xtpcpp (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