2005-09-02  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.8.7

	* polchem-defs/protein: added sulphation and oxidation modifications

2005-09-01  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Makefile.am: Put back the sgml source file for the man
	page. This is to comply with the Debian Free Software Guidelines.

	* polchem-defs/protein/Makefile.am (MONICONS): added
	oxidation.{png,svg} and oxidation-text.svg to the distribution

2005-08-31  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Removed the full URL to the source package on the web site from
	the debian/copyright file.

2005-07-18  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.8.6
	
	* Makefile.am: removed the polyxmass.7 target as the
	docbook-to-man utility is not present in other distributions. The
	man page gets distributed as is and is not recomputed at each make.

2005-03-21  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.8.5 which is concomitant with the first release of
	Debian packages.

	* autogen.sh : changed the file so that all the autotools-related
	files are updated neatly.

2005-03-08  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* autogen.sh (CFLAGS): added -O2 for the optimization.  Added
	--add-missing --force-missing for the automake call, so that the
	last system-wide files are always used.

2005-02-06  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.8.4

	* configure.in: Removed the dependency on pkg-config, as
	polyxmass-common is no more relying on this feature...

	* Makefile.am (EXTRA_DIST): Removed the installation instructions
	for the polymxmass-common.pc file.

2005-02-02  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* pol-seqs/protein-fragments-sample.pxm: same as below, and same
	for all the sequences available today on my system.
	
	* pol-seqs/protein-sample.pxm: changed DTD to include an attribute
	to the <polseqdata> element to hold the version of the polymer
	sequence file format. Something like <polseqdata version="0.1">.

	* polchem-defs/protein/peptide.xml: same as below, as the DTD is
	the same.

	* polchem-defs/protein/protein.xml: changed DTD to include an
	attribute to the <polchemdefdata> element to hold the version of
	the polymer chemistry definition file format. Sometthing like
	<polchemdefdata version="0.1">.


	NOTE HERE THAT THE 0.8.3 RELEASE WAS MADE WITHOUT LOGGING IT.

2004-12-07  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* pol-seqs/protein-sample.pxm: changed the "LE_Acetylation" to
	"Acetylation".

	* polchem-defs/protein/protein.xml: removed the "LE_Acetylation"
	that is not actually useful with the new algorithm used to perform
	electrical charge/pI calculations.

	* polchem-defs/protein/acidobasic.xml: added this file for
	handling the computing of electrical charge / isoelectric point in
	polymer sequences.

2004-11-06  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polchem-defs/protein/protein.xml: Added a "LE_Acetylation"
	chemical modification that's going to be useful to make the
	difference between the acetylated alphaNH2 of a N-terminal Lysine,
	and the epsilonNH2 of a N-terminal Lysine. This is going to be
	very useful in the calculations of pI/net charge and so on.

2004-10-23  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.8.2

	* configure.in: removed the hard-coded "${sysconfdir}=/etc" so
	that Fink scripts can be created easily. Thanks to Mark Fink for
	pointing the problem to me.
	
	* config-files/Makefile.am: removed the ${sbindir}/script calls
	since the catalogue/dictionary parsing process has changed in the
	polyxmass-bin package.

	* whole_package: the config-files directory now contains files of
	which the names should follow the following syntax: 
	- the catalog files for polymer chemistry definitions should have
	a name ending in polchem-defs-cat.
	- the catalog files for atom definitions should have a name ending
	in atom-defs-cat.
	- the dictionary files making the link between a polymer chemistry
	definition name and the atom definition name to be used should
	have a name ending in polchem-defs-atom-defs-dic.

	These changes are to bring polyxmass-data in conformity with the
	new way the polyxmass binary program parses the catalogue and
	dictionary files.

2004-10-07  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.8.1 with the following changes: - the
	  monomer-modif.dic file is now renamed monicons.dic, and its
	  syntax is changed to simplify it.  - the sounds directory is
	  added to the polymer chemistry definition data directory and
	  sound files are added to it along with a dictionary "sounds.dic"
	  file.

2004-08-25  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.8.0 with a number of changes in the polymer chemistry
	definitions.

	* configure.in (CONFDIR): will be /etc/polyxmass if no
	--sysconfdir has been passed to the configure script.
	
2004-07-24  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.7.1
	
	* changed name of package from polyxmassdata to polyxmass-data,
	since now userman is no more in this package; it will be in
	polyxmass-doc.

2004-07-23  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Makefile.am (EXTRA_DIST): removed polyxmass-data.spec.

	* configure.in: changed PACKAGE name from polyxmassdata to
	polyxmass-data. This is so that the source stuff is almost
	colinear with the Debian package naming conventions. All file
	names were changed according to the same token.

2004-02-13  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* userman: transformed the pdf files in userman/figures/vector
	into png files, so that no font availability problems would be
	encountered when reading the polyxmass.pdf file.

2004-02-12  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* configure.in: modified the CONFDIR main configuration variable
	to now hold the "${packageprefix}/share/polyxmass.d" string. That
	will be the new location of the whole GNU polyxmass configuration
	files. This change was elicited by the making of Debian packages.

2004-01-26  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Makefile.am (polyxmassdata_mandir): corrected wrong location of
	the installed man page from $(prefix)/man/man1 to
	$(prefix)/share/man/man1.

2004-01-25  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* added a new man page to the package. Note that this man page is
	now fully part of GNU polyxmassdata, and not of the Debian
	GNU/Linux package. It is being prepared in an sgml form and then
	converted to man with the command 'docbook-to-man
	polyxmassdata.sgml > polyxmassdata.man' in the file autogen.sh.

	* The user manual pdf file now is installed in
	$(prefix)/share/doc/$(PACKAGE)/pdf/, while all the texfiles and
	all the figures required to prepare that document are located in
	$(prefix)/share/doc/$(PACKAGE)/userman. This is to comply with the
	Debian GNU/Linux policy for the documentation material.

2004-01-24  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.6.4 

	* all GNUification of the polyxmassdata package. Modifications in
	some of the polymer sequence examples to show the annotation
	feature.

2004-01-19  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* all the polseqs/*.pxm files have been changed so that what was
	before a <prop> element with <name>COMMENT</name> have become a
	<prop> element that is actually a note of name COMMENT. That is
	because we have dropped support for the "COMMENT"-named prop
	object in libpxmchem/pxmchem-polymer.c file and in the
	pxmchem-plugin.c. See these files to check the differences.

2004-01-04  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polseqs/protein-sample.pxm: added a default attribute to the
	<data> element (type), so that the PxmNote objects can be stored
	easily as text data, still knowing what kind of data they were in
	the first place (str=string, int=integer, flt=float,
	dbl=double). Default is "str". This should be compatible with
	earlier sequences.
	

2003-11-14  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.6.3

	* Added a note example in the protein-sample.pxm file so that
	users can check that annotation new feature.
	
	* Improved the documentation so that it now better reflects new
	features in the polyxedit module (annotation features).

2003-10-28  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.6.2

	* Modifications in view of new release. Mainly, modifications in
	the documentation.

2003-09-30  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* userman/basics-polchem.tex (subsubsection*{Nucleic Acid
	Fragmentation}): corrected an error in the doc, where the z
	fragments' mass calculation was badly defined.
	(paragraph{\emph{y} fragment series} The calculation is
	mathematically): corrected an error in the doc, where the y
	fragments' mass calculation was badly defined.

2003-08-05  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.6.1

	* user_manual: bunch of bug fixes. Changed the polyxcalc chapter
	to reflect changes in the way polyxcalc understands the
	chempad.conf chemical pad configuration files.

2003-08-02  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* protein/chempad.conf: removed the chempad_rows$3 exactly for the
	same reason as described below.

	* chempad.conf: removed the chempad_rows$3 line, now polyxcalc can
	layout the chemical pad using only either a chempad_rows$x
	specification or a chempad_columns$x specification.

2003-07-29  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* user_manual: removed all the files that were remaining from the
	old doc version. These files did not make it into the new version
	of the doc. Changed the userman/Makefile.am file accordingly.

2003-07-27  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* release 0.6.0
	
	* user_manual: big progress in the user manual. Changes include
	adding a full chapter about polyxmassdata with a detailed
	description of the way the polyxmass computer framework can cope
	with an arbitrary number of different polymer chemistries.
	
	* configure.in: changed AC_INIT([polyxmassdata], 0.6.0... to
	AC_INIT(polyxmassdata, 0.6.0...

2003-07-21  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* all.package : the polyxmass' software suite configuration
	directory where the modules' config files are stored is now
	$(prefix)/etc/polyxmass.d, instead of hard coded
	/etc/polyxmass.d. This way people who do not administer their *nix
	machines can still install the software and use it fully. Thanks
	to Mark Tracy for pointing this bug to me. That's a big step that
	requires that all the modules in the polyxmass software suite be
	updated accordingly. Hence the big leap to 0.6.0.

2003-07-17  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* release 0.5.1 

	* userman: almost all the documentation about polyxdef and
	polyxcalc. Still need to complete the polyxedit chapter, add a
	chapter on the configuration of the filesystem hierarchy...

2003-06-25  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* userman: added the userman directory where the polyxmass userman
	files are stored so that they can be recompiled by the user.

2003-05-xx  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* release 0.5.0

