1massxpert (3.6.1-1) unstable; urgency=low 2 3 * New upstream version: Fix programming error detected by using GCC-6. 4 Thanks to Lucas Nussbaum <lucas@debian.org> (Closes: 831089). 5 6 -- Filippo Rusconi <lopippo@debian.org> Tue, 19 Jul 2016 12:16:20 +0200 7 8massxpert (3.6.0-1) unstable; urgency=medium 9 10 * New upstream version which modifies the way masses are calculated for 11 fragment oligomers so as to allow negative ionization mode 12 fragmentation experiments. The user needs to review the polymer 13 chemistry definitions so that they account for the new workings: the 14 formula of the fragmentation patterns needs to yield a neutral species 15 (typically by removing H from the original FragSpec formula: appending 16 -H to it should do). The ionization of the fragments is then performed 17 using the current ionization rule defined in the editor window of 18 massXpert. Updated the manual to document all these changes. 19 20 -- Filippo Rusconi <lopippo@debian.org> Sat, 19 Sep 2015 15:00:32 +0200 21 22massxpert (3.5.0-2) unstable; urgency=medium 23 24 * Closes: #777998. 25 26 -- Filippo Rusconi <lopippo@debian.org> Thu, 09 Jul 2015 16:43:00 +0200 27 28massxpert (3.5.0-1) unstable; urgency=medium 29 30 * Fixes to the code errors spotted by gcc-5.1.1 (20150622). Not closing 31 the bug number #777998 as requested by the reporter (Matthias Klose 32 <doko@debian.org>); 33 34 * New upstream version 3.5.0 with finished Qt5 port; 35 36 * Build-Depends: change to qtbase5-dev (>= 5.3.2+dfsg-5), libqt5svg5-dev 37 (>= 5.3.2-2), and cmake (>= 3.2.2-2); 38 39 * Standards-Version: bump up to 3.9.6. No changes needed; 40 41 * moved upstream to upstream/metadata (Thanks Andreas Tille, although I 42 had done this long ago, Mon Aug 18, without pushing, sadly). 43 44 -- Filippo Rusconi <lopippo@debian.org> Wed, 01 Jul 2015 22:37:23 +0200 45 46massxpert (3.4.1-1) unstable; urgency=low 47 48 * This new package happens to close a bug which needed no fixes 49 (Closes: #701319) 50 * debian/control: set Standards-Version: 3.9.4 51 * debian/control: set standard vcs uri's 52 * debian/compat: set value 9 (hardening stuff automagically handled) 53 * debian/rules: update the hardening stuff according to using v9 of 54 debhelper 55 * debian/control: set debhelper dependency version to 9.20130630 56 * massxpert.desktop: Icon=massxpert-icon-32 (no extension for filename) 57 * massxpert.desktop: Categories=Science (one categ. only) 58 59 -- Filippo Rusconi <lopippo@debian.org> Mon, 01 Jul 2013 14:25:27 +0200 60 61massxpert (3.4.0-2) UNRELEASED; urgency=medium 62 63 * Team upload 64 * Moved debian/upstream to debian/upstream/metadata 65 66 -- Andreas Tille <tille@debian.org> Fri, 31 Oct 2014 18:55:26 +0100 67 68massxpert (3.4.0-1) unstable; urgency=low 69 70 * New upstream release: 71 72 - Implemented the primary selection clipboard copy in the sequence 73 editor window; 74 75 - Implemented feature that allows one to enter a coordinates string in 76 the sequence editor window so as to select a specific sequence or make 77 a multi-region selection or make a multi-selection region. 78 79 - Refactored the mz lab GUI so as to greatly simplify its use. 80 81 - Update of the french translation. 82 83 -- Filippo Rusconi <lopippo@debian.org> Tue, 25 Dec 2012 22:04:33 +0100 84 85massxpert (3.3.0-1) unstable; urgency=low 86 87 * New upstream release implementing new ways to import mass data in the 88 m/z lists of the mzLab. Updated the documentation. 89 90 -- Filippo Rusconi <lopippo@debian.org> Tue, 04 Dec 2012 21:00:17 +0100 91 92massxpert (3.2.4-1) unstable; urgency=low 93 94 * debian/control: add Build-Depends: dpkg-dev (>= 1.16.1~) as lintian 95 complained about transitive dependencies that should be made explicit. 96 97 * Added new modifications in the protein-1-letter chemistry definition. 98 99 -- Filippo Rusconi <lopippo@debian.org> Wed, 17 Oct 2012 20:37:47 +0200 100 101massxpert (3.2.3-1) unstable; urgency=low 102 103 * debian/rules: setting DPKG_EXPORT_BUILDFLAGS=1 to implement the Debian 104 hardening guidelines. 105 106 * Modification in the dna.xml file to better document the photocleavable 107 biotin modification 108 109 -- Filippo Rusconi <lopippo@debian.org> Fri, 08 Jun 2012 11:09:47 +0200 110 111massxpert (3.2.2-1) unstable; urgency=low 112 113 * Upstream release: 114 115 - Fix warning messages from gcc, complaining about set variable 116 values, but unused variables. Replaced corresponding Q_ASSERT() calls 117 to qFatal() ones. 118 119 -- Filippo Rusconi <lopippo@debian.org> Mon, 14 May 2012 17:28:42 +0200 120 121massxpert (3.2.1-1) unstable; urgency=low 122 123 * Upstream release: 124 125 - fix a bug in the definition of the protein chemical modifications 126 TNB and DTNB; 127 128 * Add debian/upstream to document a reference to a paper describing this 129 software; 130 * Fix problem with failing symbolic link between the massxpert and -dbg 131 doc directories (lintian W binaries-have-file-conflict); 132 * Bump-up Standards Version number to 3.9.3 from 3.9.1. 133 134 -- Filippo Rusconi <lopippo@debian.org> Thu, 10 May 2012 15:57:45 +0200 135 136massxpert (3.2.0-2) unstable; urgency=low 137 138 * debian/control: configure packaging for debug symbols (new 139 massxpert-dbg binary package added). 140 141 -- Filippo Rusconi <lopippo@debian.org> Thu, 24 Nov 2011 13:42:48 +0100 142 143massxpert (3.2.0-1) unstable; urgency=low 144 145 * Upstream release: 146 147 - Added feature to simulate fragmentations of oligomers that contain 148 cross-links. 149 150 - Updated the user manual to document the new feature. 151 152 -- Filippo Rusconi <lopippo@debian.org> Sat, 22 Oct 2011 21:45:33 +0200 153 154massxpert (3.1.0-1) unstable; urgency=low 155 156 * Upstream release: 157 158 - Updated the user manual since a long time, documenting part of the 159 features implemented since last manual update; 160 161 - Implemented automatic naming of XpertMiner input data dialog 162 windows; 163 164 - Implemented export of XpertMiner output data into new input data 165 dialog windows, so as to be able to chain calculations; 166 167 - Refactored isotopic cluster calculation code; 168 169 - Implemented a new spectrum calculation feature that simulates a 170 complete spectrum starting from a list of oligomers obtained by 171 cleavage of a polymer sequence. An isotopic cluster can be computed 172 for each oligomer in the list or not. If not, the mono or avg mass can 173 be used to compute the peak shape; 174 175 - Implemented a new spectrum calculation feature that simulates a 176 complete spectrum starting from a list of analytes obtained by 177 calculating a m/z ratio series with a elemental formula as the 178 starting point. 179 180 -- Filippo Rusconi <lopippo@debian.org> Mon, 29 Aug 2011 19:01:23 +0200 181 182massxpert (3.0.0-1) unstable; urgency=low 183 184 * Upstream release: 185 186 - Major rework of the XpertMiner module; 187 - Bug fixes; 188 - Feature improvements. 189 190 -- Filippo Rusconi <lopippo@debian.org> Thu, 21 Jul 2011 22:51:24 +0200 191 192massxpert (2.9.0-1) unstable; urgency=low 193 194 * New upstream release: 195 196 - Switched to the TableView data display method the whole XpertMiner 197 module. This allows for easier code maintaining and for clearer 198 graphical user interface. 199 200 - Refactored code in the MzLabInputOligomerTreeView class code to 201 improve quality and readability. 202 203 - Improved the XpertMiner window layout for more clarity. 204 205 - Added feature to call a calculator window right from the sequence 206 editor window with either whole/selected sequence masses preseeded. 207 208 -- Filippo Rusconi <lopippo@debian.org> Sun, 17 Jul 2011 18:43:48 +0200 209 210massxpert (2.8.0-1) unstable; urgency=low 211 212 * New upstream release: 213 214 - Switched to the TableView mass search oligomer display (was using 215 TreeView); 216 217 -- Filippo Rusconi <lopippo@debian.org> Mon, 11 Jul 2011 14:52:08 +0200 218 219massxpert (2.7.0-1) unstable; urgency=low 220 221 * New upstream release: 222 223 - Switched to the TableView fragmentation oligomer display (was using 224 TreeView); 225 226 - Added feature by which it is now possible to stack fragmentation 227 oligomers from different fragmentation calculations, thus providing a 228 way to have a single list of fragments calculated in different 229 ways. 230 231 -- Filippo Rusconi <lopippo@debian.org> Mon, 04 Jul 2011 22:47:50 +0200 232 233massxpert (2.6.0-1) unstable; urgency=low 234 235 * New upstream release: 236 237 - Completely refactored the code for the isotopic cluster 238 simulator. Increased speed calculation by a factor ~8. In particular, 239 the simulator now handles handsomely the heavily-charged large 240 polymers. It can use the gaussian or the lorentzian mathemical model 241 to compute the curves. 242 243 -- Filippo Rusconi <lopippo@debian.org> Wed, 29 Jun 2011 07:48:37 +0200 244 245massxpert (2.5.2-1) unstable; urgency=low 246 247 * New upstream release: 248 249 - Fix regression causing a crash when fragmenting oligomers in any 250 kind of situation. This fix is critical. 251 252 -- Filippo Rusconi <lopippo@debian.org> Mon, 06 Jun 2011 02:34:46 +0200 253 254massxpert (2.5.1-1) unstable; urgency=low 255 256 * Modified the email address of the uploader to my debian address 257 lopippo@debian.org. 258 * Removed the DM-Upload-Allowed bit. 259 260 * New upstream release: 261 262 - Fix serious bug that crashed the program upon recleaving a polymer 263 within the same CleavageDlg window. That bug appeared related to the 264 upgrade of the Qt libraries as it crept without modifications of the 265 massXpert source code. The cleavage oligomers are now displayed in a 266 QTableView widget instead of a QTreeView widget which simplified a lot 267 both the code and the graphics display of the data. 268 269 - Fix problems with the reliability of the cleavage details that were 270 provided as feedback when an oligomer from the tree/table view was 271 selected. 272 273 -- Filippo Rusconi <lopippo@debian.org> Sun, 05 Jun 2011 19:08:29 +0200 274 275massxpert (2.5.0-1) unstable; urgency=low 276 277 * New upstream release: 278 279 - Implement feature allowing one to apply formulas commonly found 280 during fragmentation, like loss of water or loss of ammonia, to each 281 fragment oligomer computed for any given fragmentation pattern. 282 283 -- Filippo Rusconi <rusconi-debian@laposte.net> Sun, 22 May 2011 21:25:17 +0200 284 285massxpert (2.4.4-1) unstable; urgency=low 286 287 * New upstream release: 288 289 - Fix FTBFS with gcc-4.6 -Werror (this package builds with -Werror, 290 and GCC 4.6 triggers new warnings) reported by Matthias Klose 291 <doko@debian.org> (Closes: #625382). 292 293 -- Filippo Rusconi <rusconi-debian@laposte.net> Wed, 04 May 2011 22:50:03 +0200 294 295massxpert (2.4.3-1) unstable; urgency=low 296 297 * Upstream release. 298 299 - Rewrote the Formula's elementalComposition() so that the order of 300 the atoms is in the CHNO->alphabetic conventional order; 301 302 - Added ion charge proton to the formula of the z fragmentation 303 specification; 304 305 - Added feature: when running the mz calculations dialog from the 306 sequence editor window, the masses are automatically set in the dialog 307 window 308 309 -- Filippo Rusconi <rusconi-debian@laposte.net> Sat, 19 Feb 2011 19:11:35 +0100 310 311massxpert (2.4.2-1) unstable; urgency=low 312 313 * New upstream release: 314 315 - Fix bug (Closes: #611142) due to insufficient checking of the array 316 boundary upon clicking on the sequence editor outside of the vignettes. 317 318 - debian/control : Standards-Version: 3.9.1. 319 320 -- Filippo Rusconi <rusconi-debian@laposte.net> Tue, 25 Jan 2011 23:26:23 +0100 321 322massxpert (2.4.1-1) unstable; urgency=low 323 324 * Fix bug due to returning false when should return a string. Thanks to 325 Mathias Klose <doko@ubuntu.com> for reporting the bug, and to Stéphane 326 Téletchéa <steletch@free.fr> for reporting the same in private 327 (Closes: #607723). 328 329 -- Filippo Rusconi <rusconi-debian@laposte.net> Tue, 04 Jan 2011 16:21:03 +0100 330 331massxpert (2.4.0-1) unstable; urgency=low 332 333 * Upstream release: 334 335 - Monoisotopic mass is now the mass of the isotope of highest 336 abundance and not of lowest mass. This won't change anything for 337 biopolymers, as all the chemical elements used there have their 338 lightest isotope of highest abundance; 339 340 - Update the french translation; 341 342 - Add two peptide example files. 343 344 -- Filippo Rusconi <rusconi-debian@laposte.net> Fri, 10 Dec 2010 11:16:30 +0100 345 346massxpert (2.3.6-1) unstable; urgency=low 347 348 * Upstream release: 349 350 - Add a warning when the user is trying a polymer cleavage on a region 351 not encompassing all the cross-linked monomers; 352 353 - Fix a linker flag for the MacOSX PPC build; 354 355 - Fix a GUI bug in the sequence editor window 356 (gui/monomerCodeEvaluator.cpp). 357 358 -- Filippo Rusconi <rusconi-debian@laposte.net> Mon, 10 May 2010 20:16:34 +0200 359 360massxpert (2.3.5-1) unstable; urgency=low 361 362 * Upstream release: 363 364 - Add feature to compute the mass differences between any two monomers 365 in the polymer chemistry definition; 366 367 - Update the user manual to document the new feature. 368 369 -- Filippo Rusconi <rusconi-debian@laposte.net> Thu, 29 Apr 2010 15:13:50 +0200 370 371massxpert (2.3.0-1) unstable; urgency=low 372 373 * Upstream release: 374 375 - Add feature to allow cleaving polymer sequences only in the 376 currently selected region of the sequence; 377 378 - Improvements in the GUI of the cleavage dialog window; 379 380 - Fix one bug in the constructor of the CalcOptions object, which 381 failed to correctly initialize the CoordinateList member data; 382 383 - Update the documentation (user manual) to describe the new cleavage 384 feature. 385 386 -- Filippo Rusconi <rusconi-debian@laposte.net> Tue, 27 Apr 2010 14:20:25 +0200 387 388massxpert (2.2.0-1) unstable; urgency=low 389 390 * Upstream release: 391 392 - Fix bug with polymer sequence not saving a modified name in the 393 sequence editor window; 394 395 - Implemented a protein sequence importer for PDB cristallographic 396 data; 397 398 - Update the french translation; 399 400 -- Filippo Rusconi <rusconi-debian@laposte.net> Tue, 20 Apr 2010 22:37:24 +0200 401 402massxpert (2.1.1-1) unstable; urgency=low 403 404 * Upstream release: 405 - Fix programming error: use of an uninitialised variable. 406 407 * debian/rules: remove the 'dh_desktop -a' call. 408 409 -- Filippo Rusconi <rusconi-debian@laposte.net> Wed, 13 Jan 2010 20:49:30 +0100 410 411massxpert (2.1.0-1) unstable; urgency=low 412 413 * Upstream release: 414 415 - Show the current selection coordinates in the sequence editor window; 416 417 - Fixed nasty bug due to reusing freed memory. Interestingly, that bug 418 only showed up on MOSX; 419 420 - Code cleanup (amongs which a number of C-style casts were moved to 421 C++-reinterpret_cast's; 422 423 - Fix memory leaks; 424 425 - Fix programming style glitches. 426 427 -- Filippo Rusconi <rusconi-debian@laposte.net> Tue, 22 Dec 2009 15:44:58 +0100 428 429massxpert (2.0.9-1) unstable; urgency=low 430 431 * Upstream release: 432 433 - Fixed a bug causing a crash in corner polymer cleavage cases. 434 435 * Switched to source format 3.0 (quilt); 436 437 -- Filippo Rusconi <rusconi-debian@laposte.net> Thu, 26 Nov 2009 20:51:48 +0100 438 439massxpert (2.0.8-1) unstable; urgency=low 440 441 * New upstream release: 442 443 - data : fix dna polymer chemistry definition to include 444 phosphorothioates; 445 446 - Added feature to regularly recall to the user to cite massXpert in 447 the About dialog window; 448 449 - data: ix monomer definition for uracile; 450 451 - New version of the massxpert.spec taken from Thomas Spura 452 <tomspur@fedoraproject.org> 453 454 - data: added deuterium to atom definitions; 455 456 - Enable installing the plugins in a specific directory (to help with 457 distributions willing to put shared binaries in /usr/lib64); 458 459 - XpertMiner : fix potentially massive memory leaks. Thanks cppcheck; 460 461 - Code documentation and cleanup; 462 463 - XpertCalc: formulas that were added to the memory of the calculator 464 can now be removed; 465 466 - XpertCalc : implemented per polymer chemistry definition handling of 467 window geometry settings; 468 469 - data: mprove fragmentation definitions for dna; 470 471 - Fix bug due to not really checking the formula syntax while it was 472 reported as validated; 473 474 - Formulas now accept a double-quote-enclosed title and spaces. 475 476 * debian/copyright: add blurb about location of the GPL-3 license on 477 Debian systems. 478 479 480 -- Filippo Rusconi <rusconi-debian@laposte.net> Sat, 21 Nov 2009 20:04:21 +0100 481 482massxpert (2.0.7-1) unstable; urgency=low 483 484 * New upstream release: 485 486 * Fix problem with version numbering in the previous release; 487 488 * Fix absence of the corresponding .orig.tar.gz (made erroneously a 489 native package). 490 491 -- Filippo Rusconi <rusconi-debian@laposte.net> Mon, 05 Oct 2009 22:54:42 +0200 492 493 494massxpert (2.0.6.-1) unstable; urgency=low 495 496 * Upstream release: 497 498 - Fixes to nroff formatting of the man pages (thanks to Daniel Leidert 499 for suggestions); 500 501 - XpertCalc: added possibility to insert formulas in the formula line 502 edit by Ctrl-clicking buttons in the chemical keypad; 503 504 - XpertCalc: added possibility to surround formulas with spaces for 505 much better readability in case of complex structures. This is 506 performed by Shit-Ctrl-cliking on the chemical pad buttons; 507 508 - XpertCalc: automatically seed m/z calculation dialog window with 509 masses from the XpertCalc main window; 510 511 - XpertEdit: bug fix in the sequence editor's feedback to the user 512 upon entering a bad monomer code character. When a new valid character 513 is entered this old error message is removed; 514 515 - XpertCalc: added lots of useful buttons to the dna chemical pad 516 configuration file; 517 518 - Added bibliographical reference to the massXpert paper in 519 _Bioinformatics_ to the man pages; 520 521 - XpertCalc: added possibility to store formula in a drop-down list so 522 as to be able to recall them in ulterior calculations; 523 524 - XpertCalc: implemented new feature by which it is possible to set a 525 title to a formula like the following : "initial-dimer" C5H6O9P3, 526 which will be interpreted as formula "C5H6O9P3". 527 528 - Sequence editing plugins: added possibility to perform more 529 sophisticated translation, like from codon to 1-letter code or from 530 codon to 3-letters code (protein chemistry); 531 532 - XpertEdit: the tool box (available monomers/mass calculation engine 533 configuration) now saves its position; 534 535 - Improved the CMake-based build system to automatically build the 536 binary and the data if nothing is specified on the configuration 537 command line (usermanual is not built by default; thanks to Pere 538 Constans for reporting); 539 540 - Bunch of code tidying and memory leaks fixing (thanks to cppcheck, 541 as suggested by Pere Constans); 542 543 - XpertEdit: fixed wrong behaviour in the whole/selected sequence 544 logic in the mass search dialog window; 545 546 - XpertEdit: fixed the multi-character code disambiguation mechanism 547 in the sequence editor's available codes tool box widget: it's 548 triggered by hitting Ctrl-Enter; 549 550 - Xpertedit/XpertDef: improved feedback to the user on file save 551 operation errors; 552 553 - XpertEdit/XpertDef: added possibility to show non-*.mxp/non-*.xml 554 files in the openfile dialogs; 555 556 - XpertEdit: improved fragmentation with multiply-charged fragments: 557 When there are multiply-charged fragments, the mass now takes into 558 account the ionization rule that sits in the sequence editor windows's 559 calculation engine configuration. 560 561 - Added Doxygen configuration file. Docs generated outside of the 562 source tree. 563 564 - XpertEdit: fix bug in elementalComposition() that would fail when 565 count is negative. Added simplify() function that calls 566 elementalComposition() in turn. Also fixed the way atomCount objects 567 are added to the list of such objects : when an atomCount object 568 reaches a 0-count, it gets removed from the list. 569 570 - XpertCalc: added possibility to simplify a complex set of formulas 571 into a single factorized formula. 572 573 574 -- Filippo Rusconi <rusconi-debian@laposte.net> Mon, 05 Oct 2009 10:55:32 +0200 575 576 577massxpert (2.0.5-1) unstable; urgency=low 578 579 * Upstream release: 580 581 - Bug fix release : one serious bug was fixed, whereby the program 582 would crash upon re-cleaving a polymer sequence in the same cleavage 583 dialog window. This bug was already present (and silent) in previous 584 versions, but became crash-inducing upon upgrade of the version of the 585 Qt libraries from 4.4.x (x=3, if I recall correctly) to present 586 version 4.5.2. 587 588 -- Filippo Rusconi <rusconi-debian@laposte.net> Fri, 18 Sep 2009 13:49:13 +0200 589 590 591massxpert (2.0.4-1) unstable; urgency=low 592 593 * Upstream release: 594 595 - Performed an extensive cleaning work on the messages to the user and 596 in the GUI messages. Updated the french translation accordingly. Fixes 597 in the GUI stuff itself (like setting line edit widgets to read-only 598 where necessary); 599 600 - XpertCalc: allow pasting the chempad's button's formula in the 601 formula line edit widget instead of immediately accounting it in the 602 results masses; 603 604 - XpertCalc: remove spaces from the formula entered in the calculator 605 window; 606 607 - XpertCalc: rework the chemical pad specification to allow grouping 608 of buttons and their coloring along with coloring of the group boxes; 609 610 - XpertCalc: update all the chemical pad configuration files of the 611 distribution to the new format (chem_pad.conf files); 612 613 - User manual: update to document the new features of the calculator; 614 615 - XpertCalc: fixed a bug due to not really clearing seed/result masses 616 when later using the chemical pad; 617 618 * massxpert.1 man page: specify better the location of the GPL-3 file on 619 Debian systems. 620 621 * Bump Standards-Version to 3.8.3. 622 623 * debian/rules: remove the CFLAGS = -Wall -g setting as it is already set. 624 625 * debian/rules: change CFLAGS to CXXFLAGS. 626 627 -- Filippo Rusconi <rusconi-debian@laposte.net> Tue, 01 Sep 2009 15:45:56 +0200 628 629 630massxpert (2.0.3-1) unstable; urgency=low 631 632 * debian/control: Rename binary package from massxpert-bin to massxpert 633 and remove Section: science field (inherits from the source package); 634 635 * debian/control: Move all the Build-Depends-Indep dependencies 636 (texlive-latex-recommended,qtexlive-fonts-recommended) to 637 Build-Depends dependencies (Closes: #528086) to work around the 638 builders bug. For more details, see bugs: 639 640 - Bug #528086: massxpert_2.0.0-1(mips/unstable): FTBFS: 641 missing build dependency 642 643 - Bug #521918: pbuilder --build --binary-arch invokes 'build' target. 644 645 * debian/control: Remove no more required Build-Depends-Indep 646 latex-related cm-super-minimal package (thanks to removing 647 dependencies in the UseLATEX.cmake file; 648 649 * debian/control: Add Vcs-Git and Vcs-Browser fields; 650 651 * debian/control: Set Uploaders to Filippo Rusconi 652 <rusconi-debian@laposte.net>; 653 654 * debian/control: Set Maintainer to The Debichem Group 655 <debichem-devel@lists.alioth.debian.org>; 656 657 * debian/rules: Remove old unused variables; 658 659 * debian/rules: Fully separated the arch/indep targets which build and 660 install stuff in different directories; 661 662 * debian/rules: .PHONY targets are now individually specified (so as not 663 to forget them when targets change); 664 665 * debian/control: remove unrequired Build-Depends-Indep packages; 666 667 * debian/watch: added file; 668 669 * debian/control: massxpert-bin to massxpert renaming: 670 Conflict/Replace massxpert-bin 671 672 * New upstream release (worked a lot with Lionel Elie Mamane): 673 674 - gui/massxpert_fr.ts: updated the french translation; 675 676 - usermanual/front-matter.tex & usermanual/massxpert.tex: remove user 677 manual dependency on LaTeX package "textcomp", so as not to embed 678 Type3 fonts in the PDF file. Replaced (C) with \copyright. Small 679 typographical fixes. 680 681 - usermanual/UseLATEX.cmake: remove other non-essential software 682 requirements to reduce dependencies; 683 684 -- Filippo Rusconi <rusconi-debian@laposte.net> Wed, 10 Jun 2009 14:33:04 +0200 685 686massxpert (2.0.2-1) UNRELEASED; urgency=low 687 688 * New upstream release (worked a lot with Lionel Elie Mamane): 689 690 - usermanual/CMakeLists.txt: remove the "-Werror" flag as almost any 691 LaTeX compilation produces warnings; 692 693 - gui/application.cpp: set sensible values for the default decimal 694 places to use to display numerical data on the first program run; 695 696 - usermanual/UseLATEX.cmake: update Copyright notice to reflect the 697 fact that the file was modified by me; 698 - lib/configSettings.cpp: remove unncessary configuration settings 699 feedback messages, other improvements; 700 701 - gui/main.cpp: remove unnecessary feedback for the loading of 702 translation files; 703 704 - Added 'Close' button to aboutDlg dialog window. 705 706 -- Filippo Rusconi <rusconi-debian@laposte.net> Fri, 15 May 2009 18:00:22 +0200 707 708massxpert (2.0.1-1) UNRELEASED; urgency=low 709 710 * New upstream release: bug fix release and other improvements. 711 712 - Clean source tree; 713 714 - lib/configSettings.cpp: fix typo (thanks Lionel Mamane); 715 716 - Modify usermanual build process to use UseLATEX.cmake; 717 718 - Fix bug due to not taking into account the locale while making 719 textual mass lists starting from oligomer items in treeviews. 720 721 - Fix locale-specific input/output inconsistencies; 722 723 - Improved the simulations' result export as text; 724 725 - usermanual/UseLATEX.cmake: removed the requirement of 726 /usr/bin/convert from ImageMagick as we do not need it: using pdflatex 727 and only png-format graphics files; 728 729 -- Filippo Rusconi <rusconi-debian@laposte.net> Wed, 15 Apr 2009 21:17:17 +0200 730 731massxpert (2.0.0-1) unstable; urgency=low 732 733 * Standards version is 3.8.1. 734 735 * Bumped debian/compat to 7. 736 737 * Entirely reworked debian/rules, which now has build-arch and 738 build-indep fully separated targets totally fitting the Build-Depends 739 and Build-Depends-Indep fields of debian/control. 740 741 * New upstream release: 742 743 - Fixed bug in XpertDef due to not verifying upon removal of a 744 modification if it is used by a cross-linker. Crashes. Report by Ron 745 Bakus (UCSD domain edu). 746 747 - Fixed bug with storing polymer sequences and polymer chemistry 748 definitions with crippled XML; 749 750 - Added configurability to the number of decimal places used to 751 display values for pH/pKa, atoms/isotopes, oligomers, polymers; 752 753 - Fixed regression with un-cross-linking; 754 755 - Fixed bug with calculation of right-end fragment boundaries; 756 757 - Big work within the XpertMiner module; 758 759 - Huge internal work with the ionization paradigm in particular within 760 the fragmentation framework. 761 762 * Fixes with the debian/* so that the source package now build three 763 packages: massxpert-bin, massxpert-data, massxpert-doc. 764 765 * A bunch of improvements in the Debian packaging thanks to Lionel 766 Mamane mentoring (parallel support in rules and others). 767 768 * Sponsored upload done by Lionel Elie Mamane <lmamane@debian.org> 769 770 -- Filippo Rusconi <rusconi-debian@laposte.net> Tue, 31 Mar 2009 23:06:14 +0200 771 772massxpert (1.7.8-1) unstable; urgency=low 773 774 * New upstream release: 775 776 - Implemented multi-cleavages; 777 778 - Updated the User Manual 779 780 -- Filippo Rusconi <massxpert-maintainer@massxpert.org> Tue, 08 Jul 2008 13:09:31 +0200 781 782massxpert (1.7.7-1) unstable; urgency=low 783 784 * New upstream release: 785 786 - Implemented multi-region selections; 787 788 - Updated the User Manual. 789 790 -- Filippo Rusconi <massxpert-maintainer@massxpert.org> Fri, 04 Jul 2008 13:35:35 +0200 791 792massxpert (1.7.6-1) unstable; urgency=low 793 794 * New upstream release: 795 796 - Moved the project to GNU GPL version 3; 797 798 - Fixes for GUI bugs; 799 800 - Fixes with the localization of double values in the GUI; 801 802 - First implementation of the mzLab (still experimental feature); 803 804 - Classes rework with better handling of ionization throughout the whole project; 805 806 - Code cleanup, better handling of constness in the whole project; 807 808 - Updated the User Manual. 809 810 -- Filippo Rusconi <massxpert-maintainer@massxpert.org> Wed, 28 May 2008 15:18:37 +0200 811 812massxpert (1.7.5-1) unstable; urgency=low 813 814 * New upstream release: 815 816 - Code cleanup throughout the code redesign of some classes and addition 817 of Ion class; 818 819 - Implemented namespace massXpert throughout the project; 820 821 - Update of the french translation; 822 823 - Bug fixes; 824 825 -- Filippo Rusconi <massxpert-maintainer@massxpert.org> Thu, 24 Apr 2008 21:12:56 +0200 826 827massxpert (1.7.4-1) unstable; urgency=low 828 829 * New upstream release: 830 831 - Implemented new means to define fragmentation specifications that 832 involve the decomposition of the fragmented monomer's side chain; 833 834 - Fixed memory leak and bugs; 835 836 - Updated the french translation and the user manual. 837 838 -- Filippo Rusconi <massxpert-maintainer@massxpert.org> Wed, 02 Apr 2008 22:59:50 +0200 839 840massxpert (1.7.3-1) unstable; urgency=low 841 842 * Upstream release with main new feature: the filtering implemented for 843 the previous version was extended also for the fragmentation and mass 844 searching oligomer data; 845 846 * Improved the use of the filtering feature thanks to modifications in 847 the graphical user interface; 848 849 * Implemented check that a cross-link name cannot be used already as a 850 modification name (and vice versa); 851 852 * Fixes to regressions that crept in during last version developments 853 and code cleanup; 854 855 * Update of the documentation; 856 857 -- Filippo Rusconi <massxpert-maintainer@massxpert.org> Sun, 30 Mar 2008 17:34:27 +0200 858 859massxpert (1.7.2-1) unstable; urgency=low 860 861 * Upstream release with main new figure: the oligomer data from a 862 polymer sequence cleavage might be filtered live and in-place using a 863 sortingProxy treeview (powerful feature of the Qt library); 864 865 * User manual update; 866 867 * Minor bugfixes. 868 869 -- Filippo Rusconi <massxpert-maintainer@massxpert.org> Tue, 25 Mar 2008 22:11:17 +0100 870 871massxpert (1.7.1-1) unstable; urgency=low 872 873 * Upstream release with main new feature: intra-molecular cross-links. 874 875 * Bug fixes and small improvements here and there. 876 877 * Modified dh_shlibs line to exclude the plugins from the scan, as these 878 are private libraries with no SONAME. 879 880 -- Filippo Rusconi <massxpert-maintainer@massxpert.org> Tue, 18 Mar 2008 22:24:36 +0100 881 882massxpert (1.7.0-1) unstable; urgency=low 883 884 * Upstream bug-fix release. 885 886 * Fixed crash caused by elemental compositions calculations using 887 manually-defined polymer sequence modifications (thanks to as 888 calculations session with Fatima Boutimah in my lab); 889 890 * Modified the polymer sequence file format so as to be able to save 891 polymer sequence modifications with a fully qualified <mdf> (see 892 polChemDef format) element. This allows storing the modifications with 893 full qualification (and not only name) even when the modification is 894 manually-defined. 895 896 * Added man massxpert-doc.7 page documenting the User manual. 897 898 -- Filippo Rusconi <massxpert-maintainer@massxpert.org> Thu, 21 Feb 2008 14:28:55 +0100 899 900massxpert (1.6.9-1) unstable; urgency=low 901 902 * Upstream release with more flexible monomer modification procedure 903 (big inner code changes not visible by the user). 904 905 * Update the documentation. 906 907 * Extended copyright to 2008. 908 909 -- Filippo Rusconi <massxpert-maintainer@massxpert.org> Fri, 15 Feb 2008 10:48:49 +0100 910 911massxpert (1.6.8-1) unstable; urgency=low 912 913 * Upstream release with some small modifications in the debian packaging 914 (massxpert.1 man page an massxpert.desktop are installed differently 915 so that these files might also be used when generating rpm packages); 916 917 * The user manual now installs properly in /usr/share/doc/massxpert-doc 918 and not /usr/share/doc/massxpert, as was the case before. Also, the 919 user manual was updated so as to reflect the new polymer chemistry 920 definition GUI design. 921 922 * Removed the lintian override file, as I finally found why two of the 923 three plugins would make lintian complain about 924 shlib-with-non-pic-code. 925 926 * Fully rewritten the polymer chemistry definition graphical interface. 927 928 * Some bug fixes here and there. 929 930 -- Filippo Rusconi <massxpert-maintainer@massxpert.org> Tue, 18 Dec 2007 11:39:06 +0100 931 932massxpert (1.6.7-1) unstable; urgency=low 933 934 * Upstream release with the following modifications: 935 936 * CMake'ization of the source tree. 937 938 * Fixed bug with calculation net charges with any given pH. 939 940 * Standards-Version: 3.7.2 941 942 -- Filippo Rusconi <massxpert-maintainer@massxpert.org> Sun, 09 Dec 2007 18:40:55 +0100 943 944massxpert (1.6.6-1) unstable; urgency=low 945 946 * Upstream release with the following modifications: 947 948 * Update the french translation and the user manual to reflect the 949 new features of the cleavage- and fragmentation-base oligomer 950 generation. 951 952 * The oligomers from cleavage and fragmentation might now be calculated 953 as multi-charged oligomers 954 955 * Implemented the fragmentation stuff in new class MxpFragmenter and 956 removed the corresponding code from the fragmentation dialog 957 class. Also, made the same use of QList<MxpOligomerList *> * instead 958 of two nested QList objects as previously performed with the cleavage 959 code in the fragmentation code. 960 961 * Implemented ionization level ranges for oligomers, starting with the 962 cleavage application bits 963 * Reimplemented the gui polymer sequence cleaving stuff to use the 964 modified MxpCleaver object 965 * Reimplemented the cleaver object to use the new oligomer list object 966 967 * Implemented and added to library 'list of oligomers' new class: 968 MxpOligomerList derived from QList<MxpOligomer *> 969 970 -- Filippo Rusconi <massxpert-maintainer@massxpert.org> Sun, 23 Sep 2007 14:26:47 +0200 971 972massxpert (1.6.5-1) unstable; urgency=low 973 974 * Upstream release with the following modifications: 975 976 * Added possibiliy to restrict monomer modifications to given 977 monomers. If the user tries to modify a monomer with a modification 978 that is not supported for it, the modification does not occur and the 979 user gets a message. Implemented a mechanism by which these monomer 980 modification limitations can be overridden. 981 982 * Fixed bug with parsing atom symbols with more than 2 characters. 983 984 * Added fake atoms so as to to allow defining formulas with precise 985 masses. 986 987 * Fixed bug with creation of default monomer modification vignette and 988 setting it to the hash with a bad key. That would lead to bad 989 reference counting and crashes upon unmodification of more than one 990 modified monomer. 991 992 * Better feedback messages to the sequence editor window's statusBar 993 while doing initial sequence drawing. 994 995 * Updated french translation. 996 997 * Reverted to version 2 of the GPL as the Qt libraries are not using the 998 'version 2 or any later version' wording. 999 1000 -- Filippo Rusconi <massxpert-maintainer@polyxmass.org> Sun, 19 Aug 2007 16:51:09 +0200 1001 1002massxpert (1.6.4-1) unstable; urgency=low 1003 1004 * Upstream release with the following modifications: 1005 1006 * Translated the application into french. Took advantage of the 1007 translation work to uniformize the messages and the labels on the UI 1008 widgets. 1009 1010 * Bug fixes with modifications declared in some polymer chemisty 1011 definitions but not available as graphics files or not registered in 1012 the modification_dictionary. 1013 1014 * Added default modification vignette, so that when a modification 1015 is defined without assigning a corresponding vignette the program 1016 does not crash. 1017 1018 * Switch to 4.3.0 for MS-Windows also. 1019 1020 * Minor bugfixes 1021 1022 -- Filippo Rusconi <massxpert-maintainer@polyxmass.org> Tue, 24 Jul 2007 22:06:00 +0200 1023 1024massxpert (1.6.3-1) unstable; urgency=low 1025 1026 * New upstream release. 1027 1028 * Fixed glitches in some fields of the debian/control file. 1029 1030 * Fixed problems with the modification vignettes and declarations of 1031 modifications in the modification_dictionary of some polymer 1032 chemistry definition. 1033 1034 * Many improvements in the user manual. 1035 1036 * Improved handling of polymer sequence modifications. 1037 1038 * Improvements the GUI and in the calculator recorder output. 1039 1040 * Added possibility to modify a polymer sequence arbitrarily by 1041 entering a chemical formula and not by choosing a modification in 1042 the polymer chemistry definition. 1043 1044 * Switch to 4.3.0 as the Qt dependency, which showed some glitches 1045 in the handling of the sequence editor graphics view that were 1046 fixed. 1047 1048 -- Filippo Rusconi <massxpert-maintainer@polyxmass.org> Thu, 19 Jul 2007 14:55:47 +0200 1049 1050massxpert (1.6.1-1) unstable; urgency=low 1051 1052 * Added new feature to the XpertEdit module: a mass list 1053 laboratory. Updated the documentation. 1054 1055 -- Filippo Rusconi <massxpert-maintainer@massxpert.org> Sun, 1 Jul 2007 18:49:17 +0200 1056 1057massxpert (1.6.0-rc2-1) unstable; urgency=low 1058 1059 * Initial release. 1060 1061 -- Filippo Rusconi <massxpert-maintainer@massxpert.org> Sun, 1 Jul 2007 18:49:17 +0200 1062 1063