## File: ChangeLog

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polyxmass-doc 0.8.5-2
 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185 2005-03-21 Filippo Rusconi * Release 0.8.5 with modifications related to packaging the material in such a way that the pdf file can be compiled, and so that the pdf file itself is not shipped. This release is concomitant with the release of Debian packages. * autogen.sh : changed the file so that all the autotools-related files are updated neatly. 2005-03-08 Filippo Rusconi * 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. 2005-02-16 Filippo Rusconi * userman/Makefile.am (EXTRA_DIST): removed polyxmass.pdf from the distributed material, as it should be compiled. (clean): added *.pdf as pdf files should be removed since they should be compiled from scratch. 2005-02-12 Filippo Rusconi * userman/installation-overview.tex (section*{Installation On A \OSname{Mac~OS~X} System With \software{Fink}}): modified the paragraph on Fink installation according to a text provided by Dr Mark Tracy. 2004-12-07 Filippo Rusconi * Release 0.8.3 with a new section about the electrical charge/isoelectric point calculations and detailed documentation of the acidobasic.xml file format. 2004-02-13 Filippo Rusconi * 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 * configure.in: modified the CONFDIR main configuration variable to now hold the "${packageprefix}/share/polyxmass.d" string. That will be the new location of the whole GNU polyxmass configuration files. This change was elicited by the making of Debian packages. 2004-01-26 Filippo Rusconi * Makefile.am (polyxmassdata_mandir): corrected wrong location of the installed man page from$(prefix)/man/man1 to $(prefix)/share/man/man1. 2004-01-25 Filippo Rusconi * added a new man page to the package. Note that this man page is now fully part of GNU polyxmassdata, and not of the Debian GNU/Linux package. It is being prepared in an sgml form and then converted to man with the command 'docbook-to-man polyxmassdata.sgml > polyxmassdata.man' in the file autogen.sh. * The user manual pdf file now is installed in$(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 * 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 * all the polseqs/*.pxm files have been changed so that what was before a element with COMMENT have become a 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 * polseqs/protein-sample.pxm: added a default attribute to the 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 * 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 * Release 0.6.2 * Modifications in view of new release. Mainly, modifications in the documentation. 2003-09-30 Filippo Rusconi * 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 * 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 * 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$x specification. 2003-07-29 Filippo Rusconi * user_manual: removed all the files that were remaining from the old doc version. These files did not make it into the new version of the doc. Changed the userman/Makefile.am file accordingly. 2003-07-27 Filippo Rusconi * release 0.6.0 * user_manual: big progress in the user manual. Changes include adding a full chapter about polyxmassdata with a detailed description of the way the polyxmass computer framework can cope with an arbitrary number of different polymer chemistries. * configure.in: changed AC_INIT([polyxmassdata], 0.6.0... to AC_INIT(polyxmassdata, 0.6.0... 2003-07-21 Filippo Rusconi * all.package : the polyxmass' software suite configuration directory where the modules' config files are stored is now$(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 * 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 * 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 * release 0.5.0