1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062
|
massxpert (3.6.1-1) unstable; urgency=low
* New upstream version: Fix programming error detected by using GCC-6.
Thanks to Lucas Nussbaum <lucas@debian.org> (Closes: 831089).
-- Filippo Rusconi <lopippo@debian.org> Tue, 19 Jul 2016 12:16:20 +0200
massxpert (3.6.0-1) unstable; urgency=medium
* New upstream version which modifies the way masses are calculated for
fragment oligomers so as to allow negative ionization mode
fragmentation experiments. The user needs to review the polymer
chemistry definitions so that they account for the new workings: the
formula of the fragmentation patterns needs to yield a neutral species
(typically by removing H from the original FragSpec formula: appending
-H to it should do). The ionization of the fragments is then performed
using the current ionization rule defined in the editor window of
massXpert. Updated the manual to document all these changes.
-- Filippo Rusconi <lopippo@debian.org> Sat, 19 Sep 2015 15:00:32 +0200
massxpert (3.5.0-2) unstable; urgency=medium
* Closes: #777998.
-- Filippo Rusconi <lopippo@debian.org> Thu, 09 Jul 2015 16:43:00 +0200
massxpert (3.5.0-1) unstable; urgency=medium
* Fixes to the code errors spotted by gcc-5.1.1 (20150622). Not closing
the bug number #777998 as requested by the reporter (Matthias Klose
<doko@debian.org>);
* New upstream version 3.5.0 with finished Qt5 port;
* Build-Depends: change to qtbase5-dev (>= 5.3.2+dfsg-5), libqt5svg5-dev
(>= 5.3.2-2), and cmake (>= 3.2.2-2);
* Standards-Version: bump up to 3.9.6. No changes needed;
* moved upstream to upstream/metadata (Thanks Andreas Tille, although I
had done this long ago, Mon Aug 18, without pushing, sadly).
-- Filippo Rusconi <lopippo@debian.org> Wed, 01 Jul 2015 22:37:23 +0200
massxpert (3.4.1-1) unstable; urgency=low
* This new package happens to close a bug which needed no fixes
(Closes: #701319)
* debian/control: set Standards-Version: 3.9.4
* debian/control: set standard vcs uri's
* debian/compat: set value 9 (hardening stuff automagically handled)
* debian/rules: update the hardening stuff according to using v9 of
debhelper
* debian/control: set debhelper dependency version to 9.20130630
* massxpert.desktop: Icon=massxpert-icon-32 (no extension for filename)
* massxpert.desktop: Categories=Science (one categ. only)
-- Filippo Rusconi <lopippo@debian.org> Mon, 01 Jul 2013 14:25:27 +0200
massxpert (3.4.0-2) UNRELEASED; urgency=medium
* Team upload
* Moved debian/upstream to debian/upstream/metadata
-- Andreas Tille <tille@debian.org> Fri, 31 Oct 2014 18:55:26 +0100
massxpert (3.4.0-1) unstable; urgency=low
* New upstream release:
- Implemented the primary selection clipboard copy in the sequence
editor window;
- Implemented feature that allows one to enter a coordinates string in
the sequence editor window so as to select a specific sequence or make
a multi-region selection or make a multi-selection region.
- Refactored the mz lab GUI so as to greatly simplify its use.
- Update of the french translation.
-- Filippo Rusconi <lopippo@debian.org> Tue, 25 Dec 2012 22:04:33 +0100
massxpert (3.3.0-1) unstable; urgency=low
* New upstream release implementing new ways to import mass data in the
m/z lists of the mzLab. Updated the documentation.
-- Filippo Rusconi <lopippo@debian.org> Tue, 04 Dec 2012 21:00:17 +0100
massxpert (3.2.4-1) unstable; urgency=low
* debian/control: add Build-Depends: dpkg-dev (>= 1.16.1~) as lintian
complained about transitive dependencies that should be made explicit.
* Added new modifications in the protein-1-letter chemistry definition.
-- Filippo Rusconi <lopippo@debian.org> Wed, 17 Oct 2012 20:37:47 +0200
massxpert (3.2.3-1) unstable; urgency=low
* debian/rules: setting DPKG_EXPORT_BUILDFLAGS=1 to implement the Debian
hardening guidelines.
* Modification in the dna.xml file to better document the photocleavable
biotin modification
-- Filippo Rusconi <lopippo@debian.org> Fri, 08 Jun 2012 11:09:47 +0200
massxpert (3.2.2-1) unstable; urgency=low
* Upstream release:
- Fix warning messages from gcc, complaining about set variable
values, but unused variables. Replaced corresponding Q_ASSERT() calls
to qFatal() ones.
-- Filippo Rusconi <lopippo@debian.org> Mon, 14 May 2012 17:28:42 +0200
massxpert (3.2.1-1) unstable; urgency=low
* Upstream release:
- fix a bug in the definition of the protein chemical modifications
TNB and DTNB;
* Add debian/upstream to document a reference to a paper describing this
software;
* Fix problem with failing symbolic link between the massxpert and -dbg
doc directories (lintian W binaries-have-file-conflict);
* Bump-up Standards Version number to 3.9.3 from 3.9.1.
-- Filippo Rusconi <lopippo@debian.org> Thu, 10 May 2012 15:57:45 +0200
massxpert (3.2.0-2) unstable; urgency=low
* debian/control: configure packaging for debug symbols (new
massxpert-dbg binary package added).
-- Filippo Rusconi <lopippo@debian.org> Thu, 24 Nov 2011 13:42:48 +0100
massxpert (3.2.0-1) unstable; urgency=low
* Upstream release:
- Added feature to simulate fragmentations of oligomers that contain
cross-links.
- Updated the user manual to document the new feature.
-- Filippo Rusconi <lopippo@debian.org> Sat, 22 Oct 2011 21:45:33 +0200
massxpert (3.1.0-1) unstable; urgency=low
* Upstream release:
- Updated the user manual since a long time, documenting part of the
features implemented since last manual update;
- Implemented automatic naming of XpertMiner input data dialog
windows;
- Implemented export of XpertMiner output data into new input data
dialog windows, so as to be able to chain calculations;
- Refactored isotopic cluster calculation code;
- Implemented a new spectrum calculation feature that simulates a
complete spectrum starting from a list of oligomers obtained by
cleavage of a polymer sequence. An isotopic cluster can be computed
for each oligomer in the list or not. If not, the mono or avg mass can
be used to compute the peak shape;
- Implemented a new spectrum calculation feature that simulates a
complete spectrum starting from a list of analytes obtained by
calculating a m/z ratio series with a elemental formula as the
starting point.
-- Filippo Rusconi <lopippo@debian.org> Mon, 29 Aug 2011 19:01:23 +0200
massxpert (3.0.0-1) unstable; urgency=low
* Upstream release:
- Major rework of the XpertMiner module;
- Bug fixes;
- Feature improvements.
-- Filippo Rusconi <lopippo@debian.org> Thu, 21 Jul 2011 22:51:24 +0200
massxpert (2.9.0-1) unstable; urgency=low
* New upstream release:
- Switched to the TableView data display method the whole XpertMiner
module. This allows for easier code maintaining and for clearer
graphical user interface.
- Refactored code in the MzLabInputOligomerTreeView class code to
improve quality and readability.
- Improved the XpertMiner window layout for more clarity.
- Added feature to call a calculator window right from the sequence
editor window with either whole/selected sequence masses preseeded.
-- Filippo Rusconi <lopippo@debian.org> Sun, 17 Jul 2011 18:43:48 +0200
massxpert (2.8.0-1) unstable; urgency=low
* New upstream release:
- Switched to the TableView mass search oligomer display (was using
TreeView);
-- Filippo Rusconi <lopippo@debian.org> Mon, 11 Jul 2011 14:52:08 +0200
massxpert (2.7.0-1) unstable; urgency=low
* New upstream release:
- Switched to the TableView fragmentation oligomer display (was using
TreeView);
- Added feature by which it is now possible to stack fragmentation
oligomers from different fragmentation calculations, thus providing a
way to have a single list of fragments calculated in different
ways.
-- Filippo Rusconi <lopippo@debian.org> Mon, 04 Jul 2011 22:47:50 +0200
massxpert (2.6.0-1) unstable; urgency=low
* New upstream release:
- Completely refactored the code for the isotopic cluster
simulator. Increased speed calculation by a factor ~8. In particular,
the simulator now handles handsomely the heavily-charged large
polymers. It can use the gaussian or the lorentzian mathemical model
to compute the curves.
-- Filippo Rusconi <lopippo@debian.org> Wed, 29 Jun 2011 07:48:37 +0200
massxpert (2.5.2-1) unstable; urgency=low
* New upstream release:
- Fix regression causing a crash when fragmenting oligomers in any
kind of situation. This fix is critical.
-- Filippo Rusconi <lopippo@debian.org> Mon, 06 Jun 2011 02:34:46 +0200
massxpert (2.5.1-1) unstable; urgency=low
* Modified the email address of the uploader to my debian address
lopippo@debian.org.
* Removed the DM-Upload-Allowed bit.
* New upstream release:
- Fix serious bug that crashed the program upon recleaving a polymer
within the same CleavageDlg window. That bug appeared related to the
upgrade of the Qt libraries as it crept without modifications of the
massXpert source code. The cleavage oligomers are now displayed in a
QTableView widget instead of a QTreeView widget which simplified a lot
both the code and the graphics display of the data.
- Fix problems with the reliability of the cleavage details that were
provided as feedback when an oligomer from the tree/table view was
selected.
-- Filippo Rusconi <lopippo@debian.org> Sun, 05 Jun 2011 19:08:29 +0200
massxpert (2.5.0-1) unstable; urgency=low
* New upstream release:
- Implement feature allowing one to apply formulas commonly found
during fragmentation, like loss of water or loss of ammonia, to each
fragment oligomer computed for any given fragmentation pattern.
-- Filippo Rusconi <rusconi-debian@laposte.net> Sun, 22 May 2011 21:25:17 +0200
massxpert (2.4.4-1) unstable; urgency=low
* New upstream release:
- Fix FTBFS with gcc-4.6 -Werror (this package builds with -Werror,
and GCC 4.6 triggers new warnings) reported by Matthias Klose
<doko@debian.org> (Closes: #625382).
-- Filippo Rusconi <rusconi-debian@laposte.net> Wed, 04 May 2011 22:50:03 +0200
massxpert (2.4.3-1) unstable; urgency=low
* Upstream release.
- Rewrote the Formula's elementalComposition() so that the order of
the atoms is in the CHNO->alphabetic conventional order;
- Added ion charge proton to the formula of the z fragmentation
specification;
- Added feature: when running the mz calculations dialog from the
sequence editor window, the masses are automatically set in the dialog
window
-- Filippo Rusconi <rusconi-debian@laposte.net> Sat, 19 Feb 2011 19:11:35 +0100
massxpert (2.4.2-1) unstable; urgency=low
* New upstream release:
- Fix bug (Closes: #611142) due to insufficient checking of the array
boundary upon clicking on the sequence editor outside of the vignettes.
- debian/control : Standards-Version: 3.9.1.
-- Filippo Rusconi <rusconi-debian@laposte.net> Tue, 25 Jan 2011 23:26:23 +0100
massxpert (2.4.1-1) unstable; urgency=low
* Fix bug due to returning false when should return a string. Thanks to
Mathias Klose <doko@ubuntu.com> for reporting the bug, and to Stéphane
Téletchéa <steletch@free.fr> for reporting the same in private
(Closes: #607723).
-- Filippo Rusconi <rusconi-debian@laposte.net> Tue, 04 Jan 2011 16:21:03 +0100
massxpert (2.4.0-1) unstable; urgency=low
* Upstream release:
- Monoisotopic mass is now the mass of the isotope of highest
abundance and not of lowest mass. This won't change anything for
biopolymers, as all the chemical elements used there have their
lightest isotope of highest abundance;
- Update the french translation;
- Add two peptide example files.
-- Filippo Rusconi <rusconi-debian@laposte.net> Fri, 10 Dec 2010 11:16:30 +0100
massxpert (2.3.6-1) unstable; urgency=low
* Upstream release:
- Add a warning when the user is trying a polymer cleavage on a region
not encompassing all the cross-linked monomers;
- Fix a linker flag for the MacOSX PPC build;
- Fix a GUI bug in the sequence editor window
(gui/monomerCodeEvaluator.cpp).
-- Filippo Rusconi <rusconi-debian@laposte.net> Mon, 10 May 2010 20:16:34 +0200
massxpert (2.3.5-1) unstable; urgency=low
* Upstream release:
- Add feature to compute the mass differences between any two monomers
in the polymer chemistry definition;
- Update the user manual to document the new feature.
-- Filippo Rusconi <rusconi-debian@laposte.net> Thu, 29 Apr 2010 15:13:50 +0200
massxpert (2.3.0-1) unstable; urgency=low
* Upstream release:
- Add feature to allow cleaving polymer sequences only in the
currently selected region of the sequence;
- Improvements in the GUI of the cleavage dialog window;
- Fix one bug in the constructor of the CalcOptions object, which
failed to correctly initialize the CoordinateList member data;
- Update the documentation (user manual) to describe the new cleavage
feature.
-- Filippo Rusconi <rusconi-debian@laposte.net> Tue, 27 Apr 2010 14:20:25 +0200
massxpert (2.2.0-1) unstable; urgency=low
* Upstream release:
- Fix bug with polymer sequence not saving a modified name in the
sequence editor window;
- Implemented a protein sequence importer for PDB cristallographic
data;
- Update the french translation;
-- Filippo Rusconi <rusconi-debian@laposte.net> Tue, 20 Apr 2010 22:37:24 +0200
massxpert (2.1.1-1) unstable; urgency=low
* Upstream release:
- Fix programming error: use of an uninitialised variable.
* debian/rules: remove the 'dh_desktop -a' call.
-- Filippo Rusconi <rusconi-debian@laposte.net> Wed, 13 Jan 2010 20:49:30 +0100
massxpert (2.1.0-1) unstable; urgency=low
* Upstream release:
- Show the current selection coordinates in the sequence editor window;
- Fixed nasty bug due to reusing freed memory. Interestingly, that bug
only showed up on MOSX;
- Code cleanup (amongs which a number of C-style casts were moved to
C++-reinterpret_cast's;
- Fix memory leaks;
- Fix programming style glitches.
-- Filippo Rusconi <rusconi-debian@laposte.net> Tue, 22 Dec 2009 15:44:58 +0100
massxpert (2.0.9-1) unstable; urgency=low
* Upstream release:
- Fixed a bug causing a crash in corner polymer cleavage cases.
* Switched to source format 3.0 (quilt);
-- Filippo Rusconi <rusconi-debian@laposte.net> Thu, 26 Nov 2009 20:51:48 +0100
massxpert (2.0.8-1) unstable; urgency=low
* New upstream release:
- data : fix dna polymer chemistry definition to include
phosphorothioates;
- Added feature to regularly recall to the user to cite massXpert in
the About dialog window;
- data: ix monomer definition for uracile;
- New version of the massxpert.spec taken from Thomas Spura
<tomspur@fedoraproject.org>
- data: added deuterium to atom definitions;
- Enable installing the plugins in a specific directory (to help with
distributions willing to put shared binaries in /usr/lib64);
- XpertMiner : fix potentially massive memory leaks. Thanks cppcheck;
- Code documentation and cleanup;
- XpertCalc: formulas that were added to the memory of the calculator
can now be removed;
- XpertCalc : implemented per polymer chemistry definition handling of
window geometry settings;
- data: mprove fragmentation definitions for dna;
- Fix bug due to not really checking the formula syntax while it was
reported as validated;
- Formulas now accept a double-quote-enclosed title and spaces.
* debian/copyright: add blurb about location of the GPL-3 license on
Debian systems.
-- Filippo Rusconi <rusconi-debian@laposte.net> Sat, 21 Nov 2009 20:04:21 +0100
massxpert (2.0.7-1) unstable; urgency=low
* New upstream release:
* Fix problem with version numbering in the previous release;
* Fix absence of the corresponding .orig.tar.gz (made erroneously a
native package).
-- Filippo Rusconi <rusconi-debian@laposte.net> Mon, 05 Oct 2009 22:54:42 +0200
massxpert (2.0.6.-1) unstable; urgency=low
* Upstream release:
- Fixes to nroff formatting of the man pages (thanks to Daniel Leidert
for suggestions);
- XpertCalc: added possibility to insert formulas in the formula line
edit by Ctrl-clicking buttons in the chemical keypad;
- XpertCalc: added possibility to surround formulas with spaces for
much better readability in case of complex structures. This is
performed by Shit-Ctrl-cliking on the chemical pad buttons;
- XpertCalc: automatically seed m/z calculation dialog window with
masses from the XpertCalc main window;
- XpertEdit: bug fix in the sequence editor's feedback to the user
upon entering a bad monomer code character. When a new valid character
is entered this old error message is removed;
- XpertCalc: added lots of useful buttons to the dna chemical pad
configuration file;
- Added bibliographical reference to the massXpert paper in
_Bioinformatics_ to the man pages;
- XpertCalc: added possibility to store formula in a drop-down list so
as to be able to recall them in ulterior calculations;
- XpertCalc: implemented new feature by which it is possible to set a
title to a formula like the following : "initial-dimer" C5H6O9P3,
which will be interpreted as formula "C5H6O9P3".
- Sequence editing plugins: added possibility to perform more
sophisticated translation, like from codon to 1-letter code or from
codon to 3-letters code (protein chemistry);
- XpertEdit: the tool box (available monomers/mass calculation engine
configuration) now saves its position;
- Improved the CMake-based build system to automatically build the
binary and the data if nothing is specified on the configuration
command line (usermanual is not built by default; thanks to Pere
Constans for reporting);
- Bunch of code tidying and memory leaks fixing (thanks to cppcheck,
as suggested by Pere Constans);
- XpertEdit: fixed wrong behaviour in the whole/selected sequence
logic in the mass search dialog window;
- XpertEdit: fixed the multi-character code disambiguation mechanism
in the sequence editor's available codes tool box widget: it's
triggered by hitting Ctrl-Enter;
- Xpertedit/XpertDef: improved feedback to the user on file save
operation errors;
- XpertEdit/XpertDef: added possibility to show non-*.mxp/non-*.xml
files in the openfile dialogs;
- XpertEdit: improved fragmentation with multiply-charged fragments:
When there are multiply-charged fragments, the mass now takes into
account the ionization rule that sits in the sequence editor windows's
calculation engine configuration.
- Added Doxygen configuration file. Docs generated outside of the
source tree.
- XpertEdit: fix bug in elementalComposition() that would fail when
count is negative. Added simplify() function that calls
elementalComposition() in turn. Also fixed the way atomCount objects
are added to the list of such objects : when an atomCount object
reaches a 0-count, it gets removed from the list.
- XpertCalc: added possibility to simplify a complex set of formulas
into a single factorized formula.
-- Filippo Rusconi <rusconi-debian@laposte.net> Mon, 05 Oct 2009 10:55:32 +0200
massxpert (2.0.5-1) unstable; urgency=low
* Upstream release:
- Bug fix release : one serious bug was fixed, whereby the program
would crash upon re-cleaving a polymer sequence in the same cleavage
dialog window. This bug was already present (and silent) in previous
versions, but became crash-inducing upon upgrade of the version of the
Qt libraries from 4.4.x (x=3, if I recall correctly) to present
version 4.5.2.
-- Filippo Rusconi <rusconi-debian@laposte.net> Fri, 18 Sep 2009 13:49:13 +0200
massxpert (2.0.4-1) unstable; urgency=low
* Upstream release:
- Performed an extensive cleaning work on the messages to the user and
in the GUI messages. Updated the french translation accordingly. Fixes
in the GUI stuff itself (like setting line edit widgets to read-only
where necessary);
- XpertCalc: allow pasting the chempad's button's formula in the
formula line edit widget instead of immediately accounting it in the
results masses;
- XpertCalc: remove spaces from the formula entered in the calculator
window;
- XpertCalc: rework the chemical pad specification to allow grouping
of buttons and their coloring along with coloring of the group boxes;
- XpertCalc: update all the chemical pad configuration files of the
distribution to the new format (chem_pad.conf files);
- User manual: update to document the new features of the calculator;
- XpertCalc: fixed a bug due to not really clearing seed/result masses
when later using the chemical pad;
* massxpert.1 man page: specify better the location of the GPL-3 file on
Debian systems.
* Bump Standards-Version to 3.8.3.
* debian/rules: remove the CFLAGS = -Wall -g setting as it is already set.
* debian/rules: change CFLAGS to CXXFLAGS.
-- Filippo Rusconi <rusconi-debian@laposte.net> Tue, 01 Sep 2009 15:45:56 +0200
massxpert (2.0.3-1) unstable; urgency=low
* debian/control: Rename binary package from massxpert-bin to massxpert
and remove Section: science field (inherits from the source package);
* debian/control: Move all the Build-Depends-Indep dependencies
(texlive-latex-recommended,qtexlive-fonts-recommended) to
Build-Depends dependencies (Closes: #528086) to work around the
builders bug. For more details, see bugs:
- Bug #528086: massxpert_2.0.0-1(mips/unstable): FTBFS:
missing build dependency
- Bug #521918: pbuilder --build --binary-arch invokes 'build' target.
* debian/control: Remove no more required Build-Depends-Indep
latex-related cm-super-minimal package (thanks to removing
dependencies in the UseLATEX.cmake file;
* debian/control: Add Vcs-Git and Vcs-Browser fields;
* debian/control: Set Uploaders to Filippo Rusconi
<rusconi-debian@laposte.net>;
* debian/control: Set Maintainer to The Debichem Group
<debichem-devel@lists.alioth.debian.org>;
* debian/rules: Remove old unused variables;
* debian/rules: Fully separated the arch/indep targets which build and
install stuff in different directories;
* debian/rules: .PHONY targets are now individually specified (so as not
to forget them when targets change);
* debian/control: remove unrequired Build-Depends-Indep packages;
* debian/watch: added file;
* debian/control: massxpert-bin to massxpert renaming:
Conflict/Replace massxpert-bin
* New upstream release (worked a lot with Lionel Elie Mamane):
- gui/massxpert_fr.ts: updated the french translation;
- usermanual/front-matter.tex & usermanual/massxpert.tex: remove user
manual dependency on LaTeX package "textcomp", so as not to embed
Type3 fonts in the PDF file. Replaced (C) with \copyright. Small
typographical fixes.
- usermanual/UseLATEX.cmake: remove other non-essential software
requirements to reduce dependencies;
-- Filippo Rusconi <rusconi-debian@laposte.net> Wed, 10 Jun 2009 14:33:04 +0200
massxpert (2.0.2-1) UNRELEASED; urgency=low
* New upstream release (worked a lot with Lionel Elie Mamane):
- usermanual/CMakeLists.txt: remove the "-Werror" flag as almost any
LaTeX compilation produces warnings;
- gui/application.cpp: set sensible values for the default decimal
places to use to display numerical data on the first program run;
- usermanual/UseLATEX.cmake: update Copyright notice to reflect the
fact that the file was modified by me;
- lib/configSettings.cpp: remove unncessary configuration settings
feedback messages, other improvements;
- gui/main.cpp: remove unnecessary feedback for the loading of
translation files;
- Added 'Close' button to aboutDlg dialog window.
-- Filippo Rusconi <rusconi-debian@laposte.net> Fri, 15 May 2009 18:00:22 +0200
massxpert (2.0.1-1) UNRELEASED; urgency=low
* New upstream release: bug fix release and other improvements.
- Clean source tree;
- lib/configSettings.cpp: fix typo (thanks Lionel Mamane);
- Modify usermanual build process to use UseLATEX.cmake;
- Fix bug due to not taking into account the locale while making
textual mass lists starting from oligomer items in treeviews.
- Fix locale-specific input/output inconsistencies;
- Improved the simulations' result export as text;
- usermanual/UseLATEX.cmake: removed the requirement of
/usr/bin/convert from ImageMagick as we do not need it: using pdflatex
and only png-format graphics files;
-- Filippo Rusconi <rusconi-debian@laposte.net> Wed, 15 Apr 2009 21:17:17 +0200
massxpert (2.0.0-1) unstable; urgency=low
* Standards version is 3.8.1.
* Bumped debian/compat to 7.
* Entirely reworked debian/rules, which now has build-arch and
build-indep fully separated targets totally fitting the Build-Depends
and Build-Depends-Indep fields of debian/control.
* New upstream release:
- Fixed bug in XpertDef due to not verifying upon removal of a
modification if it is used by a cross-linker. Crashes. Report by Ron
Bakus (UCSD domain edu).
- Fixed bug with storing polymer sequences and polymer chemistry
definitions with crippled XML;
- Added configurability to the number of decimal places used to
display values for pH/pKa, atoms/isotopes, oligomers, polymers;
- Fixed regression with un-cross-linking;
- Fixed bug with calculation of right-end fragment boundaries;
- Big work within the XpertMiner module;
- Huge internal work with the ionization paradigm in particular within
the fragmentation framework.
* Fixes with the debian/* so that the source package now build three
packages: massxpert-bin, massxpert-data, massxpert-doc.
* A bunch of improvements in the Debian packaging thanks to Lionel
Mamane mentoring (parallel support in rules and others).
* Sponsored upload done by Lionel Elie Mamane <lmamane@debian.org>
-- Filippo Rusconi <rusconi-debian@laposte.net> Tue, 31 Mar 2009 23:06:14 +0200
massxpert (1.7.8-1) unstable; urgency=low
* New upstream release:
- Implemented multi-cleavages;
- Updated the User Manual
-- Filippo Rusconi <massxpert-maintainer@massxpert.org> Tue, 08 Jul 2008 13:09:31 +0200
massxpert (1.7.7-1) unstable; urgency=low
* New upstream release:
- Implemented multi-region selections;
- Updated the User Manual.
-- Filippo Rusconi <massxpert-maintainer@massxpert.org> Fri, 04 Jul 2008 13:35:35 +0200
massxpert (1.7.6-1) unstable; urgency=low
* New upstream release:
- Moved the project to GNU GPL version 3;
- Fixes for GUI bugs;
- Fixes with the localization of double values in the GUI;
- First implementation of the mzLab (still experimental feature);
- Classes rework with better handling of ionization throughout the whole project;
- Code cleanup, better handling of constness in the whole project;
- Updated the User Manual.
-- Filippo Rusconi <massxpert-maintainer@massxpert.org> Wed, 28 May 2008 15:18:37 +0200
massxpert (1.7.5-1) unstable; urgency=low
* New upstream release:
- Code cleanup throughout the code redesign of some classes and addition
of Ion class;
- Implemented namespace massXpert throughout the project;
- Update of the french translation;
- Bug fixes;
-- Filippo Rusconi <massxpert-maintainer@massxpert.org> Thu, 24 Apr 2008 21:12:56 +0200
massxpert (1.7.4-1) unstable; urgency=low
* New upstream release:
- Implemented new means to define fragmentation specifications that
involve the decomposition of the fragmented monomer's side chain;
- Fixed memory leak and bugs;
- Updated the french translation and the user manual.
-- Filippo Rusconi <massxpert-maintainer@massxpert.org> Wed, 02 Apr 2008 22:59:50 +0200
massxpert (1.7.3-1) unstable; urgency=low
* Upstream release with main new feature: the filtering implemented for
the previous version was extended also for the fragmentation and mass
searching oligomer data;
* Improved the use of the filtering feature thanks to modifications in
the graphical user interface;
* Implemented check that a cross-link name cannot be used already as a
modification name (and vice versa);
* Fixes to regressions that crept in during last version developments
and code cleanup;
* Update of the documentation;
-- Filippo Rusconi <massxpert-maintainer@massxpert.org> Sun, 30 Mar 2008 17:34:27 +0200
massxpert (1.7.2-1) unstable; urgency=low
* Upstream release with main new figure: the oligomer data from a
polymer sequence cleavage might be filtered live and in-place using a
sortingProxy treeview (powerful feature of the Qt library);
* User manual update;
* Minor bugfixes.
-- Filippo Rusconi <massxpert-maintainer@massxpert.org> Tue, 25 Mar 2008 22:11:17 +0100
massxpert (1.7.1-1) unstable; urgency=low
* Upstream release with main new feature: intra-molecular cross-links.
* Bug fixes and small improvements here and there.
* Modified dh_shlibs line to exclude the plugins from the scan, as these
are private libraries with no SONAME.
-- Filippo Rusconi <massxpert-maintainer@massxpert.org> Tue, 18 Mar 2008 22:24:36 +0100
massxpert (1.7.0-1) unstable; urgency=low
* Upstream bug-fix release.
* Fixed crash caused by elemental compositions calculations using
manually-defined polymer sequence modifications (thanks to as
calculations session with Fatima Boutimah in my lab);
* Modified the polymer sequence file format so as to be able to save
polymer sequence modifications with a fully qualified <mdf> (see
polChemDef format) element. This allows storing the modifications with
full qualification (and not only name) even when the modification is
manually-defined.
* Added man massxpert-doc.7 page documenting the User manual.
-- Filippo Rusconi <massxpert-maintainer@massxpert.org> Thu, 21 Feb 2008 14:28:55 +0100
massxpert (1.6.9-1) unstable; urgency=low
* Upstream release with more flexible monomer modification procedure
(big inner code changes not visible by the user).
* Update the documentation.
* Extended copyright to 2008.
-- Filippo Rusconi <massxpert-maintainer@massxpert.org> Fri, 15 Feb 2008 10:48:49 +0100
massxpert (1.6.8-1) unstable; urgency=low
* Upstream release with some small modifications in the debian packaging
(massxpert.1 man page an massxpert.desktop are installed differently
so that these files might also be used when generating rpm packages);
* The user manual now installs properly in /usr/share/doc/massxpert-doc
and not /usr/share/doc/massxpert, as was the case before. Also, the
user manual was updated so as to reflect the new polymer chemistry
definition GUI design.
* Removed the lintian override file, as I finally found why two of the
three plugins would make lintian complain about
shlib-with-non-pic-code.
* Fully rewritten the polymer chemistry definition graphical interface.
* Some bug fixes here and there.
-- Filippo Rusconi <massxpert-maintainer@massxpert.org> Tue, 18 Dec 2007 11:39:06 +0100
massxpert (1.6.7-1) unstable; urgency=low
* Upstream release with the following modifications:
* CMake'ization of the source tree.
* Fixed bug with calculation net charges with any given pH.
* Standards-Version: 3.7.2
-- Filippo Rusconi <massxpert-maintainer@massxpert.org> Sun, 09 Dec 2007 18:40:55 +0100
massxpert (1.6.6-1) unstable; urgency=low
* Upstream release with the following modifications:
* Update the french translation and the user manual to reflect the
new features of the cleavage- and fragmentation-base oligomer
generation.
* The oligomers from cleavage and fragmentation might now be calculated
as multi-charged oligomers
* Implemented the fragmentation stuff in new class MxpFragmenter and
removed the corresponding code from the fragmentation dialog
class. Also, made the same use of QList<MxpOligomerList *> * instead
of two nested QList objects as previously performed with the cleavage
code in the fragmentation code.
* Implemented ionization level ranges for oligomers, starting with the
cleavage application bits
* Reimplemented the gui polymer sequence cleaving stuff to use the
modified MxpCleaver object
* Reimplemented the cleaver object to use the new oligomer list object
* Implemented and added to library 'list of oligomers' new class:
MxpOligomerList derived from QList<MxpOligomer *>
-- Filippo Rusconi <massxpert-maintainer@massxpert.org> Sun, 23 Sep 2007 14:26:47 +0200
massxpert (1.6.5-1) unstable; urgency=low
* Upstream release with the following modifications:
* Added possibiliy to restrict monomer modifications to given
monomers. If the user tries to modify a monomer with a modification
that is not supported for it, the modification does not occur and the
user gets a message. Implemented a mechanism by which these monomer
modification limitations can be overridden.
* Fixed bug with parsing atom symbols with more than 2 characters.
* Added fake atoms so as to to allow defining formulas with precise
masses.
* Fixed bug with creation of default monomer modification vignette and
setting it to the hash with a bad key. That would lead to bad
reference counting and crashes upon unmodification of more than one
modified monomer.
* Better feedback messages to the sequence editor window's statusBar
while doing initial sequence drawing.
* Updated french translation.
* Reverted to version 2 of the GPL as the Qt libraries are not using the
'version 2 or any later version' wording.
-- Filippo Rusconi <massxpert-maintainer@polyxmass.org> Sun, 19 Aug 2007 16:51:09 +0200
massxpert (1.6.4-1) unstable; urgency=low
* Upstream release with the following modifications:
* Translated the application into french. Took advantage of the
translation work to uniformize the messages and the labels on the UI
widgets.
* Bug fixes with modifications declared in some polymer chemisty
definitions but not available as graphics files or not registered in
the modification_dictionary.
* Added default modification vignette, so that when a modification
is defined without assigning a corresponding vignette the program
does not crash.
* Switch to 4.3.0 for MS-Windows also.
* Minor bugfixes
-- Filippo Rusconi <massxpert-maintainer@polyxmass.org> Tue, 24 Jul 2007 22:06:00 +0200
massxpert (1.6.3-1) unstable; urgency=low
* New upstream release.
* Fixed glitches in some fields of the debian/control file.
* Fixed problems with the modification vignettes and declarations of
modifications in the modification_dictionary of some polymer
chemistry definition.
* Many improvements in the user manual.
* Improved handling of polymer sequence modifications.
* Improvements the GUI and in the calculator recorder output.
* Added possibility to modify a polymer sequence arbitrarily by
entering a chemical formula and not by choosing a modification in
the polymer chemistry definition.
* Switch to 4.3.0 as the Qt dependency, which showed some glitches
in the handling of the sequence editor graphics view that were
fixed.
-- Filippo Rusconi <massxpert-maintainer@polyxmass.org> Thu, 19 Jul 2007 14:55:47 +0200
massxpert (1.6.1-1) unstable; urgency=low
* Added new feature to the XpertEdit module: a mass list
laboratory. Updated the documentation.
-- Filippo Rusconi <massxpert-maintainer@massxpert.org> Sun, 1 Jul 2007 18:49:17 +0200
massxpert (1.6.0-rc2-1) unstable; urgency=low
* Initial release.
-- Filippo Rusconi <massxpert-maintainer@massxpert.org> Sun, 1 Jul 2007 18:49:17 +0200
|