i2masschroq (0.4.54-1) unstable; urgency=low * This is a new package (source and binary ones) that is an exact replicate of xtpcpp but with the name change to i2MassChroQ. This name change is required because of the publication that is being prepared to describe this software by this new name. -- Filippo Rusconi Fri, 18 Mar 2022 11:20:45 +0100 xtpcp (0.4.53-1) unstable; urgency=low * New package to ensure non-source-only upload (xtpcpp-tools is new). -- Filippo Rusconi Wed, 16 Mar 2022 21:40:28 +0100 xtpcpp (0.4.52-1) unstable; urgency=low * New upstream version depending on libpappsomspp >= 0.8.49. * Added a new command line tool. * New xtpcpp-tools package replacing the xtpcpp-tandemwrapper. * Written new user manual section and improved others. -- Filippo Rusconi Wed, 16 Mar 2022 16:01:28 +0100 xtpcpp (0.4.51-1) unstable; urgency=medium * New upstream release now building on top of libpappsomspp 0.8.48 (Closes: #1005151, thanks to Adrian Bunk ). [ Filippo Rusconi ] * betterment of the whole manual * rename the binary package from tandemwrapper to xtpcpp-tandemwrapper [ Olivier Langella ] * replacement of old sax based XML parsers for tandem presets and HTCondor * new test on XML parsers * new formula column added in the peptide ODS output -- Filippo Rusconi Wed, 09 Feb 2022 15:33:40 +0100 xtpcpp (0.4.49-1~bullseye1) bullseye; urgency=medium [ Olivier Langella ] * gui label fix * duplicated xml group ids in proticdbml fixed thanks to Kevin ROGER [ Filippo Rusconi ] * going forward with the user manual, almost done -- Olivier Langella Thu, 13 Jan 2022 09:32:56 +0100 xtpcpp (0.4.48-1~bullseye1) bullseye; urgency=medium * fix XIC reextract bug -- Olivier Langella Tue, 11 Jan 2022 09:31:29 +0100 xtpcpp (0.4.47-1~bullseye1) bullseye; urgency=medium * refactoring MCQ settings for timsTOF * select R binary path in preferences * fix grantlee plugin problem for win64 installation thanks to Kevin ROGER -- Olivier Langella Fri, 07 Jan 2022 09:12:11 +0100 xtpcpp (0.4.46-1~bullseye2) bullseye; urgency=medium * fix mess between xtpcpp and tandemwrapper install instructions -- Olivier Langella Mon, 03 Jan 2022 11:07:56 +0100 xtpcpp (0.4.46-1~bullseye1) bullseye; urgency=medium [ Olivier Langella ] * tandemwrapper added to xtpcpp distribution * new tandem parser, fix for tdf sample name * remove quantile filter integration for timsTOF pro * lots of fix to integrate R process into xtpcpp: basic XIC analysis available in production [ Filippo Rusconi ] * going forward with the user manual -- Olivier Langella Mon, 03 Jan 2022 09:26:54 +0100 xtpcpp (0.4.45-1~bullseye1) bullseye; urgency=medium [ Olivier Langella ] * display ion sequence in peptide detail status bar [ Filippo Rusconi ] * going forward with the user manual -- Olivier Langella Tue, 21 Dec 2021 08:56:40 +0100 xtpcpp (0.4.44-1~bullseye1) bullseye; urgency=medium [ Olivier Langella ] * fix fragment ion tags bearing phospho acid loss [ Filippo Rusconi ] * going forward with the user manual (phophoproteomics) -- Olivier Langella Thu, 16 Dec 2021 13:25:05 +0100 xtpcpp (0.4.43-2~bullseye1) bullseye; urgency=medium * new libpappsomspp library -- Olivier Langella Sat, 11 Dec 2021 16:29:18 +0100 xtpcpp (0.4.43-1~bullseye1) bullseye; urgency=medium * new package for bullseye -- Olivier Langella Fri, 26 Nov 2021 15:08:12 +0100 xtpcpp (0.4.43-1) unstable; urgency=low * New upstream release (see below). * d/control and company: Add required dependencies for the user manual and all the d/ to package and ship the user manual. * The package xtpcpp-doc now ships the user manual in HTML and PDF formats. * d/watch: add the file pointing to the forgemia GitLab instance. * d/control: add graphviz to build deps for the dot binary. * Standards-Version: 4.6.0 -- Filippo Rusconi Fri, 12 Nov 2021 16:32:16 +0100 xtpcpp (0.4.42-1~buster1) buster; urgency=medium * better tandem run wrapper progression windows * fix issue #73 * new support for timsTOF compression type 1 -- Olivier Langella Fri, 05 Nov 2021 16:36:57 +0100 xtpcpp (0.4.41-1~buster1) buster; urgency=medium * MCQR intergration work * display and export ion mobility informations -- Olivier Langella Tue, 05 Oct 2021 15:38:42 +0200 xtpcpp (0.4.40-2~buster1) buster; urgency=medium * a bit of refactoring to ensure MCQR dialog on MassChroQ data -- Olivier Langella Sat, 25 Sep 2021 06:47:04 +0200 xtpcpp (0.4.40-1~buster1) buster; urgency=medium * fix MassChroQ process control problem -- Olivier Langella Fri, 24 Sep 2021 09:01:27 +0200 xtpcpp (0.4.39-1~buster1) buster; urgency=medium * better MCQR integration added by Thomas Renne * output format added for MassChroQ v2.4 -- Olivier Langella Wed, 15 Sep 2021 14:36:02 +0200 xtpcpp (0.4.38-1~buster1) buster; urgency=medium * MCQR statistics on spectral count data available (https://forgemia.inra.fr/pappso/xtpcpp/-/merge_requests/57) , Thomas Renne -- Olivier Langella Tue, 24 Aug 2021 16:18:37 +0200 xtpcpp (0.4.37-1~buster1) buster; urgency=medium * Specific sequence count bug fixed (introduced in 0.4.35) -- Olivier Langella Wed, 21 Jul 2021 14:59:33 +0200 xtpcpp (0.4.36-1~buster1) buster; urgency=medium * deepprot FDR computation bug fixed * protein list accession search bug fixed * msrun store bug fixed * msrun id problem fixed in the mzIdentML parser -- Olivier Langella Mon, 19 Jul 2021 16:06:53 +0200 xtpcpp (0.4.35-1~buster1) buster; urgency=medium * better stop process interface * unique fasta files in sample output * sample names in simple output * better performances to count specific spectra * add spectral count analysis of SDS experiment with MCQR, Thomas Renne * documentation progress: fundamentals in bottom up proteomics, exploring identification data, Filippo Rusconi -- Olivier Langella Fri, 16 Jul 2021 15:03:40 +0200 xtpcpp (0.4.34-2~buster1) buster; urgency=medium * fix #68 * better stop API management -- Olivier Langella Wed, 30 Jun 2021 13:05:19 +0200 xtpcpp (0.4.34-1~buster1) buster; urgency=medium * first MCQR integration, Thomas Renne * NSAF bug fix #65 * concurency problem fixed for submonitor * specific output "simple" dedicated to OMS results study -- Olivier Langella Wed, 30 Jun 2021 09:42:22 +0200 xtpcpp (0.4.33-1~buster1) buster; urgency=medium * documentation progress: protein list, peptide list, detail, xic, Filippo Rusconi * MassChroQ execution using signals and slots * better MSGF+ support #66 * UNIMOD conversion to PSI mod * fix for issue #67 concerning TimsTOF data support reported by Aaron Wiles -- Olivier Langella Sun, 27 Jun 2021 10:19:18 +0200 xtpcpp (0.4.32-1~buster1) buster; urgency=medium * fix XIC generation using scan index problem -- Olivier Langella Tue, 15 Jun 2021 09:18:08 +0200 xtpcpp (0.4.31-1~buster1) buster; urgency=medium * new PAPPSOms++ library * user interface cleaning, Filippo Rusconi * starting documentation using docbook, Filippo Rusconi -- Olivier Langella Fri, 11 Jun 2021 09:13:12 +0200 xtpcpp (0.4.30-1~buster1) buster; urgency=medium * using new tandem error exception * using tandemwrapper for any tandem identification in an HTCondor job -- Olivier Langella Thu, 20 May 2021 11:56:44 +0200 xtpcpp (0.4.29-1~buster1) buster; urgency=medium * new XIC extractor API * begining documentation * new spectrum index column * tandem execution progress messages and stop * use tandem wrapper with mzML -- Olivier Langella Wed, 12 May 2021 18:19:26 +0200 xtpcpp (0.4.28-1~buster1) buster; urgency=medium * crash fix * better deepprot studio * new widgets to handle OBO terms -- Olivier Langella Wed, 21 Apr 2021 15:33:19 +0200 xtpcpp (0.4.27-1~buster1) buster; urgency=medium * first version of a working DeepProt studio -- Olivier Langella Mon, 05 Apr 2021 17:26:14 +0200 xtpcpp (0.4.26-1~buster2) buster; urgency=medium * little glitch -- Olivier Langella Fri, 02 Apr 2021 15:22:18 +0200 xtpcpp (0.4.26-1~buster1) buster; urgency=medium * improvements for the Bruker's user meeting -- Olivier Langella Thu, 01 Apr 2021 15:10:34 +0200 xtpcpp (0.4.26-1) unstable; urgency=low * New upstream version now depending on librdata and libgrantlee5. * Standards-Version: 4.5.1 (no change done). -- Filippo Rusconi Tue, 02 Mar 2021 20:51:39 +0100 xtpcpp (0.4.25-1~buster1) buster; urgency=medium * fix for issue #52 https://forgemia.inra.fr/pappso/xtpcpp/-/issues/52 -- Olivier Langella Wed, 10 Mar 2021 13:05:48 +0100 xtpcpp (0.4.24-1~buster1) buster; urgency=medium * TimsTOF XIC extraction and display * Display mobility coordinates on timstof identified peptides -- Olivier Langella Thu, 04 Mar 2021 13:19:00 +0100 xtpcpp (0.4.23-1~buster1) buster; urgency=medium * better mzIdentML file parsing * thread concurency problem fixed * display mzformat in peptide view -- Olivier Langella Wed, 24 Feb 2021 10:20:46 +0100 xtpcpp (0.4.22-1~buster1) buster; urgency=medium * config filename reversed to xtpcpp -- Olivier Langella Mon, 08 Feb 2021 14:27:40 +0100 xtpcpp (0.4.21-1~buster1) buster; urgency=medium * mgf absolute file path -- Olivier Langella Fri, 05 Feb 2021 13:43:40 +0100 xtpcpp (0.4.20-1~buster1) buster; urgency=medium * fix recongnizing mgf files in tdf directory -- Olivier Langella Fri, 05 Feb 2021 10:46:18 +0100 xtpcpp (0.4.19-1~buster1) buster; urgency=medium * MCQR work, integration is coming using librdata * MzIdentML parser is back * Handles DeepProt Open Modification Search results files * New XPIP structure to store alignment parameters -- Olivier Langella Mon, 01 Feb 2021 14:11:11 +0100 xtpcpp (0.4.18-1) unstable; urgency=low * New upstream version fixing a number of upstream-reported bugs. * Now depends on libpappsomspp 0.8.15. -- Filippo Rusconi Wed, 06 Jan 2021 15:48:09 +0100 xtpcpp (0.4.18-1~buster1) buster; urgency=medium * fix for issue https://forgemia.inra.fr/pappso/xtpcpp/-/issues/44 * use of latest PAPPSOms++ library 0.8.14 -- Olivier Langella Thu, 17 Dec 2020 10:41:20 +0100 xtpcpp (0.4.17-1~buster1) buster; urgency=medium * buster package * bunch of fixed issues #27 #40 #41 #42 (XIC data file export, better xtandem preset ui, mgf batch, masschroq parameter alignment files fixed) -- Olivier Langella Thu, 10 Dec 2020 14:45:20 +0100 xtpcpp (0.4.16-1) unstable; urgency=low * New version that requires libpappsomspp 0.8.13. * Fix bug #976512 (Closes: #976512). Thanks to Lucas Nussbaum for the report. * Fix bug reported by Vagrant Cascadian . Thanks for the report! (Closes: #976071). -- Filippo Rusconi Tue, 08 Dec 2020 20:48:29 +0100 xtpcpp (0.4.15-1) buster; urgency=medium * little fix concerning masschroq binary file path -- Olivier Langella Tue, 24 Nov 2020 16:32:12 +0100 xtpcpp (0.4.14-1) buster; urgency=medium * fix for issue #38 -- Olivier Langella Thu, 19 Nov 2020 10:10:18 +0100 xtpcpp (0.4.13-1) buster; urgency=medium * fixed issue #37 -- Olivier Langella Thu, 19 Nov 2020 09:16:34 +0100 xtpcpp (0.4.12-1) buster; urgency=medium * new features added by Thomas Renne -- Olivier Langella Wed, 18 Nov 2020 16:21:03 +0100 xtpcpp (0.4.11-1) buster; urgency=medium * new tandemrun wrapper -- Olivier Langella Wed, 18 Nov 2020 14:15:58 +0100 xtpcpp (0.4.10-1) buster; urgency=medium * new CondorProcess API * new MassChroQ GUI to execute MassChroQ -- Olivier Langella Tue, 17 Nov 2020 14:22:16 +0100 xtpcpp (0.4.9-2) UNRELEASED; urgency=low * Changed the maintainer to debichem team as the code is now in https://salsa.debian.org/debichem-team/xtpcpp. * Add Thomas Renne as Copyright holder for GPL3+ code in 2019,2020. * Add the corresponding VCS fields (see above). -- Filippo Rusconi Mon, 09 Nov 2020 20:55:49 +0100 xtpcpp (0.4.9-1) unstable; urgency=low * First package to be uploaded to NEW. * Some additions by Filippo Rusconi, like d/u/metadata or d/s/format. * Standards-Version: 4.5.0, no changes required. -- Filippo Rusconi Fri, 06 Nov 2020 12:21:05 +0100 xtpcpp (0.4.8-1) buster; urgency=medium * fix for issues masschroqml, ptm island view -- Olivier Langella Mon, 02 Nov 2020 11:10:53 +0100 xtpcpp (0.4.7-1) buster; urgency=medium * deep refactoring concerning msrun statistics -- Olivier Langella Thu, 15 Oct 2020 16:48:37 +0200 xtpcpp (0.4.6-1) buster; urgency=medium * mfg support for timsdata temporarily removed * more checks tandemwrapper run -- Olivier Langella Fri, 09 Oct 2020 16:07:27 +0200 xtpcpp (0.4.5-1) buster; urgency=medium * alginment GUI stuff * timstof support -- Olivier Langella Thu, 08 Oct 2020 11:35:20 +0200 xtpcpp (0.4.4-6) buster; urgency=medium * new fix for issue #31 -- Olivier Langella Thu, 01 Oct 2020 10:07:36 +0200 xtpcpp (0.4.4-5) buster; urgency=medium * new point mutation notation feature fix #32 -- Olivier Langella Tue, 29 Sep 2020 16:24:05 +0200 xtpcpp (0.4.4-4) buster; urgency=medium * fix for issue #31 -- Olivier Langella Mon, 28 Sep 2020 10:20:55 +0200 xtpcpp (0.4.4-3) buster; urgency=medium * new package to fix issue #31 -- Olivier Langella Thu, 24 Sep 2020 16:05:03 +0200 xtpcpp (0.4.4-2) buster; urgency=medium * new package to fix issue #31 -- Olivier Langella Thu, 24 Sep 2020 15:20:04 +0200 xtpcpp (0.4.4-1) buster; urgency=medium * maximum number of file reached, test for issue #31 -- Olivier Langella Thu, 24 Sep 2020 13:21:31 +0200 xtpcpp (0.4.3-1) buster; urgency=medium * fix for issue #28 : new column in PTM tables and exports to count spectra bearing modifications -- Olivier Langella Wed, 16 Sep 2020 10:55:19 +0200 xtpcpp (0.4.2-1) buster; urgency=medium * fix for issue #26 : bug in compar specific unique sequence sheet -- Olivier Langella Wed, 02 Sep 2020 09:14:53 +0200 xtpcpp (0.4.1-1) buster; urgency=medium * better PTM support * no tims preset required * boost not needed * loss of mzIdentML support * export chemical formula in masschroqML output -- Olivier Langella Wed, 22 Jul 2020 16:53:04 +0200 xtpcpp (0.4.0-2) buster; urgency=medium * display all digits of XIC areas -- Olivier Langella Mon, 08 Jun 2020 17:59:22 +0200 xtpcpp (0.4.0-1) buster; urgency=medium * fixed issue #23 -- Olivier Langella Fri, 29 May 2020 16:58:10 +0200 xtpcpp (0.3.9-2) buster; urgency=medium * fix issue #22 * no more dependency with libpwiz and libboost -- Olivier Langella Thu, 28 May 2020 09:46:44 +0200 xtpcpp (0.3.9-1) buster; urgency=medium * lots of improvements made by Thomas Renne -- Olivier Langella Tue, 19 May 2020 16:25:15 +0200 xtpcpp (0.3.8-1) unreleased; urgency=low * New upstream version. Packaging tweaks. -- Filippo Rusconi Mon, 04 May 2020 11:37:03 +0200 xtpcpp (0.3.7-3) buster; urgency=medium * no console in windows version * pseudo centroid for tandem wrapper -- Olivier Langella Mon, 20 Apr 2020 08:31:29 +0200 xtpcpp (0.3.7-2) buster; urgency=medium * important fix in lib PAPPSOms++ -- Olivier Langella Sun, 12 Apr 2020 17:14:51 +0200 xtpcpp (0.3.7-1) buster; urgency=medium * allow column move (peptide list, protein list, ptm list, ptm peptide list) * edition of centroid parameters in tandem settings for tims tof reader * defining alignment groups * cross compilation with MXE -- Olivier Langella Fri, 10 Apr 2020 22:05:08 +0200 xtpcpp (0.3.6-1) buster; urgency=medium * timstof support -- Olivier Langella Wed, 04 Mar 2020 16:59:21 +0100 xtpcpp (0.3.5-1ubuntu1) bionic; urgency=medium * tandem error messages -- Olivier Langella Mon, 10 Feb 2020 10:58:19 +0100 xtpcpp (0.3.4-1) buster; urgency=medium * several issues fixed by Thomas Renne * mascot dat parser work -- Olivier Langella Wed, 29 Jan 2020 10:22:48 +0100 xtpcpp (0.3.3-1) buster; urgency=medium * new spreadsheet output for PSMs -- Olivier Langella Tue, 14 Jan 2020 10:33:42 +0100 xtpcpp (0.3.2-2ubuntu1) bionic; urgency=medium * ubuntu 18.04 package -- Olivier Langella Fri, 10 Jan 2020 22:39:39 +0000 xtpcpp (0.3.2-2) buster; urgency=medium * new pappsoms++ library -- Olivier Langella Wed, 08 Jan 2020 22:22:40 +0100 xtpcpp (0.3.2-1) buster; urgency=medium * better ms run identification view * prapagation of the project name -- Olivier Langella Mon, 06 Jan 2020 11:26:14 +0100 xtpcpp (0.3.1-3) buster; urgency=medium * bunch of little bug fix -- Olivier Langella Fri, 20 Dec 2019 14:21:34 +0100 xtpcpp (0.3.1-2) buster; urgency=medium * merge of latest changes from forge mia -- Olivier Langella Thu, 19 Dec 2019 22:34:59 +0100 xtpcpp (0.3.1-1) buster; urgency=medium * new features coded by Thomas Renne * new msrun list windows * instant msrun statistics * many GUI fix -- Olivier Langella Thu, 19 Dec 2019 22:26:05 +0100 xtpcpp (0.2.40-2) buster; urgency=medium * buster package -- Olivier Langella Thu, 12 Sep 2019 20:25:49 +0200 xtpcpp (0.2.40-1) stretch; urgency=medium * find spectrum directly by index if scan numbers are not supported * MassChroqML output without peptide labels in comments * new UI to choose removal contaminant mode * new FDR computation : decoy/target * FDR driven peptide theshold, available for Tandem and Mascot results -- Olivier Langella Thu, 12 Sep 2019 09:10:45 +0200 xtpcpp (0.2.38-4) stretch; urgency=medium * scoring, pluggable scoring added -- Olivier Langella Tue, 18 Jun 2019 13:37:52 +0200 xtpcpp (0.2.38-3) stretch; urgency=medium * refine, maximum missed cleavage sites added -- Olivier Langella Tue, 18 Jun 2019 13:28:02 +0200 xtpcpp (0.2.38-2) stretch; urgency=medium * protein, use minimal annotation parameter added -- Olivier Langella Tue, 18 Jun 2019 11:43:37 +0200 xtpcpp (0.2.38-1) stretch; urgency=medium * new button to look for the best MS run to use as reference in alignment * accepts to run TPP modified version of X!Tandem, using specific parameters (DIA requirements) * new PAPPSOms++ library -- Olivier Langella Mon, 17 Jun 2019 13:53:16 +0200 xtpcpp (0.2.37-2) stretch; urgency=medium * sum/max extraction bug fixed, thanks to Marlène and Thierry -- Olivier Langella Tue, 28 May 2019 16:06:10 +0200 xtpcpp (0.2.37-1) stretch; urgency=medium * new PAPPSOms++ library -- Olivier Langella Fri, 24 May 2019 11:53:47 +0200 xtpcpp (0.2.36-1) stretch; urgency=medium * proticdbml fix * new tandem.exe setup control * better error message for tandem run process -- Olivier Langella Tue, 16 Apr 2019 15:03:10 +0200 xtpcpp (0.2.35-2) stretch; urgency=medium * fix libodsstream problem -- Olivier Langella Mon, 25 Mar 2019 11:27:19 +0100 xtpcpp (0.2.35-1) stretch; urgency=medium * mutation support * peprepro filter -- Olivier Langella Mon, 25 Mar 2019 10:46:03 +0100 xtpcpp (0.2.34-2) stretch; urgency=medium * fix filename bug -- Olivier Langella Tue, 19 Mar 2019 08:53:24 +0100 xtpcpp (0.2.34-1) stretch; urgency=medium * fix ppm range in MassChroqML export (thanks to Thierry Balliau) * new features asked by Plateforme Post-génomique de la Pitié Salpétrière - P3S (Solenne Chardonnet, Cédric Pionneau) * write protein list view as is in ODS file * write peptide list view as is in ODS file * new ui menu in peptide and protein list wiew * ppm delta added in ODS spectra sheet export * display Nter and Cter peptide flanking regions in ODS and list views -- Olivier Langella Mon, 18 Mar 2019 11:06:11 +0100 xtpcpp (0.2.33-1) stretch; urgency=medium * scroll area for small screens * xic extraction method (sum or max) * resilient ODS on failure * global settings windows * xic extractor reader choice -- Olivier Langella Mon, 25 Feb 2019 13:29:57 +0100 xtpcpp (0.2.32-1) stretch; urgency=medium * moving to refactored PAPPSOms++ library * bug fixed in FASTA exports -- Olivier Langella Wed, 06 Feb 2019 11:48:02 +0100 xtpcpp (0.2.31-2) stretch; urgency=medium * user agent created, variable to disable htpp get version -- Olivier Langella Fri, 01 Feb 2019 14:36:56 +0100 xtpcpp (0.2.31-1) stretch; urgency=medium * new Fasta file exports by groups and subgroups * better MassChroqML output : check MS run file paths, set output result files, set alignment/xic exctraction/peak detection parameters -- Olivier Langella Mon, 28 Jan 2019 15:13:20 +0100 xtpcpp (0.2.30-1) stretch; urgency=medium * new ODS spreadsheet dedicated to peptidomic : comparison of the number of spectra for each peptide in each sample -- Olivier Langella Mon, 14 Jan 2019 10:43:00 +0100 xtpcpp (0.2.29-4) stretch; urgency=medium * new PAPPSOms++ library -- Olivier Langella Tue, 08 Jan 2019 16:19:34 +0100 xtpcpp (0.2.29-3) stretch; urgency=medium * new pappsomspp library -- Olivier Langella Wed, 02 Jan 2019 21:52:00 +0100 xtpcpp (0.2.29-1) stretch; urgency=medium * modification to be qcustomplot 2.0.1 compliant * accept labeling method containing an empty label -- Olivier Langella Sat, 15 Dec 2018 16:51:44 +0100 xtpcpp (0.2.28-3) stretch; urgency=medium * mascot takes all query candidates * fix thread wait loading spectrum -- Olivier Langella Fri, 07 Dec 2018 10:44:46 +0100 xtpcpp (0.2.28-2) stretch; urgency=medium * take only first spectrum psm in mascot parser -- Olivier Langella Tue, 27 Nov 2018 09:21:43 +0100 xtpcpp (0.2.28-1) stretch; urgency=medium * improved mascot dat parser * ability to choose TSV as export file format * icon added for Windows * more checks on tandem binary path * dependency added on package tandem-mass -- Olivier Langella Mon, 26 Nov 2018 15:29:21 +0100 xtpcpp (0.2.27-1) stretch; urgency=medium * look for sequence LI -- Olivier Langella Tue, 13 Nov 2018 14:58:53 +0100 xtpcpp (0.2.26-1) stretch; urgency=medium * display distinctively the FDR on peptides and on PSM -- Olivier Langella Fri, 09 Nov 2018 10:50:11 +0100 xtpcpp (0.2.25-2) stretch; urgency=medium * new version number 0.2.25 -- Olivier Langella Fri, 02 Nov 2018 15:31:01 +0100 xtpcpp (0.2.25-1) stretch; urgency=medium * mascot parser fix for single fasta file * protein mass including alanine * X!Tandem version check * FDR written as percentage in ODS files * compute peptide FDR directly on peptides (no protein validation) -- Olivier Langella Fri, 02 Nov 2018 14:26:19 +0100 xtpcpp (0.2.24-3) stretch; urgency=medium * fix for temporary directory under condor -- Olivier Langella Mon, 29 Oct 2018 11:14:33 +0100 xtpcpp (0.2.24-2) stretch; urgency=medium * ODS output fix -- Olivier Langella Fri, 19 Oct 2018 16:57:33 +0200 xtpcpp (0.2.24-1) stretch; urgency=medium * new compar ODS output dedicated to labeled experiments * SEVERE bug fix concerning protein Evalue computation (reported by T. Balliau) -- Olivier Langella Fri, 19 Oct 2018 16:13:10 +0200 xtpcpp (0.2.23-2) stretch; urgency=medium * fix version number -- Olivier Langella Tue, 16 Oct 2018 11:13:36 +0200 xtpcpp (0.2.23-1) stretch; urgency=medium * checking tandem.exe installation * new controls to select decoy sequences and avoid bug signaled by C. Henry and T. Balliau * new temporary folder handler for HTCondor jobs -- Olivier Langella Tue, 16 Oct 2018 10:57:47 +0200 xtpcpp (0.2.22-3) stretch; urgency=medium * major mzIdentML improvements for MS-GF+ -- Olivier Langella Wed, 03 Oct 2018 22:32:56 +0200 xtpcpp (0.2.22-2) stretch; urgency=medium * minor fix -- Olivier Langella Wed, 03 Oct 2018 11:08:30 +0200 xtpcpp (0.2.22-1) stretch; urgency=medium * better Mascot parser * new placeholder for contaminant widget * refresh evalue when choosing threshold * display contaminant checkbox in protein view * release MSrun after reading -- Olivier Langella Tue, 02 Oct 2018 13:56:06 +0200 xtpcpp (0.2.21-4) stretch; urgency=medium * make sure that we look for MSrun in the right place -- Olivier Langella Mon, 03 Sep 2018 16:29:47 +0200 xtpcpp (0.2.21-3) stretch; urgency=medium * smart file path guess -- Olivier Langella Fri, 31 Aug 2018 11:49:39 +0200 xtpcpp (0.2.21-2) stretch; urgency=medium * gui text fix (proteins => peptides) * find readable msRun file -- Olivier Langella Wed, 29 Aug 2018 09:26:21 +0200 xtpcpp (0.2.21-1) stretch; urgency=medium * ODS column consistency checked, more auto documentation -- Olivier Langella Fri, 17 Aug 2018 13:51:19 +0200 xtpcpp (0.2.20-1) stretch; urgency=medium * TIC columns added in ODS report -- Olivier Langella Fri, 13 Jul 2018 09:31:03 +0200 xtpcpp (0.2.19-1) stretch; urgency=medium * fix in mzidentml reader and pepxml reader to be able to load files from MSfragger -- Olivier Langella Mon, 09 Jul 2018 13:36:40 +0200 xtpcpp (0.2.18-1) stretch; urgency=medium * pepxml support * XPIP change : each peptide is related has is own identification engine id * better xic extractor cache by msrun * possibility to display specific identification engine attributes (omssa, comet,msgf+...) -- Olivier Langella Thu, 05 Jul 2018 13:50:31 +0200 xtpcpp (0.2.17-1) stretch; urgency=medium * new window to edit detection parameters * new PAPPSO library API to read MS run files -- Olivier Langella Sat, 02 Jun 2018 18:09:53 +0200 xtpcpp (0.2.16-3) stretch; urgency=medium * fix masschroq out put msrun reference -- Olivier Langella Sat, 26 May 2018 07:05:21 +0200 xtpcpp (0.2.16-2) stretch; urgency=medium * falling back to simple pwiz xic extractor -- Olivier Langella Sat, 26 May 2018 06:47:15 +0200 xtpcpp (0.2.16-1) stretch; urgency=medium * new buffered XIC extractor -- Olivier Langella Fri, 25 May 2018 09:08:47 +0200 xtpcpp (0.2.15-2) stretch; urgency=medium * lib pappsomspp change -- Olivier Langella Thu, 17 May 2018 22:18:27 +0200 xtpcpp (0.2.15-1) stretch; urgency=medium * new xic extractor API, spectral count export fallback, compar bug fixed -- Olivier Langella Wed, 16 May 2018 11:36:53 +0200 xtpcpp (0.2.14-2) stretch; urgency=medium * avoid libodsstream bug in compar sheets -- Olivier Langella Mon, 14 May 2018 13:01:39 +0200 xtpcpp (0.2.14-1) stretch; urgency=medium * NSAF compar export -- Olivier Langella Fri, 04 May 2018 09:14:35 +0200 xtpcpp (0.2.13-1) stretch; urgency=medium * XIC peak borders -- Olivier Langella Mon, 16 Apr 2018 13:34:17 +0200 xtpcpp (0.2.12-2) stretch; urgency=medium * ppm delta bug fix -- Olivier Langella Wed, 28 Mar 2018 10:55:01 +0200 xtpcpp (0.2.12-1) stretch; urgency=medium * GUI improvements -- Olivier Langella Mon, 26 Mar 2018 16:14:42 +0200 xtpcpp (0.2.11-1) stretch; urgency=medium * MASCOT dat parser * contaminant widget -- Olivier Langella Tue, 13 Mar 2018 16:01:10 +0100 xtpcpp (0.2.10-4) stretch; urgency=medium * bug fix when no peak has been detected for a peptide -- Olivier Langella Wed, 14 Feb 2018 10:20:28 +0100 xtpcpp (0.2.10-3) stretch; urgency=medium * new PAPPSOms++ library -- Olivier Langella Mon, 12 Feb 2018 16:45:57 +0100 xtpcpp (0.2.10-2) stretch; urgency=medium * fix library package name -- Olivier Langella Sun, 11 Feb 2018 18:08:26 +0100 xtpcpp (0.2.10-1) stretch; urgency=medium * better UI and XIC viewer -- Olivier Langella Sun, 11 Feb 2018 08:02:37 +0100 xtpcpp (0.2.9-2) stretch; urgency=medium * extract XIC in other MS runs -- Olivier Langella Mon, 29 Jan 2018 09:53:12 +0100 xtpcpp (0.2.8-1) stretch; urgency=medium * better PTM island mode -- Olivier Langella Thu, 25 Jan 2018 10:06:17 +0100 xtpcpp (0.2.7-1) stretch; urgency=medium * bug fixed on long protein label with reversed sequences -- Olivier Langella Tue, 23 Jan 2018 15:57:47 +0100 xtpcpp (0.2.6-1) stretch; urgency=medium * new XIC viewer -- Olivier Langella Thu, 18 Jan 2018 16:28:07 +0100 xtpcpp (0.2.5-2) stretch; urgency=medium * disable warning message in xpip export -- Olivier Langella Wed, 10 Jan 2018 16:19:17 +0100 xtpcpp (0.2.5-1) stretch; urgency=medium * search on msrun and scan, better individual mode, better widgets -- Olivier Langella Wed, 10 Jan 2018 14:50:52 +0100 xtpcpp (0.2.4-1) stretch; urgency=medium * new peptide widget -- Olivier Langella Wed, 03 Jan 2018 11:44:36 +0100 xtpcpp (0.2.3-2) stretch; urgency=medium * new mass delta, new FDR, new histogram -- Olivier Langella Wed, 20 Dec 2017 11:20:52 +0100 xtpcpp (0.2.3-1) stretch; urgency=medium * better FDR and mass delta computing -- Olivier Langella Sun, 17 Dec 2017 18:19:11 +0100 xtpcpp (0.2.2-2) stretch; urgency=medium * new pappsomspp library -- Olivier Langella Fri, 15 Dec 2017 11:38:38 +0100 xtpcpp (0.2.2-1) stretch; urgency=medium * better xpip format input and output -- Olivier Langella Mon, 04 Dec 2017 10:54:31 +0100 xtpcpp (0.2.1-1) stretch; urgency=medium * huge refactoring * new xpip output file * clear mz file list in tandem run dialog -- Olivier Langella Wed, 22 Nov 2017 15:56:02 +0100 xtpcpp (0.1.23-1) stretch; urgency=medium * better ODS and XPIP file * compute mass and number of tryptic peptides on non regular protein sequences -- Olivier Langella Wed, 15 Nov 2017 12:57:36 +0100 xtpcpp (0.1.22-2) stretch; urgency=medium * HTCondor parameter edition -- Olivier Langella Mon, 06 Nov 2017 08:44:17 +0100 xtpcpp (0.1.22-1) stretch; urgency=medium * new buttons in central widget * xpip file creation * tandem parameters added * avoid non amino acid chars in tryptic peptide count -- Olivier Langella Fri, 27 Oct 2017 16:40:50 +0200 xtpcpp (0.1.21-1) stretch; urgency=medium * tandem file check * better tandem form * multiple directory upload * monitoring grouping (and faster grouping) -- Olivier Langella Sat, 21 Oct 2017 11:58:51 +0200 xtpcpp (0.1.20-2) stretch; urgency=medium * tandem parameter form hardened -- Olivier Langella Sun, 15 Oct 2017 20:32:27 +0200 xtpcpp (0.1.20-1) stretch; urgency=medium * tandem parameters editor -- Olivier Langella Sun, 15 Oct 2017 07:50:50 +0200 xtpcpp (0.1.19-1) stretch; urgency=medium * new preset window (for tandem parameters) * divizion by zero fixed and exception added -- Olivier Langella Mon, 09 Oct 2017 09:03:30 +0200 xtpcpp (0.1.18-1) stretch; urgency=medium * MS run and identification statistics -- Olivier Langella Tue, 26 Sep 2017 10:07:10 +0200 xtpcpp (0.1.17-2) stretch; urgency=medium * fix desktop file -- Olivier Langella Fri, 22 Sep 2017 15:42:11 +0200 xtpcpp (0.1.17-1) stretch; urgency=medium * better tandem run dialog box * success message after tandem run (thanks T. Balliau) * condor/tmp_dir_autoremove parameter to keep log files * choose number of threads for tandem run * XPIP mime type associated to xtpcpp -- Olivier Langella Fri, 22 Sep 2017 14:36:15 +0200 xtpcpp (0.1.16-1) stretch; urgency=medium * qt5 switch * about dialog window * Tandem run window (local and HTCondor) -- Olivier Langella Mon, 18 Sep 2017 12:07:33 +0200 xtpcpp (0.1.15-1) stretch; urgency=medium * ptm peptide list -- Olivier Langella Thu, 17 Aug 2017 15:40:53 +0200 xtpcpp (0.1.14-2) stretch; urgency=medium * utf8 pwiz library bug workaround -- Olivier Langella Sat, 01 Jul 2017 10:37:11 +0200 xtpcpp (0.1.14-1) stretch; urgency=medium * mzidentml and pepxml support -- Olivier Langella Sat, 24 Jun 2017 22:43:53 +0200 xtpcpp (0.1.13-1) jessie; urgency=medium * progress bar, now spectral count output -- Olivier Langella Mon, 12 Jun 2017 08:59:00 +0200 xtpcpp (0.1.12-1) jessie; urgency=medium * first PTM island support -- Olivier Langella Wed, 31 May 2017 10:51:11 +0200 xtpcpp (0.1.11-2) jessie; urgency=medium * new odsstream library -- Olivier Langella Tue, 23 May 2017 23:09:30 +0200 xtpcpp (0.1.11-1) jessie; urgency=medium * proticdbml output -- Olivier Langella Sat, 20 May 2017 17:36:09 +0200 xtpcpp (0.1.10-1) jessie; urgency=medium * trick to read MGF files -- Olivier Langella Fri, 12 May 2017 10:26:42 +0200 xtpcpp (0.1.9-1) jessie; urgency=medium * MGF peak sorting, waiting dialog, new ODS sheets (samples, groups) -- Olivier Langella Tue, 09 May 2017 11:30:23 +0200 xtpcpp (0.1.8-1) jessie; urgency=medium * better peptide viewer -- Olivier Langella Fri, 05 May 2017 16:28:16 +0200 xtpcpp (0.1.7-1) jessie; urgency=medium * button to link with peptide viewer -- Olivier Langella Thu, 04 May 2017 14:47:48 +0200 xtpcpp (0.1.6-1) jessie; urgency=medium * new ODS sheet in outputs -- Olivier Langella Wed, 03 May 2017 10:28:25 +0200 xtpcpp (0.1.5-2) jessie; urgency=medium * new export options -- Olivier Langella Fri, 28 Apr 2017 10:30:20 +0200 xtpcpp (0.1.5-1) jessie; urgency=medium * new export options -- Olivier Langella Fri, 28 Apr 2017 10:18:20 +0200 xtpcpp (0.1.4-1) jessie; urgency=medium * FASTA export -- Olivier Langella Thu, 27 Apr 2017 09:19:11 +0200 xtpcpp (0.1.3-1) jessie; urgency=medium * thanks Ariane and Thierry -- Olivier Langella Tue, 25 Apr 2017 16:22:04 +0200 xtpcpp (0.1.2-1) jessie; urgency=medium * new modification editor, new FDR mass deviation behaviour, lots of improvements -- Olivier Langella Mon, 24 Apr 2017 10:17:53 +0200 xtpcpp (0.1.1-1) jessie; urgency=medium * bug fix and new features -- Olivier Langella Thu, 20 Apr 2017 11:32:40 +0200 xtpcpp (0.1.0-1) jessie; urgency=medium * first jessie package -- Olivier Langella Wed, 19 Apr 2017 10:15:33 +0200 xtpcpp (0.1.0-1~stretch) stretch; urgency=medium * first package -- Olivier Langella Tue, 18 Apr 2017 20:55:14 +0200