Commit Graph

Select branches

Hide Pull Requests

master

v1.0

v1.1

v1.2

v1.3

v1.4

v1.5

v2.0

v3.0

v4.0

v4.1

v4.2

v4.3

v4.4

Mono Color

• b1155f8100 Format -help CLI option efischer 2022-02-27 16:53:46 -06:00
• 12b003a69f Add -help CLI option efischer 2022-02-27 16:45:30 -06:00
• 32c5bcaaff Deactivate file I/O announcement for CLI efischer 2022-02-27 16:16:24 -06:00
• 2485ac4cf6 Add getters to MatchingResult efischer 2022-02-27 16:15:26 -06:00
• 05556bce0c Add units to metadata efischer 2022-02-27 16:08:59 -06:00
• a822f69ea4 Control verbose output efischer 2022-02-27 16:07:17 -06:00
• 3d1f8668ee Control verbose output efischer 2022-02-27 16:03:57 -06:00
• 40c743308b Initialize wells efischer 2022-02-27 15:54:47 -06:00
• 5246cc4a0c Re-implement command line options efischer 2022-02-27 15:35:07 -06:00
• a5f7c0641d Refactor for better encapsulation with CellSamples efischer 2022-02-27 14:51:53 -06:00
• 8ebfc1469f Refactor plate to fill its own wells in its constructor efischer 2022-02-27 14:25:53 -06:00
• b53f5f1cc0 Refactor plate to fill its own wells in its constructor efischer 2022-02-27 14:17:16 -06:00
• 974d2d650c Refactor plate to fill its own wells in its constructor efischer 2022-02-27 14:17:11 -06:00
• 6b5837e6ce Add Vose's alias method to to-dos efischer 2022-02-27 11:46:11 -06:00
• b4cc240048 Update Readme v1.5 efischer 2022-02-26 11:03:31 -06:00
• ff72c9b359 Update Readme efischer 2022-02-26 11:02:23 -06:00
• 88eb8aca50 Update Readme efischer 2022-02-26 11:01:44 -06:00
• 98bf452891 Update Readme efischer 2022-02-26 11:01:20 -06:00
• c2db4f87c1 Update Readme efischer 2022-02-26 11:00:18 -06:00
• 8935407ade Get rid of GraphML reader, those files are larger than serialized files efischer 2022-02-26 10:38:10 -06:00
• 9fcc20343d Fix GraphML writer efischer 2022-02-26 10:36:00 -06:00
• 817fe51708 Code cleanup efischer 2022-02-26 09:56:46 -06:00
• 1ea68045ce Refactor cdr3 matching to use new Vertex class efischer 2022-02-26 09:49:16 -06:00
• 75b2aa9553 testing graph attributes efischer 2022-02-26 08:58:52 -06:00
• b3dc10f287 add graph attributes to graphml writer efischer 2022-02-26 08:15:48 -06:00
• fb8d8d8785 make heap type an enum efischer 2022-02-26 08:15:31 -06:00
• ab437512e9 make Vertex serializable efischer 2022-02-26 07:45:36 -06:00
• 7b03a3cce8 bugfix efischer 2022-02-26 07:35:34 -06:00
• f032d3e852 rewrite GraphML importer/exporter efischer 2022-02-26 07:34:07 -06:00
• b604b1d3cd Changing graph to use Vertex class efischer 2022-02-26 06:19:08 -06:00
• e4d094d796 Adding GraphML output to options menu efischer 2022-02-24 17:22:07 -06:00
• f385ebc31f Update vertex class efischer 2022-02-24 16:25:01 -06:00
• 8745550e11 add MWM algorithm type to matching metadata efischer 2022-02-24 16:24:48 -06:00
• 41805135b3 remove unused import efischer 2022-02-24 16:04:30 -06:00
• 373a5e02f9 Refactor to make CellSample class more self-contained efischer 2022-02-24 16:03:49 -06:00
• 7f18311054 fix typos efischer 2022-02-24 15:55:32 -06:00
• bcb816c3e6 Reformat TODO efischer 2022-02-24 15:48:10 -06:00
• dad0fd35fd Update readme to reflect wells with random population implemented efischer 2022-02-24 15:47:08 -06:00
• 35d580cfcf Update readme to reflect wells with random population implemented efischer 2022-02-24 15:45:03 -06:00
• ab8d98ed81 Update readme to reflect new default caching behavior. v1.4 efischer 2022-02-24 15:39:15 -06:00
• 3d9890e16a Change GraphModificationFunctions to only save edges if graph data is cached efischer 2022-02-24 15:32:27 -06:00
• dd64ac2731 Change GraphModificationFunctions to interface efischer 2022-02-24 15:18:09 -06:00
• a5238624f1 Change default graph caching behavior to false efischer 2022-02-24 15:14:28 -06:00
• d8ba42b801 Fix Algorithm Options menu output efischer 2022-02-24 14:59:08 -06:00
• 8edd89d784 Added heap type selection, fixed error handling efischer 2022-02-24 14:48:19 -06:00
• 2829b88689 Update readme to reflect caching changes v1.3 efischer 2022-02-24 12:47:26 -06:00
• 108b0ec13f Improve options menu wording efischer 2022-02-24 12:42:09 -06:00
• a8b58d3f79 Output new setting when changing options efischer 2022-02-24 12:38:15 -06:00
• bf64d57731 implement option menu for file caching efischer 2022-02-24 12:30:47 -06:00
• c068c3db3c implement option menu for file caching efischer 2022-02-23 20:35:31 -06:00
• 4bcda9b66c update readme v1.2 efischer 2022-02-23 13:22:04 -06:00
• 17ae763c6c Generate populations correctly efischer 2022-02-23 10:37:40 -06:00
• decdb147a9 Cache everything efischer 2022-02-23 10:30:42 -06:00
• 74ffbfd8ac make everything use same random number generator efischer 2022-02-23 09:29:21 -06:00
• 08699ce8ce Change output order to match interactive UI efischer 2022-02-23 08:56:09 -06:00
• 69b0cc535c Error checking efischer 2022-02-23 08:55:07 -06:00
• e58f7b0a55 checking for possible divide by zero error. efischer 2022-02-23 08:54:14 -06:00
• dd2164c250 implement sample plates with random well populations efischer 2022-02-23 08:14:17 -06:00
• 7323093bdc change "getRandomNumber" to "getRandomInt" for consistency. efischer 2022-02-23 08:13:52 -06:00
• f904cf6672 add more data caching code efischer 2022-02-23 08:13:06 -06:00
• 3ccee9891b change "concentrations" to "populations" for consistency efischer 2022-02-23 08:12:48 -06:00
• 40c2be1cfb create populations string correctly efischer 2022-02-23 08:11:01 -06:00
• 4b597c4e5e remove old testing code efischer 2022-02-23 08:10:35 -06:00
• b2398531a3 Update readme efischer 2022-02-23 05:11:36 +00:00
• 8e9a250890 Cache graph data on creation v1.1 efischer 2022-02-22 22:23:55 -06:00
• e2a996c997 update readme efischer 2022-02-22 22:23:40 -06:00
• a5db89cb0b update readme efischer 2022-02-22 22:13:01 -06:00
• 1630f9ccba Moved I/O alert to file reader efischer 2022-02-22 22:11:50 -06:00
• d785aa0da2 Moved I/O alert to file reader efischer 2022-02-22 22:10:31 -06:00
• a7afeb6119 bugfixes efischer 2022-02-22 22:10:09 -06:00
• f8167b0774 Add .jar manifest to repo efischer 2022-02-22 21:45:46 -06:00
• 68ee9e4bb6 Implemented storing graphs in memory for multiple pairing experiments efischer 2022-02-22 21:30:00 -06:00
• fd2ec76b71 Realized how to store graph in memory efischer 2022-02-22 19:42:35 -06:00
• 875f457a2d reimplement CLI (in progress) efischer 2022-02-22 19:42:23 -06:00
• 906c06062f Added metadata to MatchingResult to enable CLI options efischer 2022-02-22 18:36:30 -06:00
• 90ae2ff474 Re-implemeting CLI options (in progress) efischer 2022-02-22 17:37:00 -06:00
• 7d983076f3 Add link to releases page for download efischer 2022-02-22 16:34:24 -06:00
• 4b053e6ec4 Remove artifacts from tracking to stop repo bloat. v1.0 efischer 2022-02-22 16:14:50 -06:00
• 44784b7976 Remove artifacts from tracking to stop repo bloat. efischer 2022-02-22 16:10:22 -06:00
• 7c19896dc9 update readme efischer 2022-02-22 16:09:50 -06:00
• aec7e3016f Typos in documentation efischer 2022-02-21 11:19:54 -06:00
• 5c75c1ac09 Update readme.md efischer 2022-02-21 06:53:30 +00:00
• cb1f7adece Change "peptide" references in code to "sequence", adding comments efischer 2022-02-21 00:29:34 -06:00
• 370de79546 Add performance section to readme efischer 2022-02-21 00:02:49 -06:00
• a803336f56 Add performance section to readme efischer 2022-02-21 00:01:20 -06:00
• 94b54b3416 Add performance section to readme efischer 2022-02-20 23:31:25 -06:00
• 601e141fd0 Update readme efischer 2022-02-20 22:51:49 -06:00
• 8f9c6b7d33 Update readme TODO efischer 2022-02-20 20:59:05 -06:00
• e5ddc73723 Finish reverting back to wells-as-rows efischer 2022-02-20 20:54:44 -06:00
• 9b18fac74f Invoke garbage collection efischer 2022-02-20 20:47:12 -06:00
• 63ef6aa7a0 Revert attempt to switch plate output format. It worked, but introduced a bug in graph filtering I don't want to chase down efischer 2022-02-20 20:45:35 -06:00
• 7558455f39 Correct errors in output and documentation efischer 2022-02-20 20:13:38 -06:00
• 410f0ae547 Remove testing code, add garbage collection calls efischer 2022-02-20 20:06:45 -06:00
• 1bc6a11545 Change plate reader/writer to use columns as wells efischer 2022-02-20 19:58:24 -06:00
• 2b13e10e95 Change plate reader/writer to use columns as wells efischer 2022-02-20 19:48:09 -06:00
• 4fd5baeb98 Change plate reader/writer to use columns as wells efischer 2022-02-20 19:41:06 -06:00
• b2a4e9a42b Change plate reader/writer to use columns as wells efischer 2022-02-20 19:17:56 -06:00
• d1bb49b482 Change plate reader/writer to use columns as wells efischer 2022-02-20 19:12:11 -06:00
• 9adb7dffb8 Change plate reader/writer to use columns as wells efischer 2022-02-20 19:08:04 -06:00
• 2023bb9d7e Cleanup file output, add UI verbosity efischer 2022-02-20 18:31:31 -06:00