Deisotoping options for GPTMD #1319
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rmillikin
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Aug 15, 2018
* installer * checkbox * Added Unimod Menu Bar * added features: installer, do_not_remind and Update Unimods * remove weird * weird * hm * hm * Cleaned up * add settings * add modslocation * Git final * restore * plz solve conflict * fied indent * Violent installer * indenting fixed * A Decent Installer * Fix menu option * Simplify updater * Update Product.wxs * Debug travis * Gah * Environment.GetFolderPath(Environment.SpecialFolder.ProgramFiles) * yah * Noice * Simplify * datadir menu option * Updated to Origin * MetaUpdater Added release notes * Meta Updater * Cleanup * clean_up and Update * desktop sc * package code fix * commented with Codacy checked errors and warnings on Codacy. All minor things. * Update TestScan.cs * fix * Update TestScan.cs * Update TestScan.cs * Large file test command backup * Update command * okay * Fix a few * Mkay * Update to Curr -- Appveyor * Set to release * Added Encrypted Cert * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update * update * Update CalibrationTask.cs * Update CalibrationTask.cs * yah * Bootstraper * cleanup * sln fix * bootin * Update MetaMorpheus.sln * Update MetaMorpheus.sln * bundle compile * Update MetaMorpheus.sln * Uhum * Hmhp * aha * fixup * yeah * yeah * update to upstream * XL Different crosslink sites * XL crosslink different amino acid GUI * XL Improve codeCov * XL Improve CodeCov2 * XL test Target 90% coverage * XLTest Target 90% coverage2 * XLTest Target 90% coverage3 * XL pep.XML mod position N ter refer as 0 * XL test diff crosslink site * Optimize xltest code * XL improve code quality * XL GenerateIntensityRanks() bug * Output pep.XML for Search Task * pepXML works for Search Task * pep.xml works for TPP now! * pep.xml Search Engine Tandom * Update pep.XML * PepXML update * PepXMLWriter Class * Remove useless library pepxml * Add Quantification Setting Window * QuanSetGUI * Start RealTime GUI project * Data Collect * Connection bug * Notification Event * Updata DataReceiver Notification * Dispatcher BeginInvoke * Add MetaDraw into MetaMorpheus * MetaDraw using MsDataFile * Data Receiver by TbNotification * Add Realtime database * dd * clear * cleanup dd * RealTime add parameter * Success generate ion index for real time * Check Thread * Add log4net * log in DataReceiver * DataReceiver cannot have logWatcher * Try BeginInvoke * LogWatcher BeginInvoke * Add Notification * Add Dump * check Notification 2nd * try DataReceiver.Notifications * metadraw * no sense * sync * Update Installer * MetaDraw update Product ions parameter * Update SpectrumForDataGrid * Update * MetaDraw Added * Fix Pull * MetaDraw Added * fix installer issue that caused metamorpheus to not open (#1288) * Update to mzlib 328 (#1285) * Update mzlib * Revert "Update mzlib" This reverts commit 1b3fa4f. * update mzlib * Non tomls (#1284) * test * test remove * Added column of matched intensity values * FIXED: intensitiy count for comp ions * Revisons to Intensity column add * Fixed reassign non-specific maxpeptide length * Remove conflic marker * Delete line * Change to for loops (readability) * update mzLib; fix bug in displaying matched ion info (#1292) * Smaller refactor to common parameters * Make maxThreadsPerFile privately set * FDR Filtering Prior to Protein Parsimony (#1296) * Fix all merge errors * Merge and Merge Fixes * edits * fixed issue * remove test code * brackets * Codacy Edits * rob edits * rob edit 2 * MBR with multiple proteases, has errors becasue mzLib method not yet incorporated * Make Parsimony only take into account 1% or better FDR peptides * removed regions * Fdr filtereing done with peptide with set mods accessed from psms after mathcing, before parsimony * FdrFiltering With Psms * FDR Filtering PSMs prior to parsimony * remove test code * removing extra spaces between lines * Camel Case Changes * relocate FDR filtering code to only occur if user performs parsimony * 1% and below PSMs assigned to parsimony proteins * Index out of bounds indexing engine fix (#1299) * Include troubleshooting for MSFileReader Address issue #1300 * fix "cumulative target" skipping numbers (#1302) * fix decoy skipping (#1303) * fix "cumulative target" skipping numbers * fix decoy skipping * updates * MetaDraw * try to build * try to build 2 * metadraw edits * File specific overwrote all other parameters to default (#1305) * File specific parameter overwrite fix * Remove clone * Remove useless note * remove useless resources * Revert "Remove clone" This reverts commit a706a4f. * Small fix ensures that crashes in entering indistinguishable proteins are handled (#1307) * Fix all merge errors * Merge and Merge Fixes * edits * fixed issue * remove test code * brackets * Codacy Edits * rob edits * rob edit 2 * MBR with multiple proteases, has errors becasue mzLib method not yet incorporated * Make Parsimony only take into account 1% or better FDR peptides * removed regions * Fdr filtereing done with peptide with set mods accessed from psms after mathcing, before parsimony * FdrFiltering With Psms * FDR Filtering PSMs prior to parsimony * remove test code * removing extra spaces between lines * Camel Case Changes * relocate FDR filtering code to only occur if user performs parsimony * 1% and below PSMs assigned to parsimony proteins * Fix with indistiguishable proteins. Ensuring that proteins not already present in the protein parsimony list * Update ProteinParsimonyEngine.cs * use established peptide classes to get fragments; graphical improvements; other code improvements * MetaMorpheus Add for maxThreads in MzLib change (#1310) * MetaMorpheus Add for maxThreads in MzLib change * Added maxThreads for different methods * MaxThread method add * revamp interface * Rob's MetaDraw... (#1306) * OutputNoice * haha * aha * uhum * hmph * Noice * Fixes * version check * 205 with auto_update * added features * Auto_Update * installer updated * Aha * Yah * Uhum * uhum * Wooh * revert * minor * uhum * Remove unused * noice * noice * codemaid * Yah * Cleaner * noice * hm * installer * installer * checkbox * Added Unimod Menu Bar * added features: installer, do_not_remind and Update Unimods * remove weird * weird * hm * hm * Cleaned up * add settings * add modslocation * Git final * restore * plz solve conflict * fied indent * Violent installer * indenting fixed * A Decent Installer * Fix menu option * Simplify updater * Update Product.wxs * Debug travis * Gah * Environment.GetFolderPath(Environment.SpecialFolder.ProgramFiles) * yah * Noice * Simplify * datadir menu option * Updated to Origin * MetaUpdater Added release notes * Meta Updater * Cleanup * clean_up and Update * desktop sc * package code fix * commented with Codacy checked errors and warnings on Codacy. All minor things. * Update TestScan.cs * fix * Update TestScan.cs * Update TestScan.cs * Large file test command backup * Update command * okay * Fix a few * Mkay * Update to Curr -- Appveyor * Set to release * Added Encrypted Cert * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update * update * Update CalibrationTask.cs * Update CalibrationTask.cs * yah * Bootstraper * cleanup * sln fix * bootin * Update MetaMorpheus.sln * Update MetaMorpheus.sln * bundle compile * Update MetaMorpheus.sln * Uhum * Hmhp * aha * fixup * yeah * yeah * update to upstream * XL Different crosslink sites * XL crosslink different amino acid GUI * XL Improve codeCov * XL Improve CodeCov2 * XL test Target 90% coverage * XLTest Target 90% coverage2 * XLTest Target 90% coverage3 * XL pep.XML mod position N ter refer as 0 * XL test diff crosslink site * Optimize xltest code * XL improve code quality * XL GenerateIntensityRanks() bug * Output pep.XML for Search Task * pepXML works for Search Task * pep.xml works for TPP now! * pep.xml Search Engine Tandom * Update pep.XML * PepXML update * PepXMLWriter Class * Remove useless library pepxml * Add Quantification Setting Window * QuanSetGUI * Start RealTime GUI project * Data Collect * Connection bug * Notification Event * Updata DataReceiver Notification * Dispatcher BeginInvoke * Add MetaDraw into MetaMorpheus * MetaDraw using MsDataFile * Data Receiver by TbNotification * Add Realtime database * dd * clear * cleanup dd * RealTime add parameter * Success generate ion index for real time * Check Thread * Add log4net * log in DataReceiver * DataReceiver cannot have logWatcher * Try BeginInvoke * LogWatcher BeginInvoke * Add Notification * Add Dump * check Notification 2nd * try DataReceiver.Notifications * metadraw * no sense * sync * Update Installer * MetaDraw update Product ions parameter * Update SpectrumForDataGrid * Update * MetaDraw Added * Fix Pull * MetaDraw Added * updates * MetaDraw * try to build * try to build 2 * metadraw edits * use established peptide classes to get fragments; graphical improvements; other code improvements * revamp interface * fix file loading in metadraw (#1317) * rev (#1316) * 285 (#1294) * fix installer issue that caused metamorpheus to not open (#1288) * Update to mzlib 328 (#1285) * Update mzlib * Revert "Update mzlib" This reverts commit 1b3fa4f. * update mzlib * Non tomls (#1284) * test * test remove * Added column of matched intensity values * FIXED: intensitiy count for comp ions * Revisons to Intensity column add * Fixed reassign non-specific maxpeptide length * Remove conflic marker * Delete line * Change to for loops (readability) * update mzLib; fix bug in displaying matched ion info (#1292) * File specific overwrote all other parameters to default (#1305) * File specific parameter overwrite fix * Remove clone * Remove useless note * remove useless resources * Revert "Remove clone" This reverts commit a706a4f. * Small fix ensures that crashes in entering indistinguishable proteins are handled (#1307) * Fix all merge errors * Merge and Merge Fixes * edits * fixed issue * remove test code * brackets * Codacy Edits * rob edits * rob edit 2 * MBR with multiple proteases, has errors becasue mzLib method not yet incorporated * Make Parsimony only take into account 1% or better FDR peptides * removed regions * Fdr filtereing done with peptide with set mods accessed from psms after mathcing, before parsimony * FdrFiltering With Psms * FDR Filtering PSMs prior to parsimony * remove test code * removing extra spaces between lines * Camel Case Changes * relocate FDR filtering code to only occur if user performs parsimony * 1% and below PSMs assigned to parsimony proteins * Fix with indistiguishable proteins. Ensuring that proteins not already present in the protein parsimony list * Update ProteinParsimonyEngine.cs * 286 (#1312) * fix installer issue that caused metamorpheus to not open (#1288) * Update to mzlib 328 (#1285) * Update mzlib * Revert "Update mzlib" This reverts commit 1b3fa4f. * update mzlib * Non tomls (#1284) * test * test remove * Added column of matched intensity values * FIXED: intensitiy count for comp ions * Revisons to Intensity column add * Fixed reassign non-specific maxpeptide length * Remove conflic marker * Delete line * Change to for loops (readability) * update mzLib; fix bug in displaying matched ion info (#1292) * Smaller refactor to common parameters * Make maxThreadsPerFile privately set * FDR Filtering Prior to Protein Parsimony (#1296) * Fix all merge errors * Merge and Merge Fixes * edits * fixed issue * remove test code * brackets * Codacy Edits * rob edits * rob edit 2 * MBR with multiple proteases, has errors becasue mzLib method not yet incorporated * Make Parsimony only take into account 1% or better FDR peptides * removed regions * Fdr filtereing done with peptide with set mods accessed from psms after mathcing, before parsimony * FdrFiltering With Psms * FDR Filtering PSMs prior to parsimony * remove test code * removing extra spaces between lines * Camel Case Changes * relocate FDR filtering code to only occur if user performs parsimony * 1% and below PSMs assigned to parsimony proteins * Index out of bounds indexing engine fix (#1299) * Include troubleshooting for MSFileReader Address issue #1300 * fix "cumulative target" skipping numbers (#1302) * fix decoy skipping (#1303) * fix "cumulative target" skipping numbers * fix decoy skipping * File specific overwrote all other parameters to default (#1305) * File specific parameter overwrite fix * Remove clone * Remove useless note * remove useless resources * Revert "Remove clone" This reverts commit a706a4f. * Small fix ensures that crashes in entering indistinguishable proteins are handled (#1307) * Fix all merge errors * Merge and Merge Fixes * edits * fixed issue * remove test code * brackets * Codacy Edits * rob edits * rob edit 2 * MBR with multiple proteases, has errors becasue mzLib method not yet incorporated * Make Parsimony only take into account 1% or better FDR peptides * removed regions * Fdr filtereing done with peptide with set mods accessed from psms after mathcing, before parsimony * FdrFiltering With Psms * FDR Filtering PSMs prior to parsimony * remove test code * removing extra spaces between lines * Camel Case Changes * relocate FDR filtering code to only occur if user performs parsimony * 1% and below PSMs assigned to parsimony proteins * Fix with indistiguishable proteins. Ensuring that proteins not already present in the protein parsimony list * Update ProteinParsimonyEngine.cs * MetaMorpheus Add for maxThreads in MzLib change (#1310) * MetaMorpheus Add for maxThreads in MzLib change * Added maxThreads for different methods * MaxThread method add * Rob's MetaDraw... (#1306) * OutputNoice * haha * aha * uhum * hmph * Noice * Fixes * version check * 205 with auto_update * added features * Auto_Update * installer updated * Aha * Yah * Uhum * uhum * Wooh * revert * minor * uhum * Remove unused * noice * noice * codemaid * Yah * Cleaner * noice * hm * installer * installer * checkbox * Added Unimod Menu Bar * added features: installer, do_not_remind and Update Unimods * remove weird * weird * hm * hm * Cleaned up * add settings * add modslocation * Git final * restore * plz solve conflict * fied indent * Violent installer * indenting fixed * A Decent Installer * Fix menu option * Simplify updater * Update Product.wxs * Debug travis * Gah * Environment.GetFolderPath(Environment.SpecialFolder.ProgramFiles) * yah * Noice * Simplify * datadir menu option * Updated to Origin * MetaUpdater Added release notes * Meta Updater * Cleanup * clean_up and Update * desktop sc * package code fix * commented with Codacy checked errors and warnings on Codacy. All minor things. * Update TestScan.cs * fix * Update TestScan.cs * Update TestScan.cs * Large file test command backup * Update command * okay * Fix a few * Mkay * Update to Curr -- Appveyor * Set to release * Added Encrypted Cert * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update * update * Update CalibrationTask.cs * Update CalibrationTask.cs * yah * Bootstraper * cleanup * sln fix * bootin * Update MetaMorpheus.sln * Update MetaMorpheus.sln * bundle compile * Update MetaMorpheus.sln * Uhum * Hmhp * aha * fixup * yeah * yeah * update to upstream * XL Different crosslink sites * XL crosslink different amino acid GUI * XL Improve codeCov * XL Improve CodeCov2 * XL test Target 90% coverage * XLTest Target 90% coverage2 * XLTest Target 90% coverage3 * XL pep.XML mod position N ter refer as 0 * XL test diff crosslink site * Optimize xltest code * XL improve code quality * XL GenerateIntensityRanks() bug * Output pep.XML for Search Task * pepXML works for Search Task * pep.xml works for TPP now! * pep.xml Search Engine Tandom * Update pep.XML * PepXML update * PepXMLWriter Class * Remove useless library pepxml * Add Quantification Setting Window * QuanSetGUI * Start RealTime GUI project * Data Collect * Connection bug * Notification Event * Updata DataReceiver Notification * Dispatcher BeginInvoke * Add MetaDraw into MetaMorpheus * MetaDraw using MsDataFile * Data Receiver by TbNotification * Add Realtime database * dd * clear * cleanup dd * RealTime add parameter * Success generate ion index for real time * Check Thread * Add log4net * log in DataReceiver * DataReceiver cannot have logWatcher * Try BeginInvoke * LogWatcher BeginInvoke * Add Notification * Add Dump * check Notification 2nd * try DataReceiver.Notifications * metadraw * no sense * sync * Update Installer * MetaDraw update Product ions parameter * Update SpectrumForDataGrid * Update * MetaDraw Added * Fix Pull * MetaDraw Added * updates * MetaDraw * try to build * try to build 2 * metadraw edits * use established peptide classes to get fragments; graphical improvements; other code improvements * revamp interface * oops * Deisotoping options for GPTMD (#1319) * Remove method that was moved to mzLib (#1324) * Fix weird uni prot naming conflicts (#1321) * fix UniProt naming conflicts from the PTM list * rename some stuff * appveyor * temporary console output to figure out what appveyor is doing * appveyor... * appveyor.... * appveyor..... * warning message for duplicate IDs * Warning for more than 1 variable mod (#1318) * Warning for more than 1 variable mod * Added warning from issue #1027 * Centralized * Update GlobalGuiSettings.cs * Update SearchTaskWindow.xaml.cs * Compile fix (#1325) * compile fix * fix to compile * simpler * Output file name rename/organization (#1311) * File Output Reorganization * Test changed * Fixed Tests * BinGeneration Test fix * Cleaner Code * Fixes changed * lots of changes * small fix * Q value filter (#1327) * QValueParam * Changes to file writing * Small Changes * Smaller Changes * Merge conflicts * small things * Adapt test * Fixes * Qvalue variable change * Fixes * rob edits * rob edit 2 * rob edits 3 * succiylation rename (#1331) * Fix q value filter gui (#1332) * fix q value filter gui stuff in search task * one more thing * toml parsing * Rob's MetaDraw Added Features (#1333) * MetaDraw update * Create linkedlistToBST.java * changes * Updated MetaDraw * base sequence annotation * Fix Circle * Fix Width * mod annotation stuff * change ion sides in base seq annotation * Fix NSESTAP (#1329) * Remove commonparams from postsearchanalysisparameters * Update postProcessing construction * Update NSESTAP PWSM constructor (CAUTION) * Update PSAT * Fix removal of constructor * fix XL search crash when there are no results (#1337) * temporarily disable metadraw (#1342)
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#957