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

	* Release 0.8.9. Dependent on libpolyxmass --version 0.8.9.

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

	* polyxedit-ui-cleave-results.c
	(polyxedit_cleave_results_wnd_find_button): fixed a bug due to
	automatically freeing non-allocated string from a
	g_object_set_data_full () function with g_free as (GDestroyNotify)
	function.

	* polyxedit-ui-searchmass-results.c
	(polyxedit_searchmass_results_wnd_find_button): fixed a bug due to
	automatically freeing non-allocated string from a
	g_object_set_data_full () function with g_free as (GDestroyNotify)
	function.

	* polyxedit-ui-fragment-results.c
	(polyxedit_fragment_results_wnd_find_button): fixed a bug due to
	automatically freeing non-allocated string from a
	g_object_set_data_full () function with g_free as (GDestroyNotify)
	function.

2005-08-29  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Thus, function calls in polyxmass-bin were changed also. Mainly
	compute -> calculate transitions.

2005-08-12  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Removed polyxedit.glade which is not used since a long time
	already.

	* Huge work on internationalization. The i18n framework was
	updated and the translation of the polyxmass-bin.pot file was done
	in fr.po. In the process, a great number of modifications were
	performed in the source. However, no functionality was modified
	whatsoever. Only were performed "cosmetic" and language-related
	modifications generally aimed at clarifying the wording of
	messages output to the user. The GUI was totally translated into
	french. Since french is less compact, as a language, than english,
	there might be GUI items that now are too long. I will change the
	translations on a case-by-case basis. Files were renamed
	occasionally so that their file name is more eloquent about the
	code therein.

2005-08-02  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxmass-ui-window-mngmt.c
	(polyxmass_window_mngmt_wnd_report_clipboard_button): fixed bug
	due to calling the report-making function without having a window
	item being selected in the window management treeview. The crash
	was due to the assertion report!=NULL. Thanks to Lionel Mamane for
	this bug report.
	(polyxmass_window_mngmt_wnd_delete_event): added call to
	polyxmass_timeoutmsg_messages_remove ((GtkWindow *) window); so
	that crashes are prevented when the window is closed before the
	last timed-out message has vanished.

2005-07-31  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* for whole project called intltoolize, which created
	intltool-extract.in intltool-merge.in and intltool-update.in
	symbolic links in srcdir.

	* Makefile.am (localedir): added this definition.
	(INCLUDES): added -DLOCALEDIR=\"$(localedir)\"

	* polyxmass-main.c (main): made a number of setlocale () calls
	with proper categories and locales. This is because Jérôme
	Pansanel found that polyxcalc would fail with LC_ALL=fr_FR
	(decimal separator is ',' in that locale). 

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

	* Release 0.8.8. First release compiled using gcc-4.

	* Put the -Werror flag in the INCLUDES directive of the
	src/Makefile.am file. This way, I can remove it from the
	autogen.sh file and from the configure script-related CFLAGS
	settings, and thus can get away with warnings from the configure
	checks (which GNU polyxmass are not responsible for). 

	* configure.in: incremented to 0.8.8 the requirement for
	libpolyxmass version.
	
2005-07-15  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Makefile.am: removed the call to docbook-to-man polyxmass.sgml >
	polyxmass.1 because this utility is not available on other
	distributions with the same name. So the man page is going to be
	shipped as is, without auto-regeneration during a make.

2005-07-11  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-searchmass-options.c
	(polyxedit_searchmass_opt_search_masses): improved the feedback to
	the user such that each time a new mass is being searched it is
	displayed, thus providing a feeling of the work going on.

2005-07-10  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-searchmass-results.c
	(polyxedit_searchmass_res_wnd_sort_name_column): added this
	function to sort the name column of the displayed oligomers. This
	function is required by the findmass results "name" column of the
	displaying treeview.

	* polyxedit-ui-findmass-results.c
	(polyxedit_findmass_results_wnd_make_report_text_format): improved
	the reporting format.
	(polyxedit_findmass_res_setup_oligs_treeview): improved the
	function so that depending on the kind of oligomers reported
	(cleavage or fragmentation), the proper oligomer name sorting
	function is called.
	

	* polyxedit-ui-cleave-results.c
	(polyxedit_cleave_results_wnd_make_report_text_format): improved
	the reporting format.

	* polyxedit-ui-fragment-results.c
	(polyxedit_fragment_results_wnd_make_report_text_format): improved
	the reporting format.

2005-07-08  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-seqed-window-menu.c
	(polyxedit_seqed_window_menu_chemistry_mz_ratio_calc): added the
	window registering call so that the newly created m/z ratio
	calc. window gets listed in the window of window management.

	* polyxcalc-ui-calculator.c
	(polyxcalc_ui_calculator_wnd_mz_ratio_calculator_button): added
	the window registering call so that the newly created m/z ratio
	calc. window gets listed in the window of window management.

	* polyxmass-ui-mz-ratio.c (polyxmass_mz_ratio_wnd_setup): changed
	the setup of the window so that the function now knows which
	module is calling that window. The title window is adapted to the
	situation.
	(polyxmass_mz_ratio_wnd_make_report_text_format): added this
	reporting function that I forgot to code during the last days.

2005-07-01  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-reportopt.[ch]: changed files
	polyxmass-ui-reportopt.[ch] to this new filename, since the
	reporting options will be governed differently dealing with each
	differnent module (polyxdef and polyxcalc). More modularity is
	better.

2005-06-29  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-cleave-results.c
	(polyxedit_cleave_res_wnd_sort_coordinates_column): corrected a
	bug in the sorting algorithm.
	(polyxedit_cleave_res_wnd_sort_name_column): added this function
	to sort correctly the cleavage fragments according to their
	specific name syntax.

	* polyxedit-ui-fragment-results.c
	(polyxedit_fragment_res_wnd_sort_name_column): added this function
	to sort correctly the fragmentation oligomers according to their
	specific name syntax.

2005-06-20  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-fragment-results.c
	(polyxedit_fragment_res_wnd_really_close): added this function to
	allow automatically closing the window when the corresponding
	polymer sequence editor window is closed. This is also the case
	for the following windows: fragment-options, cleave-results and
	cleave-options.

2005-06-13  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxmass-ui-filechoosers.c
	(polyxmass_filechoosers_polchemdef_select_button_clicked):
	corrected a number of bugs created during the cleaning of the
	interfaces in the polyxmass_filechoosers_show_wnd function and
	related ones (see 2005-05-22).

2005-05-27  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Modified the edit main menu item from the canvas contextual menu
	as it was a gtk stock menu not properly recognized using
	MacOSX/Fink platform. Thanks to Mark Tracy for finding this bug.

2005-05-22  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxmass-ui-filechoosers.c (polyxmass_filechoosers_show_wnd):
	cleaned interfaces to calling the different types of file choosing
	windows (atom definition, polymer chemistry definition,
	initialization of a new polymer sequence).

2005-04-25  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* configure.in : removed the test of the pkg-config version number.

	* changed the handling of all the var = strlen () calls, so that
	the returned value is of type gsize (equivalent to size_t). Then,
	the returned gsize value is ensured to be less than G_MAXINT and
	finally the value is converted to gint with a simple cast. Bug
	discoverd by Debian users on Sparc workstations.

2005-04-05  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.8.7 with a dependency to libpolyxmass >=0.8.7 (this
	release should coincide with the first Debian package release. I
	am immensely grateful to Lionel Mamane for working on that with me
	and teaching me a lot of things (often Debian GNU/Linux-related,
	but not only).

2005-04-03  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-seqed-window-menu.[ch] and
	polyxedit-ui-seqed-canvas-menu.[ch] were added to replace the
	polyxedit-ui-seqed-canvasmenu.[ch] pair. The functionality of the
	old pair of files is now distributed in the two new pairs. The
	'window' pair hold now only the functionality that is related to
	the whole polymer sequence editor window. The 'canvas' pair
	(that's the contextual menu) hold now the functionality that is
	only related to a single right-clicked monomer icon. This changed
	was suggested by Lionel Elie Mamane, and I'm grateful to him for
	this.
	

	* polyxedit-ui-seqed-wnd.c (polyxedit_seqed_wnd_setup): changed
	the colors with which the code editing feedback text is displayed:
	dark green for the currently edited (and still valid) monomer code
	feedback message and dark red for the erroneous code feedback
	message.
	(polyxedit_seqed_wnd_setup): changed also (with glade-2) the
	graphical interface of the sequence editor. Should look cleaner
	and also be easier to gain more space for the sequence by shutting
	down frames.

2005-03-29  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-seqed-menu.c
	(polyxedit_seqed_canvas_menu_view_completionslist): added this
	menuitem to the canvas contextual menu so that user not knowing
	that TAB provides the list of available monomer code completions
	can find it easily. (Thanks to Lionel Mamane for this suggestion).

2005-03-28  Filippo Rusconi  <filippo rusconi at nowhere dot org>

        * all_glade_files: changed the GtkEntry widgets to have no frame
	each time the GtkEntry has as the sole purpose to produce text for
	user's consumption. Instead, if the GtkEntry is to receive data
	from the user, then the frame is set to visible.

	* polyxedit-ui-seqed-clipboard.c
	(polyxedit_seqed_clipboard_import_wnd_setup): finalized the
	writing of all the functions that will allow the user to purify a
	badly formatted sequence to be pasted in the sequence editor. A
	number of facilities allow for an easy purification, such as
	removing all the digits and spaces in one go... an other goodies.

2005-03-27  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-seqed-clipboard.c
	(polyxedit_seqed_clipboard_selection_received): fixed a
	potentially very big memory leak due to not freeing the allocated
	array of monomers resulting from parsing the sequence string being
	imported into the sequence editor in the form of a clipboard
	paste.

	* polyxedit-ui-seqed-clipboard.[ch]: added this pair of source
	files to handle all the X Window system clipboard functions
	related to the sequence editor.

2005-03-22  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* autogen.sh (CFLAGS): removed the -z flag to CFLAGS that was a
	sequel of a previous -Wl,-z,defs flag that was to be passed to the
	linker. After this removal, a number of warning: unused variable
	appeared upon compiling polyxmass-bin. Thus code cleanup was
	performed.

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

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

	* TODO : added items as a result of a long discussion with Lionel
	Mamane.

2005-03-15  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-seqed-kbd.c (polyxedit_seqed_kbd_*_handler): In all
	the handlers, the code was improved for the case where the
	selection was destroyed by moving the cursor with the keyboard
	keys. This ensure that when a new selection is started, the
	selection's bordering monomers have the proper index value, and
	thus the proper position, which ensures that the selection polygon
	gets drawn correctly.

	* polyxedit-ui-cleave-results.c
	(polyxedit_cleave_res_oligs_treeview_row_activated): Implemented
	this function so that when the user double-clicks onto an oligomer
	item its corresponding sequence gets selected in the editor window
	so that it is easy to see where the oligomer is located.

2005-03-14  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-seqed-wnd.c
	(polyxedit_seqed_wnd_select_all_sequence): changed this function
	to polyxedit_seqed_wnd_select_sequence () with two more params:
	start_idx and end_idx, so that a single function can either select
	the whole sequence (either start_idx or end_idx == -1) or the
	sequence portion as defined by these two indices. Changed calls to
	the older function so that they still work with the new one.

2005-03-12  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-calculations-opt.c
	(polyxedit_calculations_opt_ionizerule_activate_entry): changed
	the way the recalculations are performed when the ionization data
	are changed. Previously, only the entry that received the <Enter>
	was updated, even if other text entries had changed. The mass
	results were thus counter-intuitive, as data was displayed in the
	different edit boxes, but the masses were recalculated by only
	taking into account the text entry widget(s) in which <Enter> was
	pressed. Now, logically, all the three actform, charge, level
	GtkEntry widgets are updated whenever <Entry> is pressed in
	whatever of these three widgets. Thus, mass results should always
	be consistent with what's displayed in the three GtkEntry widgets.

2005-03-10  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxcalc-ui-calculator.c
	(polyxcalc_ui_calculator_wnd_univ_chem_elem_checkbutton): fixed a
	GUI bug due to calling a gtk+ widget with a bad name.

2005-03-09  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-polymer-modif.c
	(polyxedit_ui_polymer_modif_modify_button): removed a debug_print
	statement that caused text to be output on stdout.

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.

2005-02-12  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* configure.in: changed version to 0.8.7-no release yet. Just
	making packages for Debian and discovering glitches...

	* polyxmass.sgml: corrected the <!ENTITY dhsection
	"<manvolnum>1</manvolnum>"> from 7 to 1.

	* Makefile.am (EXTRA_DIST): changed the man page name from
	polyxmass-bin.7 to polyxmass.1. Note that the install directory
	was also changed from man7 to man1. Also, the sgml page was
	changed from polyxmass-bin.sgml to polyxmass.sgml. The Makefile.am
	file was changed accordingly.

2005-02-05  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.8.6

	* whole_package: changed some functions to report errors in the
	form of g_critical messages, instead of g_error, so that no crash
	occurs when something fails. This is true for cases where the user
	tries to open files for which dependencies are not satisfied, like
	when the polyxmass-common package is not installed or when the
	installation is messed up somehow. The message that is returned is
	clear enough to let the user understand that something is not
	correct in her installation, like either polyxmass-common missing
	or some files being absent from locations where they were expected
	to be found.

	* configure.in (LIBPOLYXMASS_REQUIRED): incremented to 0.8.6

	* polyxcalc-calcctxt.c (polyxcalc_calcctxt_free): corrected a bug
	to polyxmass_timeoutmsg_messages_remove for
	calcctxt->calculator_wnd prior to checking that this window
	pointer was actually non-NULL. This yielded a crash when the
	polyxcalc_calcctxt_free() was called before that the window was
	actually correctly set up.

	* Added two new libpopt flags to ask what the current XML file
	format version is for either the polymer chemistry definition or
	the polymer sequence (--polchemdefversion and
	--polymersequenceversion).

	* whole_project: set the log handlers for critical, warning,
	message g_log messages and replaced all the calls to g_log to
	each corresponding g_critical, g_warning, g_message logging
	functions. Each such call is now handled nicely with each
	corresponding handler that sends the message to the console window
	so that the user may see the messages even if polyxmass was not
	started from a terminal.
	
	* configure.in (XXXXXX_REQUIRED): Removed the dependency on the
	polyxmass-common package. This will allow the program to be
	compile on a machine that has no data installed on it. Thanks
	Lionel Mamane for this suggestion.

2005-02-03  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxmass-ui-console.c (polyxmass_console_setup_wnd): added this
	pair of [ch] files to the project to handle the message-logging
	console window. Added the corresponding polyxmass-console.glade
	file in the srcdir/glade directory.

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

	* polyxdef-defctxt.c (polyxdef_defctxt_free): corrected a bug to
	polyxmass_timeoutmsg_messages_remove for defctxt->definition_wnd
	prior to checking that this window pointer was actually
	non-NULL. This yielded a crash when the polyxdef_defctxt_free()
	was called before that the window was actually correctly set up.

2005-01-31  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.8.5

	* polyxedit-ui-self-speak.c (whole_file: each fputs() return value
	check was corrected as the previous version was not faulty in
	GNU/Linux but was in MacOSX/Fink. This is a known bug that was
	corrected earlier elsewhere in the project (the return value of
	the fputs() function (the fputs () return value is not the same on
	all platforms). Thanks to Marc Dellinger for pointing this out.

2005-01-25  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-searchmass-results.c
	(polyxedit_searchmass_res_setup_oligs_treeview): changed to
	setting-up of the coordinates column of the treeview so that it
	gets sorted correctly by calling automatically the sorting
	function polyxedit_searchmass_res_wnd_sort_coordinates_column.
	(polyxedit_searchmass_res_wnd_sort_coordinates_column): added this
	function to ensure the coordinates [xx-yy] column would sort
	correctly according to xx when its header is clicked.

	* polyxedit-ui-mnmcompos.c
	(polyxedit_mnmcompos_wnd_setup_treeview): the "Name" and "Code"
	columns are now sortable in the treeview that shows the monomeric
	composositio of the polymer sequence.

2005-01-24  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-cleave-results.c
	(polyxedit_cleave_res_setup_oligs_treeview): changed to setting-up
	of the coordinates column of the treeview so that it gets sorted
	correctly by calling automatically the sorting function
	polyxedit_cleave_res_wnd_sort_coordinates_column.
	(polyxedit_cleave_res_wnd_sort_coordinates_column): added this
	function to ensure the coordinates [xx-yy] column would sort
	correctly according to xx when its header is clicked.

	* polyxedit-ui-seqed-wnd.c (polyxedit_seqed_wnd_delete_event):
	corrected a small bug due to passing the sequence window pointer
	to gtk_dialog_add_buttons (GTK_DIALOG (here_pointer), instead of
	the dialog window pointer.

	* polyxedit-ui-completions.c (polyxedit_completions_wnd_setup):
	the monomer "Code" and "Name" columns of the completions list are
	listed are now sortable.

	* Release 0.8.4

	* polyxedit-main.c (polyxedit_main_prepare_new_context_open_file):
	changed the error reporting from LEVEL_ERROR (that is abortion of
	the program) to LEVEL_CRITICAL when failure to open a polymer
	definition context is encountered (thanks to Mark Tracy for
	suggesting that modification).

	* Whole_program: added the polyxmass-ui-mz-ratio.[ch] pair of
	files to handle the calculation of m/z ratios. That functionality
	might be called either from the polyxcalc module or from the
	polyxedit sequence contextual menu.

2005-01-12  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-seqed-wnd.c (polyxedit_seqed_wnd_delete_event):
	corrected a bug due to calling this function from the handler of
	the Close contextual menu with a NULL window pointer. Added code
	to go searching that pointer value in the seqeditorctxt object
	pointed to by the editctxt pointer that is passed to the function.

	* in file glade/polyxedit-seqeditor.glade changed a number of
	standard items in the contextual sequence editor menu due to
	GTK_ACCEL_* error messages and crashes.

2005-01-11  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* in file glade/polyxedit-acidobasic.glade changed the graphical
	interface to ensure that fields requiring input are clearly
	detectable, in contrast with fields where data are provided as the
	result of calculations (thanks Mark Tracy for pointing this
	problem out).

2004-12-08  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* release 0.8.3

	* Removed fake dependencies on libvorbis header files, since the
	program does not use those libraries. The inclusions date back to
	the developing phase of the self-speaking feature of polymer
	sequences.

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

	* Added the functionality of electrical charge/isoelectric point
	computations for the polymer sequence. Two sets of files were
	added: polyxedit-ui-pka-ph-pi.[ch] and
	polyxedit-acidobasic.[ch]. This new feature is to be considered
	experimental.

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

	* release 0.8.2
	
2004-11-04  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxdef-ui-polchemdef.c
	(polyxdef_ui_polchemdef_wnd_setup_window): corrected a bug due to
	setting up the monomers' notebook widget twice, which resulted in
	the insertion of two new items each time the "Add" button was
	clicked in the monomers' notebook page. The proper behaviour is
	now ensured.

2004-11-03  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxdef-main.c (polyxdef_main_prepare_new_context): added a
	call to pxmchem_polchemdef_update_delim_codes () after reading a
	polymer definition from xml file, so that the delim_codes string
	is available when the user starts working on cleavage
	specifications; this string is needed because the cleavage
	specification parsing requires it.

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

	* Release 0.8.1 

	* polyxcalc-main.c (polyxcalc_main_prepare_new_context): now uses
	the polyxmass_polchemdefctxt_init_with_type () function to load
	the polymer chemistry definition that the user might have
	asked. Otherwise simply loads the atoms for the 'basic' atom
	definition.

2004-10-05  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-self-speak.c (polyxedit_self_speak_wnd_setup): same
	as below. 

	* polyxedit-ui-monomer-modif.c
	(polyxedit_ui_monomer_modif_setup_wnd): improved the user
	experience by setting up a callback mechanism that takes care of
	closing this window if the "parent" sequence editor window is
	closed. As a side effect corrected a bug that was due to not
	emptying the array of timed-out messages before closing the
	window, which had as effect the crash of the pogram when the
	time-out would happen and the window was not there anymore...

	* polyxedit-rendering.c (polyxedit_rendering_pixbuf_render_modif):
	adapted the code to comply with the new fact that the modif
	specifications are now located in another array,
	polchemdefctxt->mdfspecGPA, and no more in
	polchemdefctxt->mnmspecGPA.

2004-10-04  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-self-speak.c
	(polyxedit_self_speak_wnd_create_polseq_playlist): added the
	capability to let modifications self-speak themselves out.

	* polyxedit-main.c (polyxedit_main_prepare_new_context_open_file):
	this function now calls the
	polyxmass_polchemdefctxt_init_with_type () without duplicating the
	creation of the polchemdefctxt.
	
2004-10-02  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxmass-self-speak.c
	(polyxmass_self_speak_get_silent_sound_file_name): will parse the
	sounds.dic file and return the filename of the silent sound.

2004-09-27  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-self-speak.c: added this file to handle the
	self-speak feature for polymer sequences that become able to send
	to a playlist file all the sound filenames that are required to
	play a given polymer sequence.

	* polyxmass-self-speak.c: added this file to handle a number of
	tasks related to things like reading the monomer-sound.dic config
	file...

	* polyxedit-ui-seqed-wnd.c
	(polyxedit_seqed_wnd_export_sound_playlist): added this function
	to serve as relay between the canvas menu and the acutal function
	doing the work.

	* polyxedit-ui-seqed-menu.c
	(polyxedit_canvas_menu_edit_export_sound_playlist): simple menu
	handler for the contextual menu.

2004-09-22  Filippo Rusconi  <filippo rusconi at nowhere dot org>

 	* Release 0.8.0

2004-08-30  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-note.c
	(polyxedit_note_wnd_selected_item_propagate): corrected a bug that
	would stop propagating a note in all the monomers of the range is
	one such monomer had a "NOTE"-named property in its propGPA
	array. That is erroneous: a monomer might have as many
	"NOTE"-named properties in its propGPA array! What is not possible
	is that a monomer has two "NOTE"-name property object that have
	the same name themselves, that is that have the same (PxmNote
	*)->name string.

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

	* configure.in (CONFDIR): will be /etc/polyxmass if no
	--sysconfdir has been passed to the configure script.

	* this ChangeLog entry marks the start of the version 0.8.0 of the
	GNU polyxmass package, as it is born by pooling all my code
	previously written for modules polyxdef, polyxcalc and polyxedit
	into one single binary package: polyxmass. Below are the three
	ChangeLog files from those three modules concatenated together.

2004-07-24  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* configure.in (POLYXMASS_DATA_REQUIRED): changed requirement from
	0.7.0 to 0.7.1 since location of data files changed.

	* polyxedit-config.c: changed user_polyxdef_cfg_file from
	".polyxmass.d/polyxedit.conf" to ".polyxmass/polyxedit.conf".

	* autogen.sh (CFLAGS): added switch --sysconfdir=/etc

	* Makefile.am (polyxeditconf_datadir): now in
	$(sysconfdir)/polyxmass

	* configure.in: changed the CONFDIR specification to point to
	$(sysconfdir)/polyxmass, with autogen and configure saying
	"--sysconfdir=/etc".

2004-07-20  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.7.2

	* polyxedit-poledtctxt.c (polyxedit_poledtctxt_free): corrected
	bug due to leaving the completions' listview window around after
	the related sequence editor window was closed. Now the closing of
	the completions's listview window is automatic when the sequence
	editor window is closed.

2004-07-04  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.7.1 compiled using the new libraries Glib, Gtk+... and
	lipbolyxmass version 0.0.0.
	
	* configure.in: AC_INIT(polyxedit, 0.7.0 changed to
	AC_INIT(polyxedit, 0.7.1
	(GLIB_REQUIRED): changed from old version requirements to new
	ones. Same for all the other libraries that were upgraded.

	* polyxedit-ui-findmass-options.c
	(polyxedit_findmass_opt_setup_wnd): changed GtkOptionMenu to
	GtkComboBox because the latter one was dropped from Gtk+ v2.4.0.

	* polyxedit-ui-searchmass-options.c
	(polyxedit_searchmass_opt_setup_wnd): changed GtkOptionMenu to
	GtkComboBox because the latter one was dropped from Gtk+ v2.4.0.

	* polyxedit-globals.c (polyxedit_globals_timeout_message_set):
	changed gtk_timeout_add to g_timeout_add (due to upgrade of
	glib-2.0 and co libraries since last march).
	(polyxedit_globals_timeout_message_stop): changed
	g_object_timeout_remove into g_source_remove (due to upgrade of
	glib-2.0 and co libraries since last march).

2004-03-24  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* whole_project: remodelled all the function calls that used to be
	performed when comparing/duplicating PxmProp-related or PxmYYYY
	objects, as the framework for comparing and duplicating properties
	(PxmProp objects) has vastly been enhanced in the
	libpxmutils/libpxmchem libraries. This is a major feature
	enhancement, although not directly visible to the user. These
	changes are made with a very powerful find/replace feature in
	mind, which is to be developed soon.

	* whole_project: refactored the manner in which timed-out messages
	can be displayed in the messages_entry GtkEntry wiget. There is
	now a framework ready to be used easily that ensures that pending
	timed-out messages are removed before a window is closed. This way
	a number of crashes are avoided. The crashes due to timing-out of
	messages displayed in a GtkEntry belonging to a no longer-existing
	window are the only crashes that I have encountered in the program
	so far.

2004-03-09  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-note.c
	(polyxedit_note_wnd_selected_item_remove_range): Bogota,
	Colombia. Removed a bug due to freeing the reference monomer'prop
	object instead of removing it from each of the iterated monomers
	in the range. That bug drove to removing twice a noteval object
	out of the reference monomer's "NOTE" prop object.

2004-02-10  Filippo Rusconi  <filippo rusconi at nowhere dot org>
 
        * Release 0.7.0 without major source code changes, only changes in
	the package. The release is aimed at synchronizing all the
	packages on the same value for the milestone Debian GNU/Linux. The
	tar.gz packages are now fully synchronized with the .deb packages
	and the $(package).spec.in file in the source tarball with which
	rpm packages should be able to be prepared.
 
2004-02-03  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-note.c (polyxedit_note_wnd_note_add_button):
	corrected a number of seemingly erroneous pointer casts from
	GtkTreeModel * to GtkTreeStore * and vice-versa... These problems
	appeared when compiling with -g -O0 -z -Wl -Wall -Werror
	-D_REENTRANT.

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

	* Release 0.6.6

	* Full Gnuification of the package. A number of new developments,
	mostly in the sequence annotation field. Going to release this.

2004-01-23  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-note.c
	(polyxedit_note_wnd_reset_note_related_widgets): added this
	function to handle cases when no more selection is present in the
	treeview, and thus nothing should be visible in the note-related
	widgets. This is cosmetic, but improve the user experience with
	this complex window.

2004-01-03  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* configure.in (ALL_LINGUAS): added ALL_LINGUAS="fr" because
	automake would complain in $(srcdir) that this variable is not
	defined while still using gettext...

	* Makefile.in.in (MKINSTALLDIRS): change this file in $(srcdir)/po
	so that the make install target would not failed, not finding the
	mkinstalldirs script... See the file itself for details.

2003-12-14  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-seqed-wnd.c
	(polyxedit_seqed_wnd_lr_end_modif_button_clicked): added this
	function, in conjunction with a modification of the polymer
	sequence editor gui-defining glade file
	(glade/polyxedit-seqeditor.glade), so that the left and right
	ends' modification data can be shown/hidden using a single click
	onto the frame title (button with no border). This is similar to
	the polymer sequence data frame on top of the polymer sequence
	editor window.
	(polyxedit_seqed_wnd_setup): added a button in the left and right
	en modifs frame so that the user can call from it the polymer
	sequence modification window.

2003-11-16  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-seqed-wnd.c
	(polyxedit_seqed_wnd_update_monomer_flag): corrected a bug due to
	not unref'ing the allocated GdkGC *gc, which yielded massive
	memory leaks.

2003-11-15  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-rendering.c
	(polyxedit_rendering_monicon_make_canvas_item): changed
	(GtkSignalFunc) to G_CALLBACK ().

	* polyxedit-polseqctxt.c (polyxedit_polseqctxt_free): fixed memory
	leak due to not calling g_free (polseqctxt) (Thanks Valgrind).

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

	* Release 0.6.5 

	* configure.in updated the
	dependencies. LIB_PXMUTILS_REQUIRED=0.6.2
	LIB_PXMCHEM_REQUIRED=0.6.3 POLYXMASSDATA_REQUIRED=0.6.3

2003-11-13  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Improved the interface for the polymer sequence editor so that
	the status of the monomer under the mouse cursor is displayed
	automatically in the form of a flag with three elements. Written
	the code that updates this flag. See the documentation in the
	polyxmassdata package.
 
2003-11-12  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-seqed-wnd.c (polyxedit_seqed_wnd_canvas_event):
	corrected a nasty bug due to not bypassing a mouse click out of
	sequence drawing area follow by a drag to the sequence area,
	button release: CRASH BOOM ! The mouse event handling function has
	been corrected and its design bettered somewhat.
	(polyxedit_seqed_wnd_render_polseq): when the sequence cursor is
	drawn for the first time, it is drawn left of the very first
	monomer of the sequence. And we did not make sure that the first
	point of the selection rectangle (poledtctxt->selection_rect) had
	meaningful values. Hence crashes.

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

	* polyxedit-ui-note.c
	(polyxedit_note_wnd_monomer_note_remove_range): continued
	improving the PxmNote stuff. Now it is possible to add notes to a
	range of monomers in one go. It is also possible to change a note
	throughout a range of monomers. It is also possible to remove a
	note throughout a range of monomers. More flexible than
	that... Thanks to Mark Tracy for suggesting that feature.

	

2003-11-10  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-globals.c (polyxedit_globals_timeout_stop): corrected
	a bug that would crash the program if a timeout would be triggered
	after the window in which it was created was closed. That was a
	bad format of the call if (TRUE == G_IS_OBJECT (entry)) which was
	actually if (TRUE == G_IS_OBJECT (entry) == TRUE) -:(. Now seems
	to work. Same bug corrected in the polyxdef and polyxcalc modules.

2003-10-27  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.6.4

	* polyxedit-ui-note.c
	(polyxedit_note_wnd_edited_note_apply_button): Implementation of a
	set of functionalities aimed at allowing unlimited and flexible
	annotation to polymer sequences and/or monomers. This system is
	virtually applicable to any chemical entity that has the
	propGPA-base property system already implemented (oligomers, for
	example).

2003-10-26  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-seqed-wnd.c
	(polyxedit_seqed_wnd_get_mnm_idx_with_xy): added code to check if
	the cursor is located in the margin of the sequence display
	area. If so the index that is returned is -1 and it becomes the
	responsibility of the caller to check for that specific
	value. Functions have been changed in that respect. For example,
	the mouse button press/mouse motion handling function was changed
	to check for that -1 returned value. No action is taken if the
	returned value is -1. As soon as the mouse cursor returns in the
	sequence display area, then the mouse button press/mouse motion
	handling function takes actions properly. Also, the position of
	the last moused monomer is updated to " " if the cursor is not
	over a monomer icon.
	(polyxedit_seqed_wnd_get_mnm_idx_with_xy): same as above but when
	the y position is less than zero, which mean that the cursor in in
	the upper margin of the canvas area.
	(polyxedit_seqed_wnd_get_mnm_idx_with_xy): same but for the bottom
	of the sequence display area.

	* polyxedit-poledtctxt.h (struct _PxmPoledtctxt): changed
	last_point_idx to last_point_1_idx (global change throughout all
	the source code). Added two other variants for buttons 2 and 3 of
	the mouse.

	* Makefile.am (SUBDIRS): removed the polyxedit/doc subdirectory as
	this directory was misleading: the documentation is in the
	polyxmassdata package not in each GUI module.

	* removed from the main Makefile.am the pixmaps directory from the
	'SUBDIRS =' line.

	* removed the polyxedit/pixmaps subdirectory because it contained
	two graphics files that actually belong to the glade
	subdirectory. See below.

	* Makefile.am (GRAPHIC_FILES): in the glade subdir. added
	provision to distribute graphics files (icons, for menus, for
	example). Glade/libglade would not load graphic files in
	subdirectories of the glade dir so I removed the pixmaps directory
	alltogether. Distributed graphics go in ghe glade dir now.

2003-10-25  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-seqed-kbd.c (polyxedit_seqed_kbd_key_press_event):
	added handler for GDK_F10, that acts like right-clicking onto the
	canvas, thus eliciting the popping up of the menu.

	* polyxedit-ui-seqed-menu.c: added this pair of .c/.h files to
	handle the configuration of the menu that is popped up when the
	mouse right button is clicked in the sequence canvas. The menu
	items that were removed from the program's main window have landed
	in this contextual menu.

2003-10-24  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-seqed-wnd.c (polyxedit_seqed_wnd_canvas_event):
	added a handler that will popup the canvas' menu when the right
	button of the mouse is clicked (that's the X button mouse number
	3).

	* polyxedit-ui-main-wnd.c (polyxedit_setup_app_wnd): removed a
	number of menu handlers as these menus have been removed from the
	main program window. The menus that were removed here are now
	handled in each polymer sequence editing window, as handlers to
	the contextual menu that is popped up when the right mouse button
	is clicked onto the canvas. The model that is retained here, is
	the one that made The Gimp easy to use, that can be adapted to our
	case simpley by stating that "Each polymer sequence has its own
	menu".

2003-10-21  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.6.3

	* polyxedit-ui-seqed-wnd.c
	(polyxedit_seqed_wnd_remove_sequence_indices): this function now
	no more checks if a selection is there or not. It is the
	responsibility of the caller that it checks that there is a
	selection before calling this function. All the calling functions
	have been changed to comply with this new policy.
	(polyxedit_seqed_wnd_selection_received): corrected a bug due to
	pasting a sequence in an empty editor window, without checking
	that there was no current selection before calling the function
	that removes the selected oligomer. See above.

	* polyxedit-ui-main-wnd.c
	(polyxedit_main_select_all_menuitem_activate): added handler along
	with menu item for people who do not know that Ctrl+A works the
	same.

	* polyxedit-ui-seqed-kbd.c (polyxedit_seqed_kbd_alpha_handler):
	added code to handle the Ctrl+A keystroke that corresponds to
	selecting the whole sequence.

	* polyxedit-ui-seqed-wnd.c
	(polyxedit_seqed_wnd_update_sel_polygon): now returns TRUE if the
	selection polygon was changed, and FALSE if nothing was touched.
	(polyxedit_seqed_wnd_select_all_sequence): added this function so
	that it is easy to select all the sequence in one go.

	* polyxedit-ui-main-wnd.c (polyxedit_main_copy_menuitem_activate):
	added handler along with menu item for people who do not know that
	Ctrl+C works the same.

	* polyxedit-ui-main-wnd.c (polyxedit_main_cut_menuitem_activate):
	added handler along with menu item for people who do not know that
	Ctrl+X works the same.

	* polyxedit-ui-main-wnd.c (polyxedit_main_paste_menuitem_activate):
	added handler along with menu item for people who do not know that
	Ctrl+V works the same.

2003-10-20 Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.6.2

2003-10-20  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-seqed-wnd.c
	(polyxedit_seqed_wnd_remove_selection_polygon): removed the call
	to the function that is responsible for updating the selection
	masses, because the call could make a crash if the value of the
	present cursor location had not been previously changed...

	* polyxedit-ui-seqed-wnd.c
	(polyxedit_seqed_wnd_remove_sequence_indices): cleaned up the code
	that made all the checks pertaining to the value of the start and
	end parameters.

	* polyxedit-ui-seqed-wnd.c (polyxedit_seqed_wnd_clipboard_cut):
	new function that works.

	* polyxedit-ui-seqed-kbd.c (polyxedit_seqed_kbd_evaluate_code):
	not being able to remove the selected oligomer now is an
	abortion-worth error.
	(polyxedit_seqed_kbd_delete_handler): same as above.

	* polyxedit-ui-seqed-wnd.c
	(polyxedit_seqed_wnd_integrate_monomer_at_idx): removed the two
	function calls that elicited the recomputation of the selected and
	whole sequence masses. That task is left to the caller.

	* polyxedit-ui-seqed-kbd.c
	(polyxedit_seqed_kbd_backspace_handler): cleaned code by pooling
	at the end of the function the two mass updating function.
	(polyxedit_seqed_kbd_delete_handler): same as above.

	* polyxedit-ui-seqed-wnd.c (polyxedit_seqed_wnd_remove_monomer):
	removed the two function calls that elicited the recomputation of
	the selected and whole sequence masses, because this function is
	called by other functions before readjusting the last pointed
	monomer index, which resulted in a crash due to trying to compute
	a mass for a selection greater than the actual size of the polymer
	sequnce. The functions that call this function have to ensure that
	they call the two mass updating functions themselves. This
	function now only performs array removals.

	* polyxedit-ui-seqed-kbd.c (for all the cursor moving keystrokes):
	if selection is changed, added code to call for ownership of the
	primary X selection. That works. For the page up/down keystrokes
	that modify the selection, changed code so that scrolling is much
	more intuitive, with the cursor being always visible either at the
	bottom of the sequence canvas area or at its top depending on the
	direction of the current selection operation (downwards or
	upwards).

2003-10-18  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-seqed-kbd.c (up/down/home/end handlers): exactly
	the same as for the left_ and right_ handlers described below.
	
	* polyxedit-ui-seqed-kbd.c (polyxedit_seqed_kbd_left_handler):
	added code to allow to resume a keyboard selection process that
	was left by releasing all the keyboard keys (with a selected
	portion of the sequence). If shift is pressed and the left/right
	cursor keys are used, the selection is resumed where it was left.

	* polyxedit-ui-seqed-kbd.c (polyxedit_seqed_kbd_right_handler):
	added code to allow to resume a keyboard selection process that
	was left by releasing all the keyboard keys (with a selected
	portion of the sequence). If shift is pressed and the left/right
	cursor keys are used, the selection is resumed where it was left.

	* polyxedit-ui-seqed-wnd.c
	(polyxedit_seqed_wnd_integrate_sequence_at_point): added that
	function to handle the copy/paste/selection stuff.
	(polyxedit_seqed_wnd_integrate_monomer_at_idx): corrected bug
	-with no effect- due to using poledtctxt->last_point_idx instead
	of using the passed idx parameter value.
	(polyxedit_seqed_wnd_integrate_monomer_at_point): added that
	function that will automatically compute where the insertion has
	to be performed (which is where the point location is).
	(polyxedit_seqed_wnd_get_selection_indices): changed the behaviour
	of the window, where the start and end parameters are no more
	compulsory, so that the function is usable also just to know if a
	sequence portion is selected in the editor window. Changed all the
	function-using code accordingly.

2003-10-17  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* configure.in: corrected small glitch that gave a bad config
	directory name in the summary (end of file;
	"${sysconfdir}/polyxmass.d" (which is /etc/polyxmass.d) instead of
	the directory actually computed in this same file:
	${CONFDIR}). Thanks to Austin Acton for pointing that glitch.

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

	* Release 0.6.1

	* polyxedit-ui-seqed-wnd.c
	(polyxedit_seqed_wnd_sequence_data_button_clicked): added this
	function to handle button clicks onto the button that was added in
	place of the polymer sequence data frame's label widget. If the
	vbox inside of the frame is visible, then it is made invisible,
	and vice-versa.

	* polyxedit-seqeditor.glade: changed the graphical interface of
	the polymer sequence editor so that the user may hide the polymer
	sequence data (name and ID) by just clicking onto a button that is
	packed in place of the label of the frame widget. This button acts
	as a swith Show/Hide the contents of the frame widget.

	* polyxedit-ui-seqed-wnd.c (polyxedit_seqed_wnd_setup): added code
	to make the editor window widget aware of the new polymer sequence
	data frame widget along with its button that will act as a switch
	Show/Hide the polymer sequence data-related widgets.

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

	* Release 0.6.0

	* polyxedit-main.c (polyxedit_configure_userspec): changed code so
	that when the user has no "datadir" data directory configure in
	her own polyxedit.conf file, the userspec->datadir becomes
	automatically the "userspec->configdir/polseqs" directory, which
	means that this directory becomes the polseqs directory in the
	user's own polyxmassdata directory if it not the default installed
	one any more.

2003-07-23  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-globals.h: Changed include
	/usr/include/gtk-2.0/gdk/gdkkeysyms.h to gdk/gdkkeysyms.h (Thanks
	Mark Tracy for pointing this).

2003-07-22  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Makefile.am (INCLUDES): added -I$(prefix)/include.
	(polyxedit_LDFLAGS): added -L$(prefix)/lib. Both changes to allow
	the package to find the header files of libpxmutils, for example,
	when this lib is installed in exotic places like /opt, for
	example.

2003-07-22  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-main-wnd.c (polyxedit_main_saveas_menuitem_activate):
	corrected a small bug that prevented the file names to be
	"selected" in the file selection window's file list according to
	the pattern "*.pxm" (completion feature of the GtkFileSelection
	object). 

	* polyxedit-ui-main-wnd.c (polyxedit_main_new_menuitem_activate):
	corrected a small bug that prevented the file names to be
	"selected" in the file selection window's file list according to
	the pattern "*.pxm" (completion feature of the GtkFileSelection
	object).

	* all.package : the polyxmass software suite's configuration
	directory is now in $(prefix)/etc/polyxmass.d. All required
	changes have been performed, in particular in
	polyxedit-config.c. 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 0.5.2

2003-07-15  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-main-wnd.c (polyxedit_main_open_menuitem_activate):
	corrected a small bug that prevented the file names to be
	"selected" in the file selection window's file list according to
	the pattern "*.pxm" (completion feature of the GtkFileSelection
	object).
	(polyxedit_main_open_menuitem_activate): made the sequence file
	selection window to be able to cope with multiple files selected.

2003-06-21  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-rw-polseq.c (polyxedit_rw_polseq_read_from_filesel):
	change the G_LOG_LEVEL from ERROR (abortion of the program) to
	WARNING so that when a polymer sequence file is not found the
	program does not exit abruptly. Now the program send a message to
	the console.
	(polyxedit_rw_polseq_read): exactly as above for
	polyxedit_rw_polseq_read_from_filesel.

	* polyxedit-main.c (main): added a loop to iterate in the command
	line parameters remaining after that the registered options were
	parsed by libpopt. These "leftover" parameters are considered to
	be polymer sequence files.

2003-06-18  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* release 0.5.1

2003-06-09  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxedit-ui-seqed-wnd.c
	(polyxedit_seqed_wnd_sel_polygon_event): corrected a bug due to
	not returning FALSE, so that the canvas did think that the
	redrawing was handled fully (which is not true). This modification
	was required after the project passed to using the 2.2 version of
	the Gtk+ library and dependencies.


/* GNU polyxmass - the massist's program.
   -------------------------------------- 
   Copyright (C) 2000,2001,2002 Filippo Rusconi

   http://www.polyxmass.org

   This file is part of the "GNU polyxmass" project.

   The "GNU polyxmass" project is an official GNU project (see
   www.gnu.org) released ---in its entirety--- under the GNU General
   Public License and was started at the Centre National de la
   Recherche Scientifique (FRANCE), that granted me the formal
   authorization to publish it under this Free Software License.

   This software is free software; you can redistribute it and/or
   modify it under the terms of the GNU  General Public
   License as published by the Free Software Foundation; either
   version 2 of the License, or (at your option) any later version.
   
   This software is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
   General Public License for more details.
   
   You should have received a copy of the GNU  General Public
   License along with this software; if not, write to the
   Free Software Foundation, Inc., 59 Temple Place - Suite 330,
   Boston, MA 02111-1307, USA.
*/
2004-07-24  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* configure.in (POLYXMASS_DATA_REQUIRED): changed requirement from
	0.7.0 to 0.7.1 since location of data files changed.

	* polyxcalc-config.c: changed user_polyxdef_cfg_file from
	".polyxmass.d/polyxcalc.conf" to ".polyxmass/polyxcalc.conf".

	* autogen.sh (CFLAGS): added switch --sysconfdir=/etc

	* Makefile.am (polyxcalcconf_datadir): now in
	$(sysconfdir)/polyxmass

	* configure.in (CONFDIR): changed the CONFDIR specification to
	point to $(sysconfdir)/polyxmass, with autogen and configure
	saying "--sysconfdir=/etc". 

2004-07-03  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.7.1

	* configure.in (LIBPOLYXMASS_REQUIRED): replaced the requirements
	for libpxmutils and libpxmchem with libpolyxmass, as now the two
	former libraries have been merged into one library: libpolyxmass.

	* polyxcalc-globals.h: changed the inclusion of header files for
	libraries libpxmutils and libpxmchem as now one library is used:
	#include <libpolyxmass/libpolyxmass.h>

	* whole_project: note that the library requirements for
	libpxmutils and libpxmchem did not changed from 0.7.0 to 0.7.1.
	
	* configure.in: switch AC_INIT(polyxcalc, 0.7.0, to
	AC_INIT(polyxcalc, 0.7.1,

	* polyxcalc-ui-main.c (polyxcalc_setup_app_wnd): big set of
	changes to comply with the ever-changing Gtk+
	libraries. GtkOptionMenu is no longer working as before, so I took
	profit of the changed to improve the way polyxcalc works (mainly
	replacing unintuitive option menus with buttons laid out correctly
	in the window). Added functionality to hide widgets when these are
	of no importance to the user, so that much space can be gained
	thus reducing the footprint of the program window.

2004-06-30  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxcalc-globals.c (polyxcalc_globals_timeout_message_set):
	changed gtk_timeout_add to g_timeout_add (due to upgrade of
	glib-2.0 and co libraries since last march).
	(polyxcalc_globals_timeout_message_stop): changed
	g_object_timeout_remove into g_source_remove (due to upgrade of
	glib-2.0 and co libraries since last march).
	

2004-03-24  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* whole_project: refactored the manner in which timed-out messages
	can be displayed in the messages_entry GtkEntry wiget. There is
	now a framework ready to be used easily that ensures that pending
	timed-out messages are removed before a window is closed. This way
	a number of crashes will be avoided when timed-out messages will
	be used later (for the moment this framework is not yet used).
	
2004-02-10  Filippo Rusconi  <filippo rusconi at nowhere dot org>
 
        * Release 0.7.0 without source code changes, only changes in the
	package. The release is aimed at synchronizing all the packages on
	the same value for the milestone Debian GNU/Linux. The tar.gz
	packages are now fully synchronized with the .deb packages and the
	$(package).spec.in file in the source tarball with which rpm
	packages should be able to be prepared.
 
2004-01-24  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.6.5

	* Full GNUification of the package. No source code change.

2004-01-03  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* configure.in (ALL_LINGUAS): added ALL_LINGUAS="fr" because
	automake would complain in $(srcdir) that this variable is not
	defined while still using gettext...

	* Makefile.in.in (MKINSTALLDIRS): changed that file in
	$(srcdir)/po so that the installation would not fail at make
	install target due to not finding the mkinstalldirs target. See
	the file proper for details.

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

	* Release 0.6.4 (just recompile with new libs).

	* configure.in Updated dependencies: LIB_PXMUTILS_REQUIRED=0.6.2
	LIB_PXMCHEM_REQUIRED=0.6.3 POLYXMASSDATA_REQUIRED=0.6.3


2003-11-10  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxcalc-globals.c (polyxcalc_globals_timeout_stop): corrected
	a bug that would crash the program if a timeout would be triggered
	after the window in which it was created was closed. That was a
	bad format of the call if (TRUE == G_IS_OBJECT (entry)) which was
	actually if (TRUE == G_IS_OBJECT (entry) == TRUE) -:(. Now seems
	to work.

2003-10-27  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.6.3 (just recompile with new libs).

2003-10-22  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxcalc-ui-main.c (polyxcalc_main_new_menuitem_activate):
	memory leak fixes using memprof. Small leaks, but leaks...

2003-10-19  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.6.2: just a recompilation with requirement of
	libpxmchem lib version 0.6.1 due to a bug in that library. No
	source code changes.

2003-10-17  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* configure.in: corrected small glitch that gave a bad config
	directory name in the summary (end of file;
	"${sysconfdir}/polyxmass.d" (which is /etc/polyxmass.d) instead of
	the directory actually computed in this same file:
	${CONFDIR}). Thanks to Austin Acton for pointing that glitch.

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

	* Release 0.6.1

2003-08-04  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxcalc-ui-main.c (polyxcalc_main_wnd_delete_event): removed a
	call to destroy the recorder window if it was still present, since
	this window is set as a full datum to the data of the window, with
	a destroying function to be called whenever the program is
	closed. This call made a core dump at each closing of the program
	which was harmless but inelegant.
	
2003-08-02  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxcalc-ui-chempad.c
	(polyxcalc_chempad_fill_chempadkey_array): removed this function
	and replace its functionality (with improvements) within a new
	function: polyxcalc_chempad_parse_file().
	(polyxcalc_chempad_wnd_fill_layout): now handles the case where
	only chempad_columns or chempad_rows is defined in the
	chempad.conf file. This way the layout is computed at best. It is
	no more required that both value be defined in the conf file, as
	this was heretical from a geometrical standpoint. The
	corresponding polyxmassdata/chempad.conf and
	polyxmassdata/protein/chempad.conf files were modified by removing
	the chempad_row$3 line, retaining the chempad_columns$3 line.

	* polyxcalc-ui-chempad.h (struct _PxmChempadgeom): added this
	structure to ease the handling of the chempad geometry.

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

	* Release 0.6.0

2003-07-22  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Makefile.am (INCLUDES): added -I$(prefix)/include.
	(polyxcalc_LDFLAGS): added -L$(prefix)/lib. Both changes to allow
	the package to find the header files of libpxmutils, for example,
	when this lib is installed in exotic places like /opt, for
	example.

2003-07-22  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxcalc-ui-main.c (polyxcalc_main_new_menuitem_activate):
	corrected a small bug that prevented the file names to be
	"selected" in the file selection window's file list according to
	the pattern "*.xml" (completion feature of the GtkFileSelection
	object). 

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

	* polyxcalc-calcmass.c (polxyxcalc_calcmass_account_sequence):
	corrected bug due to freeing two times the monomer GPA in case the
	polymer sequence could not be successfully parsed and made into an
	array of monomers (thanks to Mark Tracy for reporting this).

	* polyxcalc-ui-main.c (polyxcalc_setup_app_wnd): added code to set
	to sensitive=FALSE the polymer chemistry-specific frames when no
	poldef is passed to the window setup function. This is foolproof
	code.
	(polyxcalc_main_open_poldef_from_fileselection): If a new polymer
	chemistry definition file is successfully opened, and its data
	parsed, then ensure that the polymer chemistry-specific frames
	[monomers, modifications, sequence] are effectively made
	sensitive, since the user will be able to enter
	monomer/modif/sequence requirements.

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

	* release 0.5.2

	* corrected the dependencies with respect to the libpxmutils,
	libpxmchem and polyxmassdata packages.

2003-06-21  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxcalc-ui-main.c (polyxcalc_clear_all_chem_data_activate):
	added the code to ensure that the count entry related to the
	polymer sequence would also be reset to empty. This one did not
	get erased as all the other ones.

2003-06-18  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.5.1

	* polyxcalc-ui-main.c
	(polyxcalc_remove_initial_from_result_masses_activate): added this
	function that is symmetrical to the one that adds the initial to
	result.

2003-02-04  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxcalc-globals.h (polyxcalc_globals_copy_files): removed
	declaration of this function for which no definition was given,
	since it is actually pxmutils_globals_copy_files () in the
	libpxmutils library !



/* GNU polyxmass - the massist's program.
   -------------------------------------- 
   Copyright (C) 2000,2001,2002 Filippo Rusconi

   http://www.polyxmass.org

   This file is part of the "GNU polyxmass" project.

   The "GNU polyxmass" project is an official GNU project (see
   www.gnu.org) released ---in its entirety--- under the GNU General
   Public License and was started at the Centre National de la
   Recherche Scientifique (FRANCE), that granted me the formal
   authorization to publish it under this Free Software License.

   This software is free software; you can redistribute it and/or
   modify it under the terms of the GNU  General Public
   License as published by the Free Software Foundation; either
   version 2 of the License, or (at your option) any later version.
   
   This software is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
   General Public License for more details.
   
   You should have received a copy of the GNU  General Public
   License along with this software; if not, write to the
   Free Software Foundation, Inc., 59 Temple Place - Suite 330,
   Boston, MA 02111-1307, USA.
*/
2004-07-24  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* configure.in (POLYXMASS_DATA_REQUIRED): changed requirement from
	0.7.0 to 0.7.1 since location of data files changed.

	* polyxdef-config.c: changed user_polyxdef_cfg_file from
	".polyxmass.d/polyxdef.conf" to ".polyxmass/polyxdef.conf".

	* autogen.sh (CFLAGS): added switch --sysconfdir=/etc

	* Makefile.am (polyxdefconf_datadir): now in
	$(sysconfdir)/polyxmass

	* configure.in (CONFDIR): changed the CONFDIR specification to
	point to $(sysconfdir)/polyxmass, with autogen and configure
	saying "--sysconfdir=/etc".

2004-07-03  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.7.1

	* polyxdef-globals.h: changed the inclusion of header files for
	libraries libpxmutils/libpxmchem to the location of libpolyxmass'
	header files: #include <libpolyxmass/libpolyxmass.h>

	* configure.in: switch AC_INIT(polyxdef, 0.7.0, to
	AC_INIT(polyxdef, 0.7.1,

	* configure.in (LIBPOLYXMASS_REQUIRED): replaced the requirements
	for libpxmutils and libpxmchem with libpolyxmass, as now the two
	former libraries have been merged into one library: libpolyxmass.

2004-06-30  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxdef-globals.c (polyxdef_globals_timeout_message_set):
	changed gtk_object_timeout_add to g_timeout_add (due to upgrade of
	glib-2.0 and co libraries since last march).
	(polyxdef_globals_timeout_message_stop): changed
	g_object_timeout_remove into g_source_remove (due to upgrade of
	glib-2.0 and co libraries since last march).

2004-03-24  Filippo Rusconi  <filippo rusconi at nowhere dot org>
	
	* whole_project: refactored the manner in which timed-out messages
	can be displayed in the messages_entry GtkEntry wiget. There is
	now a framework ready to be used easily that ensures that pending
	timed-out messages are removed before a window is closed. This way
	a number of crashes are avoided. The crashes due to timing-out of
	messages displayed in a GtkEntry belonging to a no longer-existing
	window are the only crashes that I have encountered in the program
	so far.

2004-02-16  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxdef-ui-main.c (polyxdef_main_save_poldef_to_file):
	corrected the test that checked the return value out of the
	fputs() call to be compliant with the MacOSX platform. This bug
	already had been corrected in the polyxedit module, but for some
	reason now is creeping up in polyxdef. Now should be OK. Once
	again thanks to Mark Tracy for pointing that bug to me.

2004-02-10  Filippo Rusconi  <filippo rusconi at nowhere dot org>
 
        * Release 0.7.0 without source code changes, only changes in the
	package. The release is aimed at synchronizing all the packages on
	the same value for the milestone Debian GNU/Linux. The tar.gz
	packages are now fully synchronized with the .deb packages and the
	$(package).spec.in file in the source tarball with which rpm
	packages should be able to be prepared.
 
2004-01-24  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.6.5
	
	* GNUification of the package. No source code changes... Now the
	development is performed under Debian GNU/Linux unstable.

2004-01-03  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* configure.in (ALL_LINGUAS): added ALL_LINGUAS="fr" because
	automake would complain in $(srcdir) that this variable is not
	defined while still using gettext...

	* Makefile.in.in (MKINSTALLDIRS): change this file in $(srcdir)/po
	so that the make install target would not failed, not finding the
	mkinstalldirs script... See the file itself for details.

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

	* Release 0.6.4 (just a recompile with new libs.)

	* configure.in: dependencies updated LIB_PXMUTILS_REQUIRED=0.6.2
	LIB_PXMCHEM_REQUIRED=0.6.3 POLYXMASSDATA_REQUIRED=0.6.3

2003-11-10  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxdef-globals.c (polyxdef_globals_timeout_stop): corrected a
	bug that would crash the program if a timeout would be triggered
	after the window in which it was created was closed. That was a
	bad format of the call if (TRUE == G_IS_OBJECT (entry)) which was
	actually if (TRUE == G_IS_OBJECT (entry) == TRUE) -:(. Now seems
	to work.

2003-10-27  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.6.3 (just a recompile with new libs.)

	* Makefile.am (glade_files_DATA): Changed the file so that
	graphics files in the glade directory are automatically
	distributed.

2003-10-19  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.6.2: just a recompilation with requirement of
	libpxmchem lib version 0.6.1 due to a bug in that library. No
	source code changes.

2003-09-11  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Release 0.6.1

2003-10-17  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* configure.in: corrected small glitch that gave a bad config
	directory name in the summary (end of file;
	"${sysconfdir}/polyxmass.d" (which is /etc/polyxmass.d) instead of
	the directory actually computed in this same file:
	${CONFDIR}). Thanks to Austin Acton for pointing that glitch.

2003-08-31  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxdef-ui-poldef.c (polyxdef_setup_poldef_wnd): fixed a bug
	that was due to trying to access an inexistent ionizerule pointer
	in the PxmPoldef that was allocated with the New menu. 

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

	* Release 0.6.0

2003-07-23  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* polyxdef-globals.h: Changed include
	/usr/include/gtk-2.0/gdk/gdkkeysyms.h to gdk/gdkkeysyms.h (Thanks
	Mark Tracy for pointing this).

2003-07-22  Filippo Rusconi  <filippo rusconi at nowhere dot org>

	* Makefile.am (INCLUDES): added -I$(prefix)/include.
	(polyxdef_LDFLAGS): added -L$(prefix)/lib. Both changes to allow
	the package to find the header files of libpxmutils, for example,
	when this lib is installed in exotic places like /opt, for
	example.

	* polyxdef-ui-main.c (polyxdef_main_open_menuitem_activate):
	corrected a small ui bug by which the *.xml pattern was not
	correctly being completed in the file selection window.

	* all.package : the polyxmass software suite's configuration
	directory is now in $(prefix)/etc/polyxmass.d. All required
	changes have been performed, in particular in
	polyxdef-config.c. 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

	* Added this ChangeLog file. 



/* GNU polyxmass - the massist's program.
   -------------------------------------- 
   Copyright (C) 2000,2001,2002 Filippo Rusconi

   http://www.polyxmass.org

   This file is part of the "GNU polyxmass" project.

   The "GNU polyxmass" project is an official GNU project (see
   www.gnu.org) released ---in its entirety--- under the GNU General
   Public License and was started at the Centre National de la
   Recherche Scientifique (FRANCE), that granted me the formal
   authorization to publish it under this Free Software License.

   This software is free software; you can redistribute it and/or
   modify it under the terms of the GNU  General Public
   License as published by the Free Software Foundation; either
   version 2 of the License, or (at your option) any later version.
   
   This software is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
   General Public License for more details.
   
   You should have received a copy of the GNU  General Public
   License along with this software; if not, write to the
   Free Software Foundation, Inc., 59 Temple Place - Suite 330,
   Boston, MA 02111-1307, USA.
*/
