https://sourceforge.net/p/cruxtoolkit/activity/Recent activity for Crux-ToolkitenThu, 13 Oct 2016 23:12:35 -0000https://sourceforge.net/p/cruxtoolkit/code/17190/Changed home page to redirect to new siteCharles E. GrantThu, 13 Oct 2016 23:12:35 -0000https://sourceforge.net/p/cruxtoolkit/code/17190/https://sourceforge.net/p/cruxtoolkit/code/17189/Last commit before transfer from svn to git. Fi...Andy LinThu, 29 Sep 2016 03:05:23 -0000https://sourceforge.net/p/cruxtoolkit/code/17189/https://sourceforge.net/p/cruxtoolkit/code/17188/Prelim commit after merging from trunk. Incopor...Andy LinMon, 26 Sep 2016 19:14:40 -0000https://sourceforge.net/p/cruxtoolkit/code/17188/https://sourceforge.net/p/cruxtoolkit/code/17187/remove lexical cast dependency from stringutilsKaipoThu, 22 Sep 2016 16:40:35 -0000https://sourceforge.net/p/cruxtoolkit/code/17187/https://sourceforge.net/p/cruxtoolkit/code/17186/update percolator test for new columnsKaipoWed, 21 Sep 2016 17:51:12 -0000https://sourceforge.net/p/cruxtoolkit/code/17186/https://sourceforge.net/p/cruxtoolkit/code/17185/Added simple percolator smoke test. Code review...Matthew TheWed, 21 Sep 2016 09:12:23 -0000https://sourceforge.net/p/cruxtoolkit/code/17185/https://sourceforge.net/p/cruxtoolkit/code/17184/update smoke tests for removing original-output...KaipoTue, 20 Sep 2016 21:23:10 -0000https://sourceforge.net/p/cruxtoolkit/code/17184/https://sourceforge.net/p/cruxtoolkit/code/17183/Summary: Some minor edits to txt-format.html.William S NobleTue, 20 Sep 2016 18:24:08 -0000https://sourceforge.net/p/cruxtoolkit/code/17183/https://sourceforge.net/p/cruxtoolkit/code/17182/Patch percolator to use its native outputKaipoTue, 20 Sep 2016 16:46:58 -0000https://sourceforge.net/p/cruxtoolkit/code/17182/https://sourceforge.net/p/cruxtoolkit/code/17181/Added cucumber tests for cascade searchAlice ChengThu, 15 Sep 2016 21:43:54 -0000https://sourceforge.net/p/cruxtoolkit/code/17181/https://sourceforge.net/p/cruxtoolkit/issues/431/Cascade search file column bugAlice ChengWed, 14 Sep 2016 22:10:54 -0000https://sourceforge.net/p/cruxtoolkit/issues/431/https://sourceforge.net/p/cruxtoolkit/code/17180/fix typoKaipoTue, 13 Sep 2016 19:59:29 -0000https://sourceforge.net/p/cruxtoolkit/code/17180/https://sourceforge.net/p/cruxtoolkit/code/17179/When constructing the stand-alone percolator co...William S NobleMon, 12 Sep 2016 14:05:46 -0000https://sourceforge.net/p/cruxtoolkit/code/17179/https://sourceforge.net/p/cruxtoolkit/code/17178/Added note that current build of Crux for OS X ...Charles E. GrantThu, 08 Sep 2016 22:56:01 -0000https://sourceforge.net/p/cruxtoolkit/code/17178/https://sourceforge.net/p/cruxtoolkit/issues/430/?limit=25#3211Thanks Bill, it is committed (r17177)KaipoThu, 08 Sep 2016 22:35:50 -0000https://sourceforge.net/p/cruxtoolkit/issues/430/?limit=25#3211https://sourceforge.net/p/cruxtoolkit/issues/430/Fix Percolator output columnsKaipoThu, 08 Sep 2016 22:35:50 -0000https://sourceforge.net/p/cruxtoolkit/issues/430/https://sourceforge.net/p/cruxtoolkit/code/17177/Add percolator pep column and fix name of match...KaipoThu, 08 Sep 2016 22:33:56 -0000https://sourceforge.net/p/cruxtoolkit/code/17177/https://sourceforge.net/p/cruxtoolkit/issues/430/?limit=25#197b/7fb9This looks good. All tests pass, and it seems to work well. Please check it in. On...William S NobleThu, 08 Sep 2016 22:30:16 -0000https://sourceforge.net/p/cruxtoolkit/issues/430/?limit=25#197b/7fb9https://sourceforge.net/p/cruxtoolkit/issues/430/?limit=25#197bHere is a patch to fix these two issues.KaipoThu, 08 Sep 2016 18:48:32 -0000https://sourceforge.net/p/cruxtoolkit/issues/430/?limit=25#197bhttps://sourceforge.net/p/cruxtoolkit/code/17176/Added missing good results file for isotope errorAlice ChengWed, 07 Sep 2016 22:45:50 -0000https://sourceforge.net/p/cruxtoolkit/code/17176/https://sourceforge.net/p/cruxtoolkit/issues/429/?limit=25#d1ae/9829I have also verified that Percolator yields about 5-fold more PSMs using the latest...William S NobleWed, 07 Sep 2016 22:15:04 -0000https://sourceforge.net/p/cruxtoolkit/issues/429/?limit=25#d1ae/9829https://sourceforge.net/p/cruxtoolkit/issues/430/?limit=25#9e81/01f1Just to confirm what we discussed in person, yes, you should use two different feature...William S NobleWed, 07 Sep 2016 22:05:23 -0000https://sourceforge.net/p/cruxtoolkit/issues/430/?limit=25#9e81/01f1https://sourceforge.net/p/cruxtoolkit/code/17175/Added Isotope ErrorAlice ChengWed, 07 Sep 2016 21:51:27 -0000https://sourceforge.net/p/cruxtoolkit/code/17175/https://sourceforge.net/p/cruxtoolkit/issues/400/tide-search fails to parse MGF file (in search-for-xlinks branch)William S NobleWed, 07 Sep 2016 21:18:25 -0000https://sourceforge.net/p/cruxtoolkit/issues/400/https://sourceforge.net/p/cruxtoolkit/code/17174/Remove some unused tide codeKaipoWed, 07 Sep 2016 19:58:43 -0000https://sourceforge.net/p/cruxtoolkit/code/17174/https://sourceforge.net/p/cruxtoolkit/issues/430/?limit=25#9e81For (1), what happens is that when we convert to pin, both distinct matches/spectrum...KaipoWed, 07 Sep 2016 19:18:26 -0000https://sourceforge.net/p/cruxtoolkit/issues/430/?limit=25#9e81https://sourceforge.net/p/cruxtoolkit/issues/429/?limit=25#d1aeI think the version is different for the binary - I get the same results (26,342...KaipoWed, 07 Sep 2016 18:27:16 -0000https://sourceforge.net/p/cruxtoolkit/issues/429/?limit=25#d1aehttps://sourceforge.net/p/cruxtoolkit/issues/430/Fix Percolator output columnsWilliam S NobleTue, 06 Sep 2016 14:53:01 -0000https://sourceforge.net/p/cruxtoolkit/issues/430/https://sourceforge.net/p/cruxtoolkit/issues/429/Percolator does not report all of the PSMsWilliam S NobleSat, 03 Sep 2016 16:31:57 -0000https://sourceforge.net/p/cruxtoolkit/issues/429/https://sourceforge.net/p/cruxtoolkit/code/17173/Update test results for percolator 3.00KaipoFri, 02 Sep 2016 21:58:52 -0000https://sourceforge.net/p/cruxtoolkit/code/17173/https://sourceforge.net/p/cruxtoolkit/code/17172/fix build for updated protocol buffers on windowsKaipoFri, 02 Sep 2016 19:11:22 -0000https://sourceforge.net/p/cruxtoolkit/code/17172/https://sourceforge.net/p/cruxtoolkit/code/17171/Merge from trunk to res-evAndy LinFri, 02 Sep 2016 18:46:13 -0000https://sourceforge.net/p/cruxtoolkit/code/17171/https://sourceforge.net/p/cruxtoolkit/issues/428/list-of-files does not work for assign-confidenceWilliam S NobleFri, 02 Sep 2016 14:43:59 -0000https://sourceforge.net/p/cruxtoolkit/issues/428/https://sourceforge.net/p/cruxtoolkit/code/17170/Summary: Fix minor mistake in parameter descrip...William S NobleFri, 02 Sep 2016 14:39:54 -0000https://sourceforge.net/p/cruxtoolkit/code/17170/https://sourceforge.net/p/cruxtoolkit/code/17169/Fixed some bugs in performance-tests. All plots...Andy LinTue, 30 Aug 2016 23:10:44 -0000https://sourceforge.net/p/cruxtoolkit/code/17169/https://sourceforge.net/p/cruxtoolkit/issues/423/?limit=25#d202committed in r17168KaipoTue, 30 Aug 2016 21:31:49 -0000https://sourceforge.net/p/cruxtoolkit/issues/423/?limit=25#d202https://sourceforge.net/p/cruxtoolkit/issues/423/Upgrade to Percolator 3.0KaipoTue, 30 Aug 2016 21:31:49 -0000https://sourceforge.net/p/cruxtoolkit/issues/423/https://sourceforge.net/p/cruxtoolkit/code/17168/Update percolator to 3.00KaipoTue, 30 Aug 2016 21:30:58 -0000https://sourceforge.net/p/cruxtoolkit/code/17168/https://sourceforge.net/p/cruxtoolkit/code/17167/Fixed global fontsYuval BossTue, 30 Aug 2016 18:50:21 -0000https://sourceforge.net/p/cruxtoolkit/code/17167/https://sourceforge.net/p/cruxtoolkit/code/17166/Add nobullet class to li elements in CreateDocsKaipoTue, 30 Aug 2016 18:47:19 -0000https://sourceforge.net/p/cruxtoolkit/code/17166/https://sourceforge.net/p/cruxtoolkit/code/17165/Rename required argument for Percolator from 'p...William S NobleTue, 30 Aug 2016 17:18:15 -0000https://sourceforge.net/p/cruxtoolkit/code/17165/https://sourceforge.net/p/cruxtoolkit/code/17164/Fixed parsing of version numbers for downloadin...Charles E. GrantMon, 29 Aug 2016 23:42:55 -0000https://sourceforge.net/p/cruxtoolkit/code/17164/https://sourceforge.net/p/cruxtoolkit/code/17163/Updated links to static Pwiz tarball and Google...Charles E. GrantMon, 29 Aug 2016 21:19:32 -0000https://sourceforge.net/p/cruxtoolkit/code/17163/https://sourceforge.net/p/cruxtoolkit/code/17162/Several small fixes, including adding a new std...William S NobleMon, 29 Aug 2016 18:02:32 -0000https://sourceforge.net/p/cruxtoolkit/code/17162/https://sourceforge.net/p/cruxtoolkit/code/17161/Did a merge with crux trunkAndy LinSat, 27 Aug 2016 16:36:19 -0000https://sourceforge.net/p/cruxtoolkit/code/17161/https://sourceforge.net/p/cruxtoolkit/code/17160/Started prepping code for score-function=BOTH. ...Andy LinSat, 27 Aug 2016 01:36:41 -0000https://sourceforge.net/p/cruxtoolkit/code/17160/https://sourceforge.net/p/cruxtoolkit/code/17159/Updated build to use Google gflags 2.1.2 downlo...Charles E. GrantSat, 27 Aug 2016 00:10:11 -0000https://sourceforge.net/p/cruxtoolkit/code/17159/https://sourceforge.net/p/cruxtoolkit/code/17158/Added gnutar requirement for OS X source buildCharles E. GrantSat, 27 Aug 2016 00:06:34 -0000https://sourceforge.net/p/cruxtoolkit/code/17158/https://sourceforge.net/p/cruxtoolkit/code/17157/Finished coding up adding amino acid frequencie...Andy LinThu, 25 Aug 2016 19:00:48 -0000https://sourceforge.net/p/cruxtoolkit/code/17157/https://sourceforge.net/p/cruxtoolkit/code/17156/started writing code for creating the residue e...Andy LinWed, 24 Aug 2016 18:19:27 -0000https://sourceforge.net/p/cruxtoolkit/code/17156/https://sourceforge.net/p/cruxtoolkit/code/17155/Redid how Crux reads in the 'score-function' pa...Andy LinMon, 22 Aug 2016 17:55:31 -0000https://sourceforge.net/p/cruxtoolkit/code/17155/https://sourceforge.net/p/cruxtoolkit/code/17154/Edited objects.h to add a scorer type for resid...Andy LinWed, 17 Aug 2016 20:27:27 -0000https://sourceforge.net/p/cruxtoolkit/code/17154/https://sourceforge.net/p/cruxtoolkit/code/17153/Update to performance test on res-ev branch. No...William S NobleWed, 17 Aug 2016 15:04:04 -0000https://sourceforge.net/p/cruxtoolkit/code/17153/https://sourceforge.net/p/cruxtoolkit/code/17152/Finished coding residue evidence when exact-p-v...Andy LinWed, 17 Aug 2016 01:34:59 -0000https://sourceforge.net/p/cruxtoolkit/code/17152/https://sourceforge.net/p/cruxtoolkit/code/17151/Updated performance tests to include residue-ev...William S NobleTue, 16 Aug 2016 21:56:18 -0000https://sourceforge.net/p/cruxtoolkit/code/17151/https://sourceforge.net/p/cruxtoolkit/code/17150/Some optimizations in the xcorr correlation fxnsjoemacTue, 16 Aug 2016 03:43:17 -0000https://sourceforge.net/p/cruxtoolkit/code/17150/https://sourceforge.net/p/cruxtoolkit/code/17149/Half-fix to make mods only occur once on a sing...sjoemacTue, 16 Aug 2016 02:53:13 -0000https://sourceforge.net/p/cruxtoolkit/code/17149/https://sourceforge.net/p/cruxtoolkit/code/17148/Did a merge with crux trunk. No merge conflicts.Andy LinMon, 15 Aug 2016 19:20:20 -0000https://sourceforge.net/p/cruxtoolkit/code/17148/https://sourceforge.net/p/cruxtoolkit/code/17147/Deleting some items not under version control t...Andy LinMon, 15 Aug 2016 18:17:26 -0000https://sourceforge.net/p/cruxtoolkit/code/17147/https://sourceforge.net/p/cruxtoolkit/code/17146/Minor spacing editsAndy LinFri, 12 Aug 2016 00:10:42 -0000https://sourceforge.net/p/cruxtoolkit/code/17146/https://sourceforge.net/p/cruxtoolkit/issues/393/?limit=25#b457Just fixed and put into the trunk all the lint errors except 1: ../../src/io/SQTWriter.cpp:61:...Alice ChengThu, 11 Aug 2016 23:45:10 -0000https://sourceforge.net/p/cruxtoolkit/issues/393/?limit=25#b457https://sourceforge.net/p/cruxtoolkit/code/17145/Updated io files to adhere to lint tests. Code ...Alice ChengThu, 11 Aug 2016 23:33:03 -0000https://sourceforge.net/p/cruxtoolkit/code/17145/https://sourceforge.net/p/cruxtoolkit/issues/427/Threading bug in cascade-search?Alice ChengThu, 11 Aug 2016 22:47:45 -0000https://sourceforge.net/p/cruxtoolkit/issues/427/https://sourceforge.net/p/cruxtoolkit/code/17144/Fixed cascade-search lock bug. See issue #427.Alice ChengThu, 11 Aug 2016 22:46:41 -0000https://sourceforge.net/p/cruxtoolkit/code/17144/https://sourceforge.net/p/cruxtoolkit/issues/427/?limit=25#cbef/f3eeYes, I have verified that (1) my test now runs to completion, (2) it get the same...William S NobleThu, 11 Aug 2016 22:43:23 -0000https://sourceforge.net/p/cruxtoolkit/issues/427/?limit=25#cbef/f3eehttps://sourceforge.net/p/cruxtoolkit/code/17143/Added Python script to summarize data in downlo...Charles E. GrantThu, 11 Aug 2016 21:57:22 -0000https://sourceforge.net/p/cruxtoolkit/code/17143/https://sourceforge.net/p/cruxtoolkit/code/17142/IT WORKS. Found a difference in TideSearchAppli...Andy LinThu, 11 Aug 2016 21:10:29 -0000https://sourceforge.net/p/cruxtoolkit/code/17142/https://sourceforge.net/p/cruxtoolkit/code/17141/IT WORKS. I think my merge with TideSearchAppli...Andy LinThu, 11 Aug 2016 21:08:08 -0000https://sourceforge.net/p/cruxtoolkit/code/17141/https://sourceforge.net/p/cruxtoolkit/issues/427/?limit=25#cbefJust figured out what was going on. It was a lock problem. There's a if () { continue;...Alice ChengThu, 11 Aug 2016 18:12:49 -0000https://sourceforge.net/p/cruxtoolkit/issues/427/?limit=25#cbefhttps://sourceforge.net/p/cruxtoolkit/issues/427/?limit=25#5aefOne of the cmd options you specified is --num-threads 1, so there shouldn't be any...Alice ChengThu, 11 Aug 2016 17:17:03 -0000https://sourceforge.net/p/cruxtoolkit/issues/427/?limit=25#5aefhttps://sourceforge.net/p/cruxtoolkit/issues/427/Threading bug in cascade-search?William S NobleThu, 11 Aug 2016 15:02:05 -0000https://sourceforge.net/p/cruxtoolkit/issues/427/https://sourceforge.net/p/cruxtoolkit/code/17140/Still getting back to normal after things went ...Andy LinThu, 11 Aug 2016 00:39:45 -0000https://sourceforge.net/p/cruxtoolkit/code/17140/https://sourceforge.net/p/cruxtoolkit/code/17139/Things went weird again....lost some code. So r...Andy LinWed, 10 Aug 2016 23:59:53 -0000https://sourceforge.net/p/cruxtoolkit/code/17139/https://sourceforge.net/p/cruxtoolkit/code/17138/Proteowizard seems to have removed Clearcore2.P...Charles E. GrantWed, 10 Aug 2016 23:44:15 -0000https://sourceforge.net/p/cruxtoolkit/code/17138/https://sourceforge.net/p/cruxtoolkit/code/17137/Did a merge with crux trunk and everything went...Andy LinWed, 10 Aug 2016 23:28:14 -0000https://sourceforge.net/p/cruxtoolkit/code/17137/https://sourceforge.net/p/cruxtoolkit/issues/426/Create smoke tests for cascade-searchWilliam S NobleWed, 10 Aug 2016 21:09:30 -0000https://sourceforge.net/p/cruxtoolkit/issues/426/https://sourceforge.net/p/cruxtoolkit/code/17136/Minor updates to cascade-search documentation.William S NobleWed, 10 Aug 2016 17:36:29 -0000https://sourceforge.net/p/cruxtoolkit/code/17136/https://sourceforge.net/p/cruxtoolkit/code/17135/Added instructions for backing up Crux SVN repo...Charles E. GrantWed, 10 Aug 2016 17:28:14 -0000https://sourceforge.net/p/cruxtoolkit/code/17135/https://sourceforge.net/p/cruxtoolkit/code/17134/Continued pulling out duplicate code in case=RE...Andy LinWed, 10 Aug 2016 01:28:30 -0000https://sourceforge.net/p/cruxtoolkit/code/17134/https://sourceforge.net/p/cruxtoolkit/code/17133/Added README describing download logging process.Charles E. GrantWed, 10 Aug 2016 00:50:01 -0000https://sourceforge.net/p/cruxtoolkit/code/17133/https://sourceforge.net/p/cruxtoolkit/code/17132/Added log file of distribution downloadsCharles E. GrantWed, 10 Aug 2016 00:42:34 -0000https://sourceforge.net/p/cruxtoolkit/code/17132/https://sourceforge.net/p/cruxtoolkit/code/17131/Fixed path to demo dataCharles E. GrantTue, 09 Aug 2016 23:05:55 -0000https://sourceforge.net/p/cruxtoolkit/code/17131/https://sourceforge.net/p/cruxtoolkit/code/17130/Summary: Fix the descriptions of delta_cn and d...William S NobleTue, 09 Aug 2016 21:52:50 -0000https://sourceforge.net/p/cruxtoolkit/code/17130/https://sourceforge.net/p/cruxtoolkit/code/17129/Fix typo in modifications column header. Update...William S NobleTue, 09 Aug 2016 20:18:26 -0000https://sourceforge.net/p/cruxtoolkit/code/17129/https://sourceforge.net/p/cruxtoolkit/issues/425/Update txt-format tableWilliam S NobleTue, 09 Aug 2016 18:56:58 -0000https://sourceforge.net/p/cruxtoolkit/issues/425/https://sourceforge.net/p/cruxtoolkit/code/17128/Summary: Update release notes re: cpos change.William S NobleTue, 09 Aug 2016 18:12:48 -0000https://sourceforge.net/p/cruxtoolkit/code/17128/https://sourceforge.net/p/cruxtoolkit/code/17127/Fix c-neg documentationKaipoTue, 09 Aug 2016 17:18:40 -0000https://sourceforge.net/p/cruxtoolkit/code/17127/https://sourceforge.net/p/cruxtoolkit/issues/424/Fix handling of mods in tide-indexWilliam S NobleTue, 09 Aug 2016 17:12:12 -0000https://sourceforge.net/p/cruxtoolkit/issues/424/https://sourceforge.net/p/cruxtoolkit/issues/423/?limit=25#1435I will try doing this now.KaipoMon, 08 Aug 2016 20:28:51 -0000https://sourceforge.net/p/cruxtoolkit/issues/423/?limit=25#1435https://sourceforge.net/p/cruxtoolkit/issues/423/Upgrade to Percolator 3.0William S NobleMon, 08 Aug 2016 20:10:41 -0000https://sourceforge.net/p/cruxtoolkit/issues/423/https://sourceforge.net/p/cruxtoolkit/code/17126/Started writing code for score-function=residue...Andy LinMon, 08 Aug 2016 18:04:37 -0000https://sourceforge.net/p/cruxtoolkit/code/17126/https://sourceforge.net/p/cruxtoolkit/issues/421/By default do not set cneg or cpos for PercolatorKaipoMon, 08 Aug 2016 17:23:47 -0000https://sourceforge.net/p/cruxtoolkit/issues/421/https://sourceforge.net/p/cruxtoolkit/code/17125/Fix for c-pos and c-neg paramsKaipoMon, 08 Aug 2016 17:23:33 -0000https://sourceforge.net/p/cruxtoolkit/code/17125/https://sourceforge.net/p/cruxtoolkit/issues/421/By default do not set cneg or cpos for PercolatorWilliam S NobleSun, 07 Aug 2016 18:04:04 -0000https://sourceforge.net/p/cruxtoolkit/issues/421/https://sourceforge.net/p/cruxtoolkit/issues/421/?limit=25#6eb4This is a slightly edited version of the patch that Kaipo sent me. Kaipo, if this...William S NobleSun, 07 Aug 2016 18:03:55 -0000https://sourceforge.net/p/cruxtoolkit/issues/421/?limit=25#6eb4https://sourceforge.net/p/cruxtoolkit/issues/420/Upgrade to Percolator 2.10William S NobleSun, 07 Aug 2016 18:02:26 -0000https://sourceforge.net/p/cruxtoolkit/issues/420/https://sourceforge.net/p/cruxtoolkit/issues/422/seg fault from tide-index in performance testWilliam S NobleSun, 07 Aug 2016 01:31:44 -0000https://sourceforge.net/p/cruxtoolkit/issues/422/https://sourceforge.net/p/cruxtoolkit/issues/422/?limit=25#9535Never mind this. I couldn't reproduce it. It seems to have been a product of an incomplete...William S NobleSun, 07 Aug 2016 01:31:27 -0000https://sourceforge.net/p/cruxtoolkit/issues/422/?limit=25#9535https://sourceforge.net/p/cruxtoolkit/issues/422/?limit=25#d69aJust ran performance tests on my mac and linux. Logs are attached below. Linux does...Alice ChengSat, 06 Aug 2016 02:31:20 -0000https://sourceforge.net/p/cruxtoolkit/issues/422/?limit=25#d69ahttps://sourceforge.net/p/cruxtoolkit/issues/422/seg fault from tide-index in performance testWilliam S NobleSat, 06 Aug 2016 01:55:10 -0000https://sourceforge.net/p/cruxtoolkit/issues/422/