0000000000000000000000000000000000000000 92166b3d892b84a9c584a7f684b3320b3b85378c Nimrod Priell <nimrod.priell@gmail.com> 1325992506 -0500	commit (initial): Initial revision, one-recognition simple simulation working
92166b3d892b84a9c584a7f684b3320b3b85378c caaaff2f81a1788c0094f9c58f91215034c99553 Nimrod Priell <nimrod.priell@gmail.com> 1325992579 -0500	commit: Added vim swap files to git ignore
caaaff2f81a1788c0094f9c58f91215034c99553 90f01afe1de403d6c7e7963352611ff1f274b14d Nimrod Priell <nimrod.priell@gmail.com> 1325992622 -0500	commit: swap files ignored at top level as well
90f01afe1de403d6c7e7963352611ff1f274b14d 7b391c070e75a8b14141563c5fb6dfb24a8af4fb Nimrod Priell <nimrod.priell@gmail.com> 1328157051 -0500	commit: Initial revision of simulation in R
7b391c070e75a8b14141563c5fb6dfb24a8af4fb 4bb75df3ae552e43389fa754d3b5528fe3aee449 Nimrod Priell <nimrod.priell@gmail.com> 1328158359 -0500	commit: Another version before heading to sleep
4bb75df3ae552e43389fa754d3b5528fe3aee449 bb9a7d50ce6faa3e565f080dd0917f8b8b1eb2c7 Nimrod Priell <nimrod.priell@gmail.com> 1329601747 -0500	commit: Initial revision of compiler with design through nupack working
bb9a7d50ce6faa3e565f080dd0917f8b8b1eb2c7 e33229e64f3f87348dfdab3a6b0f3f6941cbf435 Nimrod Priell <nimrod.priell@gmail.com> 1329603267 -0500	commit: Version with reading back sequences working
e33229e64f3f87348dfdab3a6b0f3f6941cbf435 fdfda3de20af21f6873cf1dc471720502f892431 Nimrod Priell <nimrod.priell@gmail.com> 1329604536 -0500	commit: Writing the in-file for NUPACK works
fdfda3de20af21f6873cf1dc471720502f892431 21f0bc08b29b15db65a8f27214c67e7a72a16dca Nimrod Priell <nimrod.priell@gmail.com> 1329604559 -0500	commit: Example complicated stack
21f0bc08b29b15db65a8f27214c67e7a72a16dca 5b49d0e2470994cb162dc48c55ddec28a6f95f27 Nimrod Priell <nimrod.priell@gmail.com> 1329604908 -0500	commit: Moved to argparse instead of deprecated optparse
5b49d0e2470994cb162dc48c55ddec28a6f95f27 aeeae19bb6d48635ec6a78ce324da4982f991fe1 Nimrod Priell <nimrod.priell@gmail.com> 1329626528 -0500	commit: basic pair structure plotting
aeeae19bb6d48635ec6a78ce324da4982f991fe1 2367807bc056f9a8638d06610b82322a25515aa9 Nimrod Priell <nimrod.priell@gmail.com> 1329626772 -0500	commit: added saving the plot to a PDF
2367807bc056f9a8638d06610b82322a25515aa9 f3a5fbf68908f653ee63efe2fe4f359de1c0c1b9 Nimrod Priell <nimrod.priell@gmail.com> 1329627878 -0500	commit: Fixed the plot saving path
f3a5fbf68908f653ee63efe2fe4f359de1c0c1b9 f1bc1c802e252e4b665a8a439bc3e62f5bcb358e Nimrod Priell <nimrod.priell@gmail.com> 1329628425 -0500	commit: fixed off by 1
f1bc1c802e252e4b665a8a439bc3e62f5bcb358e d26129a13c4ac9e64ebb7e801ac66e42608b0a29 Nimrod Priell <nimrod.priell@gmail.com> 1329629274 -0500	commit: Working full chain
d26129a13c4ac9e64ebb7e801ac66e42608b0a29 b4bd6332ec674bf112266601aa873f44b2b31757 Nimrod Priell <nimrod.priell@gmail.com> 1329630418 -0500	commit: The .in files were in the incorrect format, fixed it now
b4bd6332ec674bf112266601aa873f44b2b31757 d8e6f8a4ef7d083d86cdf4be8b72e5a2eb2b6570 Nimrod Priell <nimrod.priell@gmail.com> 1330062643 -0500	commit: Version with MFE generation
d8e6f8a4ef7d083d86cdf4be8b72e5a2eb2b6570 f02165cedd9c11391c82bf079c6343aaefa10c2d Nimrod Priell <nimrod.priell@gmail.com> 1330064591 -0500	commit: Added generating temperature-based energy and probability analysis
f02165cedd9c11391c82bf079c6343aaefa10c2d 439f7580ae4000f1160aa53c67aaa4cbfdcbd401 Nimrod Priell <nimrod.priell@gmail.com> 1330230324 -0500	commit: Refactored the code a little
439f7580ae4000f1160aa53c67aaa4cbfdcbd401 3f5b8d5bd1c1c57784f26d1dbbe1c78a95c9cf9a Nimrod Priell <nimrod.priell@gmail.com> 1330231091 -0500	commit: More refactoring
3f5b8d5bd1c1c57784f26d1dbbe1c78a95c9cf9a 5c23d7b49f63572eddeb598f30de9051f94d0b5e Nimrod Priell <nimrod.priell@gmail.com> 1330231375 -0500	commit: Refactored the code a little more
5c23d7b49f63572eddeb598f30de9051f94d0b5e 7974970f7bba2c809fa830b8635c8f1cd5d5cd15 Nimrod Priell <nimrod.priell@gmail.com> 1330234331 -0500	commit: Refactored the code a little more
7974970f7bba2c809fa830b8635c8f1cd5d5cd15 a1e49162e7ff5a7c0be793f3ebc8fc98a9f264ea Nimrod Priell <nimrod.priell@gmail.com> 1330234396 -0500	commit: Fixed minor bug with the R script
a1e49162e7ff5a7c0be793f3ebc8fc98a9f264ea 6072313e8a2677aaedb3e59f0f9b9b1ce29b02f6 Nimrod Priell <nimrod.priell@gmail.com> 1330320085 -0500	commit: Added probability and temperature plotting
6072313e8a2677aaedb3e59f0f9b9b1ce29b02f6 69631110bedaad595e3cd231d7e1eb2c3e60c674 Nimrod Priell <nimrod.priell@gmail.com> 1330370110 -0500	commit: Some object orientedness
69631110bedaad595e3cd231d7e1eb2c3e60c674 b38f37925239188d982751a3520da09fb9aeb856 Nimrod Priell <nimrod.priell@gmail.com> 1330371284 -0500	commit: Made it into a virtualenv python project
b38f37925239188d982751a3520da09fb9aeb856 899db70cfc50db8f1f7ef49693045bc5f0c693d0 Nimrod Priell <nimrod.priell@gmail.com> 1330373608 -0500	commit: Initial version of multi-file project
899db70cfc50db8f1f7ef49693045bc5f0c693d0 aceced488ad39f82826e2a4f1a74b0ed369e5736 Nimrod Priell <nimrod.priell@gmail.com> 1330375002 -0500	commit: Extracted out the Rscript calls
aceced488ad39f82826e2a4f1a74b0ed369e5736 28d228560895711e7763e659a7f46bb6a6e03c33 Nimrod Priell <nimrod.priell@gmail.com> 1330386339 -0500	commit: Refactored out the main part of the code
28d228560895711e7763e659a7f46bb6a6e03c33 e9fcb02f7b5e1409d67c0c585c3c33fa262803a4 Nimrod Priell <nimrod.priell@gmail.com> 1330450001 -0500	commit: Generating the tick instruction
e9fcb02f7b5e1409d67c0c585c3c33fa262803a4 22ece672c2e2070c2fd4b3fd1b0ccfd82d678509 Nimrod Priell <nimrod.priell@gmail.com> 1330453468 -0500	commit: Generalized write_analysis_file, improved the step_with_tick function
22ece672c2e2070c2fd4b3fd1b0ccfd82d678509 09d96aa6cf71b1619cdb8c9894940bf9c63fed16 Nimrod Priell <nimrod.priell@gmail.com> 1330457813 -0500	commit: added all desired structure state machine
09d96aa6cf71b1619cdb8c9894940bf9c63fed16 b3fbff6a50d8f1b2ca5a178ba67e15a67de694bf Nimrod Priell <nimrod.priell@gmail.com> 1330542891 -0500	commit: Basic example of DNA canvas
b3fbff6a50d8f1b2ca5a178ba67e15a67de694bf d575cf0f2cf6a17955d3e2aeb3467f0709f25fd2 Nimrod Priell <nimrod.priell@gmail.com> 1330543231 -0500	commit: Updated files to the unicode header for Python 2.7
d575cf0f2cf6a17955d3e2aeb3467f0709f25fd2 6a344797f4b744dac44af0b169482ccd5fe27da2 Nimrod Priell <nimrod.priell@gmail.com> 1330548221 -0500	commit: Basic templating engine works
6a344797f4b744dac44af0b169482ccd5fe27da2 abcf728f0de3bac5c7bbf200426c81d51151142b Nimrod Priell <nimrod.priell@gmail.com> 1330551660 -0500	commit: Working passing the strands to the html renderer
abcf728f0de3bac5c7bbf200426c81d51151142b 56d8db7f5a4dca70696e504d6a473db115a3c2e9 Nimrod Priell <nimrod.priell@gmail.com> 1330552493 -0500	commit: Made the javascript rendering of binding have proportionally lengthed strands
56d8db7f5a4dca70696e504d6a473db115a3c2e9 1a7854c600dbf7b5384d843d60e258f92f256004 Nimrod Priell <nimrod.priell@gmail.com> 1330553610 -0500	commit: Added coloring to the different strands
1a7854c600dbf7b5384d843d60e258f92f256004 85d9d9fb0cfe497497bee8daf5ac0f52e32d1baf Nimrod Priell <nimrod.priell@gmail.com> 1330554187 -0500	commit: Some overplotting protection
85d9d9fb0cfe497497bee8daf5ac0f52e32d1baf 829b14b09893e6bfdd9b34c9866cc40aaaf49a24 Nimrod Priell <nimrod.priell@gmail.com> 1330556305 -0500	commit: With (currently static) pairing rendering
829b14b09893e6bfdd9b34c9866cc40aaaf49a24 3d250c9e4fbe48cabc2e9cdd63f3a90076ca188a Nimrod Priell <nimrod.priell@gmail.com> 1330564444 -0500	commit: Fixed the logic for the binding sections
3d250c9e4fbe48cabc2e9cdd63f3a90076ca188a 2cabb531ddd37f38e05d00c2fe703e0a4c5919a1 Nimrod Priell <nimrod.priell@gmail.com> 1330581757 -0500	commit: Full state machine for one instruction unwinding rendered
2cabb531ddd37f38e05d00c2fe703e0a4c5919a1 e73f0596b39d6cf5cdce6ae7db9a63c31d3aae6d Nimrod Priell <nimrod.priell@gmail.com> 1330583930 -0500	commit: With presenting the pairplots
