checking fragments (in
embMolGetFrags ) for both the modified and unmodified version. This can be
readily done by adding a function that takes as a parameter a flag value
to tell it to add pyroglutamate fragments to the list alongside the
ordinary fragments.

It would be nice also to add a field to the EmbSMolFrag to take a comment
about any modification, either a simple flag or an integer code for the
modification. This can then be used in the output to inform the user.

I'll change it and send the changed files (embmol.* and emowse.* )

..d


----------------------------------
David Martin PhD
Bioinformatics Scientific Officer
Wellcome Trust Biocentre, Dundee
----------------------------------



From bauer at genprofile.com  Thu Jul  5 12:11:34 2001
From: bauer at genprofile.com (David Bauer)
Date: Thu, 05 Jul 2001 14:11:34 +0200
Subject: showseq filtering displayed features?
Message-ID: <3B445976.58628E30@genprofile.com>

Hi,

I asked some time ago that I would like to have the filtering options
(matchsource, matchtype and matchtag) which are in showfeat also
available in showseq.
I got the response that it is a good idea, but I can't see it
implemented up to now (1.13.3). Is this still somewhere on your ToDo
lists ?

Many thanks,
David.
-- 
Dr. David Bauer
GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus 
Robert-Roessle-Str. 10, D-13125 Berlin, Germany
bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151



From touro at capoeirabrasil.com.au  Fri Jul  6 00:12:04 2001
From: touro at capoeirabrasil.com.au (Bill Shui)
Date: Fri, 6 Jul 2001 10:12:04 +1000
Subject: Question on EMBOSS libraries (fwd)
In-Reply-To: <Pine.LNX.4.21.0107051644590.896-100000@plum.lsc.pku.edu.cn>
References: <Pine.LNX.4.21.0107051644590.896-100000@plum.lsc.pku.edu.cn>
Message-ID: <20010706101204.A3357@capoeira.sydney>

Hi Alan,
    Bill here, I thought I should clarify my question.

    Basically, I didn't want to use emboss to write XML reports, it should
    be handled by the database system.

    I'm writing a bioinformatics plugin to a semi-structured database system.

    The the query would not be like SQL, but of the same essence.

    I had a look at the code, but I thought it really depends on lot of acd
    files, so everytime you want to run a program, you'll have to initialise
    pretty much all of the acd settings and loading matrices, etc.


    what I want to do is that all these settings, ie. matrices and codon
    tables will be loaded into the database management system's main kernel
    at the system start up.

    such that when a user later issue a command to run a certain program,
    it need not to reinitialize all the settings. Since I"m really breaking
    up all the emboss code to suit my need, I really need to know which
    routines in the ajax library are essential for the core computation, eg.
    routines that do the actual sequence alignments.


hope this clarified my previous question.

thanks in advance.

Bill

    

On Thu, Jul 05, 2001 at 04:46:11PM +0800, Jingchu Luo wrote:
> This is the feedback I got from Alan Bleasby, the EMBOSS head.
> 
> ---------- Forwarded message ----------
> Date: Thu, 5 Jul 2001 08:41:22 +0100 (BST)
> From: ableasby at hgmp.mrc.ac.uk
> To: luojc at plum.lsc.pku.edu.cn
> Subject: Re: Question on EMBOSS libraries (fwd)
> 
> Indeed. The question is so vague though I don't know precisely
> what he wants. If you read the minutes of the last EMBOSS
> meeting (:-) last Friday then you'll see I volunteered
> to have emboss write XML reports as an option.
> 
> Cheers old chum
> 
> Alan
> 

-- 
<Reed> It is important to note that the primary reason the
       Roman Empire fail is that they had no concept of
       zero... thus they could not test the success or
       failure of their C programs.
---------------------------------------------
Bill Shui           Email:	wshui at mail.usyd.edu.au
				touro at capoeirabrasil.com.au
				bill.shui at proteomesystems.com
Bioinformatics Programmer



From gbottu at ben.vub.ac.be  Tue Jul 10 10:33:01 2001
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Tue, 10 Jul 2001 12:33:01 +0200 (MET DST)
Subject: question about sequence weights
Message-ID: <200107101033.MAA11472@bigben.vub.ac.be>

from : BEN

	Dear colleagues,
	
I have a question. The programs pretty (GCG), prettybox (GCG+egcg) and 
prettyplot (egc) all allowed to use as input a List File with a "weight"
attribute. I think that EMBOSS prettyplot does not or does it ?

	Guy Bottu




From peter.rice at uk.lionbioscience.com  Tue Jul 10 10:33:24 2001
From: peter.rice at uk.lionbioscience.com (Peter Rice)
Date: Tue, 10 Jul 2001 11:33:24 +0100
Subject: question about sequence weights
References: <200107101033.MAA11472@bigben.vub.ac.be>
Message-ID: <3B4AD9F4.41F26BA3@uk.lionbioscience.com>

Dear Guy,

> I have a question. The programs pretty (GCG), prettybox (GCG+egcg) and
> prettyplot (egc) all allowed to use as input a List File with a "weight"
> attribute. I think that EMBOSS prettyplot does not or does it ?

Was this ever used outside of SeqLab?

EMBOSS does have weights internally. It should be relatively simple to add
them to list files somehow, and even to store them in other sequence
formats (apart from MSF).

At present, you need MSF input to get the weights into EMBOSS. That is the
only sequence format that explicitly has them (so you can use seqret to
convert your list to an MSF file, and edit the weights there)

regards,

Peter

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723



From bauer at genprofile.com  Thu Jul 12 07:50:01 2001
From: bauer at genprofile.com (David Bauer)
Date: Thu, 12 Jul 2001 09:50:01 +0200
Subject: abiview
Message-ID: <3B4D56A9.FA1F66E@genprofile.com>

Hi,

we are doing some tests with the MJGeneSys BaseStation.
This machine creates output files in SCF 3.00 format. The good old ted
does not understand these tracefiles.
Are there any plans to extend abiview so it can read and display not
only ABI traces but also SCF which would be usefull also for Licor users
?

Thanks !
David.
-- 
Dr. David Bauer
GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus 
Robert-Roessle-Str. 10, D-13125 Berlin, Germany
bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151



From jkb at mrc-lmb.cam.ac.uk  Thu Jul 12 08:31:51 2001
From: jkb at mrc-lmb.cam.ac.uk (James Bonfield)
Date: Thu, 12 Jul 2001 09:31:51 +0100
Subject: abiview
In-Reply-To: <3B4D56A9.FA1F66E@genprofile.com>; from bauer@genprofile.com on Thu, Jul 12, 2001 at 09:50:01AM +0200
References: <3B4D56A9.FA1F66E@genprofile.com>
Message-ID: <20010712093151.A27762@arran.mrc-lmb.cam.ac.uk>

On Thu, Jul 12, 2001 at 09:50:01AM +0200, David Bauer wrote:
> we are doing some tests with the MJGeneSys BaseStation.
> This machine creates output files in SCF 3.00 format. The good old ted
> does not understand these tracefiles.

Ted is _OLD_. I'm suprised anyone still uses it.

The "gap4 viewer" (free to everyone, including commercial users) is
distributed on our ftp site (ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/) and also
contains Trev, a modern replacement for ted. We plan to separate this out
sometime soon so that you don't need to obtain lots of other stuff just to get 
trev - we'll just stick Trev up as a separate download.

The main file reading code from Trev (and previously Ted) is called
io_lib. The source is freely available (under something approximately a BSD
licence) on the LMB ftp site too. This supports ABI, ALF, SCF (v2 and v3) as
well as the newer highly compressed formats CTF and ZTR. We have no issues
with the Emboss team making use of this code in abiview. Io_lib, although
mainly a library, also contains some example programs which includes one to
convert between formats and to convert between SCF versions. (It 
doesn't allow writing to ABI or ALF formats; as both are proprietory we do not 
wish to create code to further their use.)

James

-- 
James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/



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From: friends at openxxx.net (friends at openxxx.net)
Date: Sun, 15 Jul 2001 02:17:32 +0100 (BST)
Subject: Hello, your friend recommended openxxx to you
Message-ID: <20010715011732.5B62417B22@mercury.hgmp.mrc.ac.uk>



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From peter.rice at uk.lionbioscience.com  Mon Jul 16 09:34:58 2001
From: peter.rice at uk.lionbioscience.com (Peter Rice)
Date: Mon, 16 Jul 2001 10:34:58 +0100
Subject: New features in ACD files for 2.0.0
Message-ID: <3B52B542.A37BAB72@uk.lionbioscience.com>

New features in ACD files for 2.0.0

1. New ACD type
   ============

1.1 Report
    ------

Feature report, intended to replace the output file for applications
that write results which can be interpreted as 'features' (start and
end positions and score, with some possible annotation). These
applications will change to store their results internally as feature
tables, and will write reports using a default format (similar to
their present output), but can be given a command line option to write
the output in any other standard feature report format.

The initial report format is GFF, or any other feature format.

Attributes will be extended - for example to specify protein or DNA
features as this now affects the valid feature formats.

Further report types will be added to produce alignment output
(-aformat and so on for the qualifiers).


Attributes:

name           report file name
extension      file name extension

Qualifiers:

-rformat       report format
-ropenfile     report file name
-rextension    file name extension
-rname         base file name



2. GUI extensions
   ==============

As proposed on the emboss-dev mailing list by James Bonfield, we now
have groups of ACD options. The basic grouping uses a 'section' and
'endsection' pair, with names to ensure correct usage. THese sections
can be nested.

Section names are intended to use a limited vocabulary so that they
can be converted to standard names in GUI interfaces. SRS, for
example, groups options in this way (see the blast launch options on
the EBI's SRS server).


2.1 Section
    -------

specified as:

section: name [ attribute: value ]

Attributes:

info     text that EMBOSS could (in future) use as a prompt
         before the first option in the section
comment  general comment, in case of need
type     type name ("frame" or "page", or undefined)

side     side specification (top, bottom, left, right) (for type: frame)
border   width of border (for type: frame only)

folder   folder name (for type: page only)


Types:

In James Bonfield's original specification, there are two special
types of section which display differently in his interface. "frame"
was intended to be the default, although this is not strictly
implemented in ajacd.c yet.

James' original descriptions (from the emboss-dev mailings, with the
attribute names updated):

=========================================================================

type       A choice between "frame" and "page".
           Defaults to frame.
           This controls whether the section should be a labelled frame or
           a page in a notebook. The distinction only really matters for
           GUI or WWW based systems. In Tcl the choice is pretty clear. In
           WWW I'd expect a frame to be a table; a page is trickier to
           implement (and may require javascript), but I've seen such
things
           done regularly.

info       A heading for the frame or page. Defaults to ""
           A page without a heading would look rather odd, but a frame
           without a heading is OK - it's just a bordered block.

folder     Only needed for type:frame.
           The notebook to associate this page to. Defaults to "", which
           implies all pages are part of the same notebook. This is only
           needed if a program wishes to make use of more than one tabbed
           notebook, in which case this is used to determine which book a
           page is within.
           *Note* James originally called this 'book'

border     Only needed for type:frame. Defaults to 1.
           The border width of the frame.

side       Only needed for type:frame. Defaults to top.
           This is used for 'frame packing'. It is only needed if we wish
           to express complex layout designs. Eg:

           +----------------------------------+
           |            Section1              |
           |   blah                           |
           |   blah                           |
           | +-------------+ +--------------+ +
           | | Section2    | | Section3     | |
           | |   blah      | |   blah       | |
           | +-------------+ +--------------+ |
           +----------------------------------+

I think perhaps the border and side attributes are overkill, and I haven't
yet 
used them except in test ACD files. Naturally all of these are really just
"hints" to the interface, which may ultimately do whatever it prefers.

=========================================================================

Note that SRS can handle these attributes reasonably well, so they
could be widely useful even if James does not eventually use them.


2.2 Other GUI hints in EMBOSS
    -------------------------

(These were already in 1.0.0)

integers and floats (and arrays) have 'increment' to specify an
increment for GUIs which go beyond typing in a number.

lists and selects have 'button' and 'maximum' to specify whether to
use a pull down menu or selectin list, or a set of radio buttons or
checkboxes. 'Maximum' is so far always 1, but there is no reason why
multiple selections would not be used in future.

2.3 Command line interface
    ----------------------

The new 'section/endsection' groups can be implemented in the command
line interface, for example by starting a new line and issuing the
'info' prompt before prompting for a value in a section. An obvious
example would be gap penalties for an alignment program.

We can expect to change the order of options in many applications to
fit them into sections. This will change the order in which programs
prompt the user, and will help us to standardise on where to place
prompts for output file and graph type.

3. Other GUIs
   ==========

GUI authors are very welcome to help in this task. Has anyone tried
rearranging the ACD options for other interfaces?

It would be useful to have a status report from each of the EMBOSS GUIs.
The current list of known EMBOSS GUIs and otehr interfaces is at:

http://www.uk.embnet.org/Software/EMBOSS/Doc/interfaces.html

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723



From touro at capoeirabrasil.com.au  Fri Jul 20 01:01:57 2001
From: touro at capoeirabrasil.com.au (Bill Shui)
Date: Fri, 20 Jul 2001 11:01:57 +1000
Subject: No subject
Message-ID: <20010720110156.A28801@capoeira.sydney>

What kind of report writing features have been implemented in EMBOSS 2.0?

thanks in advance.

Bill
-- 
The mark of a good party is that you wake up the next morning
wanting to change your name and start a new life in different
city.
                -- Vance Bourjaily, "Esquire"
---------------------------------------------
Bill Shui           Email: wshui at bigpond.net.au
			   wshui at cse.unsw.edu.au
			   touro at capoeirabrasil.com.au
			   bill.shui at proteomesystems.com
Bioinformatics Programmer