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