Fix modification bug near termini for fast nonspecific #1498
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rmillikin
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Oct 30, 2018
* fix autoupdater (#1493) * added twitter and slack follows to menu (#1495) * Fix modification bug near termini for fast nonspecific (#1498) * hyphens * test changes to score original ions instead of complementary * Faster serialize/deserialize * Revert "Faster serialize/deserialize" This reverts commit 751b427. * Revert "Faster serialize/deserialize" This reverts commit 751b427. * Fix modification bug in nonspecific * Remove comp ions in multi-termini scoring for SNES * mzlib update (#1499) * added twitter and slack follows to menu * mzlib update * mzlib update to gui * Fix nses gui (#1494) * Fix Gui * Fixes to fix the bugs from the last fixes * Clean * string set default protease to trypsin. prevents default changes if protease list is modified. * refactor default trypsin in GUI
rmillikin
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Nov 9, 2018
* Generate variant proteins for digestion in classic search * stuff * fix break * fix gptmd pruning * GPTMD on variant proteins * variantproteindigestion integrated into gui * pruned fixes * pruning sequence variant modifications * reenable catching exceptions * distinct protein accessions if there is no sequence ambiguity * little stuff * fix autoupdater (#1493) * updated local mzlib * added twitter and slack follows to menu (#1495) * Fix modification bug near termini for fast nonspecific (#1498) * hyphens * test changes to score original ions instead of complementary * Faster serialize/deserialize * Revert "Faster serialize/deserialize" This reverts commit 751b427. * Revert "Faster serialize/deserialize" This reverts commit 751b427. * Fix modification bug in nonspecific * Remove comp ions in multi-termini scoring for SNES * mzlib update (#1499) * added twitter and slack follows to menu * mzlib update * mzlib update to gui * Fix nses gui (#1494) * Fix Gui * Fixes to fix the bugs from the last fixes * Clean * string set default protease to trypsin. prevents default changes if protease list is modified. * refactor default trypsin in GUI * indexes output folder (#1500) * indexes output folder * rob edits * Add custom mod button (#1501) * start on "add custom mod" button * more error checking * cleanup * tooltips etc * QValueParam * Changes to file writing * Small Changes * Smaller Changes * Update PostSearchAnalysisTask.cs * Update TestPsm.cs * Update MetaMorpheusTask.cs * qval * Add Custom Mod Button * fix * rob edits * rob edit 2 * rob edits * Fix SNES to use notches (#1505) * Fix Gui * Fixes to fix the bugs from the last fixes * Clean * string set default protease to trypsin. prevents default changes if protease list is modified. * refactor default trypsin in GUI * Fix SNES to allow notches * fix custom mass diff acceptor parsing crash (#1508) * fix custom mass diff acceptor parsing crash * change unit test * fix public/private method stuff * parsimony speed and pruning crash fixes * Allow SNES to look at notches (round 2) (#1507) * Fix Gui * Fixes to fix the bugs from the last fixes * Clean * string set default protease to trypsin. prevents default changes if protease list is modified. * refactor default trypsin in GUI * Fix SNES to allow notches * New mass diff acceptor method for SNES to reverse calculate the notches given the observed precursor. * Update test rename from failed build. Update test to missed mono * Simplify Modern massdiffacceptor * search mods box (#1484) * my fake test * I added nothing. * Add youtube & wiki link. * youtube and wiki link update * startup message * change path. installer works after change * fixed startup message * changed text * Window close pop up * change param name * latest edits * Revert "latest edits" This reverts commit d676f5e. * output indexes to folder * Revert "output indexes to folder" This reverts commit f41ecd1. * edit message * added don't ask again button to pop up * fix method naming style * add debug ver * popup edits * remove unneccessary usings * mod search box * small format edits * initial changes * search mod boxes edits * simplified code * rob edits * rob edits 2 * remove some using statements * working on variant search tests * tests * changes * Mods revamp (#1512) * mods overhaul * installer stuff * few more edits * added a couple mods, edits * couple more edits * update mzLib * update mzlib and other responses to rmillikin * re-add peptidomics protease, fix some issues with custom mod window (#1514) * re-add peptidomics protease, fix some issues with custom mod window * gptmd search mods window stuff
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