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• 405fbf17ff improve documentation efischer 2022-02-20 17:11:39 -06:00
• 24519f4a52 improve documentation efischer 2022-02-20 17:04:25 -06:00
• 2afd01eeef improve documentation efischer 2022-02-20 15:48:11 -06:00
• 10d0b711bf improve documentation efischer 2022-02-20 15:38:40 -06:00
• 8f98baf44e improve documentation efischer 2022-02-20 15:37:39 -06:00
• d6c7c40c96 improve documentation efischer 2022-02-20 13:23:15 -06:00
• 61c14b2ecf improve documentation efischer 2022-02-20 13:20:47 -06:00
• 22fc4aedfe improve documentation efischer 2022-02-20 13:18:49 -06:00
• 5d24dc6f70 improve documentation efischer 2022-02-20 13:15:32 -06:00
• 2c01a0211c move readme efischer 2022-02-20 12:02:27 -06:00
• f2b5d9e1b7 Rename and update readme efischer 2022-02-20 11:58:12 -06:00
• 74c8cafd81 scan for filename efischer 2022-02-20 03:08:31 -06:00
• d1c37b5ccd Relocate overlap threshold filters efischer 2022-02-20 03:05:56 -06:00
• cb2c5a6024 Add plate well concentrations to output data efischer 2022-02-20 02:29:42 -06:00
• 284a5b3a40 Add plate well concentrations to output data efischer 2022-02-20 02:23:31 -06:00
• 52afb1edc2 Add plate well concentrations to output data efischer 2022-02-20 02:17:36 -06:00
• 9c52bc878a Add plate well concentrations to output data efischer 2022-02-20 02:13:13 -06:00
• 248fe4d662 Add plate well concentrations to output data efischer 2022-02-20 02:09:22 -06:00
• 5d0e60708c Add plate well concentrations to output data efischer 2022-02-20 01:53:34 -06:00
• c96b7237e9 Add plate well concentrations to output data efischer 2022-02-20 01:40:01 -06:00
• 0b28259800 Add plate well concentrations to output data efischer 2022-02-20 01:13:22 -06:00
• 837ef7bfe4 UI cleanup, some code cleanup efischer 2022-02-20 01:05:28 -06:00
• 0bebbc7602 Add missing filtering code efischer 2022-02-19 22:56:38 -06:00
• 84f7ddb696 Fix interactive output efischer 2022-02-19 22:49:50 -06:00
• c4633da9eb Correct propogation of peptide counts efischer 2022-02-19 22:33:38 -06:00
• 5b2ed165d0 Clean up interactive text, bugfix efischer 2022-02-19 22:21:09 -06:00
• 0026d8cdfe Use buffered input/output streams efischer 2022-02-19 22:04:41 -06:00
• 13fb7168bf Refactor to read/write files of graph and map data efischer 2022-02-19 21:46:01 -06:00
• 568a6be3c7 Refactoring to allow graphs from file efischer 2022-02-19 17:23:55 -06:00
• cfa473c7ce Adding parameters to filter by occupancy difference and percent overlap efischer 2022-02-19 14:06:11 -06:00
• 6faacd9a82 Adding parameters to filter by occupancy difference and percent overlap efischer 2022-02-19 14:05:26 -06:00
• ce88e170c1 Update readme with max memory flag efischer 2022-02-18 17:48:25 -06:00
• 47e23addfa Do new filtering before matching efischer 2022-02-18 17:42:05 -06:00
• b9ee31b64c Do new filtering before matching efischer 2022-02-18 17:28:24 -06:00
• bf32a55e4b Implement matching using jheaps PairingHeap efischer 2022-02-18 16:09:23 -06:00
• acff88475b Command line arguments working, need better documentation and error handling efischer 2021-11-23 12:24:48 -06:00
• 32593308df Command line arguments for CDR3 matching implemented efischer 2021-11-20 10:43:57 -06:00
• 981e24011d First attempt at command line arguments efischer 2021-11-19 17:31:18 -06:00
• 3d0a843cea Adding command line argument parsing library efischer 2021-11-18 16:19:11 -06:00
• c09ef27822 Adding command line argument parsing library efischer 2021-11-18 16:15:05 -06:00
• 2ab93dd4b7 Recording source file names in output files, allowing output of intermediate results efischer 2021-11-18 15:38:29 -06:00
• 09aa5961f3 New executable build after code refactor. efischer 2021-11-18 14:16:42 -06:00
• 34e96d3b3d Refactor to reduce code repetition efischer 2021-11-18 14:11:04 -06:00
• 2064d7e9fc Implemented parameter for CDR1 frequency efischer 2021-11-18 11:55:54 -06:00
• 4157cfb556 Usage instructions for executable .jar efischer 2021-11-16 21:27:54 -06:00
• cb6330166f Adding executable .jar efischer 2021-11-16 21:21:48 -06:00
• 2fee44d3ee removed unused imports efischer 2021-11-16 16:46:17 -06:00
• 255a3ba66c Added timing to CDR3/CDR1 matching efischer 2021-11-16 16:37:29 -06:00
• 48510a5b60 Improved efficiency by pre-filtering peptide lists before making and processing graphs efischer 2021-11-16 16:31:35 -06:00
• 26304e5dff bugfix efischer 2021-11-16 09:29:07 -06:00
• c28378632f bugfix efischer 2021-11-15 15:02:59 -06:00
• e61e384513 bugfix efischer 2021-11-15 15:01:40 -06:00
• 13b58e3204 Expanding simulation to attempt CDR3/CDR1 matching - doubles size of cells efischer 2021-11-15 15:00:11 -06:00
• c425b05d8c Expanding simulation to attempt CDR3/CDR1 matching - doubles size of cells efischer 2021-11-15 11:24:46 -06:00
• b612d65bda typos efischer 2021-11-12 11:35:11 -06:00
• 6606702aa1 added acknowledgements efischer 2021-11-12 11:34:21 -06:00
• 92add6786a Bugfix, can now do plates with <96 wells efischer 2021-11-12 11:16:21 -06:00
• e15cbc6672 All working, able to be built to .jar efischer 2021-11-12 10:41:44 -06:00
• d39fdbee3b Three ways of making graph, but [...]MatrixGenerator is fastest efischer 2021-11-10 11:18:31 -06:00
• 93cac1d38a Two ways of making graph, fixed bug with thresholds efischer 2021-11-10 09:15:03 -06:00
• 8280382ca7 Added method using matrix builder efischer 2021-11-09 21:26:10 -06:00
• 82d5500ae8 Initial Commit - works well, but too memory intensive efischer 2021-11-09 20:24:22 -06:00