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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
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