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BioJulia

Bioinformatics and Computational Biology in Julia
Collective - Host: opensource - https://opencollective.com/biojulia - Website: https://biojulia.net - Code: https://github.com/BioJulia

Moves code into src/

github.com/BioJulia/FactCheck.jl - 7a10a6af50acab9581e0d097627bf595ad1c1f0e authored over 11 years ago by Zachary Allaun <[email protected]>
Adds a small readme with a simple example

github.com/BioJulia/FactCheck.jl - 5ddd6fca4eadd012a0074f782c88bdb14ef1022e authored over 11 years ago by Zachary Allaun <[email protected]>
Simple Midje-like fact assertions

github.com/BioJulia/FactCheck.jl - f7fba5f27d735923102c614b1e6c040a656591a8 authored over 11 years ago by Zachary Allaun <[email protected]>
A little documentation.

github.com/BioJulia/Codecs.jl - ec6e2bf0568d5fd7fd6d9237f82d534481724454 authored over 11 years ago by Daniel Jones <[email protected]>
Cleanup. Base64 decoder.

github.com/BioJulia/Codecs.jl - 2808944f8daeace3b03519164a5ab6108e150801 authored over 11 years ago by Daniel Jones <[email protected]>
Add Zlib encoder/decoder.

github.com/BioJulia/Codecs.jl - ea4dc70d2bbad2407a492b4b89830d0a55b04193 authored over 11 years ago by Daniel Jones <[email protected]>
Fix encoding two byte overhangs.

github.com/BioJulia/Codecs.jl - 127075587a7f2ab8492503d74deacbd1bb3fafce authored over 11 years ago by Daniel Jones <[email protected]>
Migrate Go1 code generators

github.com/BioJulia/ragel - dde4fdf705a6c5d0081e025987e140d02622d065 authored over 11 years ago by Anton Ageev <[email protected]>
Initial work. Base64 encoder.

github.com/BioJulia/Codecs.jl - d235d5a1cdbf56ca2bf8478c76922b1a4fbe0c7c authored over 11 years ago by Daniel Jones <[email protected]>
placed calcIndexSize after the analysis pass, removed it for flat gens

github.com/BioJulia/ragel - 0f9d3ef3eee4f1547e206a9c4d1cd8a6891fbca7 authored almost 12 years ago by Adrian Thurston <[email protected]>
move the setting of key type out of calcIndex

github.com/BioJulia/ragel - a86a4ee9690c5485ec3c3df639facbe72dadf520 authored almost 12 years ago by Adrian Thurston <[email protected]>
removed the setTransPos functions, which were empty

github.com/BioJulia/ragel - f03e9187fe21d5980a94b62485ba5e837bb0abfe authored almost 12 years ago by Adrian Thurston <[email protected]>
eliminated precomutation of RedTransAp::pos

This value is determined by the code gen style and shouldn't be in the common
data structures. R...

github.com/BioJulia/ragel - df6cafdc1161888da38615c87d1cb3f64574cdaa authored almost 12 years ago by Adrian Thurston <[email protected]>
store the size of the table array type

Will use the size when calculating the size of tables of different styles.
Can't do it yet, beca...

github.com/BioJulia/ragel - ab0de4d66bb75e430e8304ddb8483ee5d9aec6f6 authored almost 12 years ago by Adrian Thurston <[email protected]>
push the upper and lower limit through the binary search in RANGE_B_SEARCH.

This change results in fewer tests when ranges are adjacent.

github.com/BioJulia/ragel - 84edbd3c94da329159feacc51f52e9436677af63 authored almost 12 years ago by Adrian Thurston <[email protected]>
added missing indentagion in RANGE_B_SEARCH

github.com/BioJulia/ragel - 23ff2423ad0a5c9c68b7f85e0c0eb604a90c5023 authored almost 12 years ago by Adrian Thurston <[email protected]>
track the lower and upper limit through the condition binary search

Instead of always using the overall lower through all branches in the bin
search, track the know...

github.com/BioJulia/ragel - 52086ef65162c6670a8cbbd6b263ce947d319fe6 authored almost 12 years ago by Adrian Thurston <[email protected]>
improvements to condition b-search

Removed the the binary search from IpGoto, can just use the one in Goto. Some
simplifications du...

github.com/BioJulia/ragel - 9f65d77a45319b3022cbc2f4057786cc1d03df79 authored almost 12 years ago by Adrian Thurston <[email protected]>
full removal of condData and keyOps globals

github.com/BioJulia/ragel - 9e885069e226709241c609638fb4c7887dd14daa authored almost 12 years ago by Adrian Thurston <[email protected]>
don't need to check _keyOps in cond key ops

github.com/BioJulia/ragel - bce417da127cfc175c3abf818b4e89c655065448 authored almost 12 years ago by Adrian Thurston <[email protected]>
removed key and cond key functions that are not in use

github.com/BioJulia/ragel - 7a5c28b349996fa393dac80248e3addc84b2d137 authored almost 12 years ago by Adrian Thurston <[email protected]>
removed non-needed operators on CondKey

github.com/BioJulia/ragel - f17e2cb10520efe7bd35c15c54e4e8b4dd47f37a authored almost 12 years ago by Adrian Thurston <[email protected]>
don't need +/- operators on CondKey

github.com/BioJulia/ragel - 133b7d54ed31b86fbdc717a7a3a5ecc5f97cca99 authored almost 12 years ago by Adrian Thurston <[email protected]>
key 'add' and 'sub' functions moved into KeyOps

github.com/BioJulia/ragel - 0ed3340f985a54b1888b21842a23a8b7e27ebdd5 authored almost 12 years ago by Adrian Thurston <[email protected]>
eliminated remaining use of key comparison operators (using global keyOps).

github.com/BioJulia/ragel - 65bc1bb9eebbd241115f2ff3b94004a9153e298a authored almost 12 years ago by Adrian Thurston <[email protected]>
more elimination of global key ops

github.com/BioJulia/ragel - 845ba548873c37e6c1942dd566bb3713864fb128 authored almost 12 years ago by Adrian Thurston <[email protected]>
more elimination of the keyOps global

github.com/BioJulia/ragel - 458765a7b737fb2e5fa076762955ae57804cf650 authored almost 12 years ago by Adrian Thurston <[email protected]>
use KeyOps in the KeySet comparison

github.com/BioJulia/ragel - 94edc41705611efee3c60f911793b59d87266823 authored almost 12 years ago by Adrian Thurston <[email protected]>
more migration to non-global keyOps and condData

github.com/BioJulia/ragel - 4abf7d2a964b2182327b663ab2423502685194ad authored almost 12 years ago by Adrian Thurston <[email protected]>
checking and using fsm contex in the FsmAp struct

Fsm operations now check the context pointer, they must point to the same
instance. Using the co...

github.com/BioJulia/ragel - 8311ab5db07ee19fbcb6e5214ea27c11fb1d176e authored almost 12 years ago by Adrian Thurston <[email protected]>
putting fsmCtx on the heap so we always get to it by a pointer

github.com/BioJulia/ragel - 2de3db35de1dcc38fa5a354cc7d978ca4e7bbc27 authored almost 12 years ago by Adrian Thurston <[email protected]>
added FsmCtx structure

The context is owned by ParseData and passed into the FsmAp constructors. Must
always use the sa...

github.com/BioJulia/ragel - ea50c0c9a361158bec1b81e40c0b338849ebb261 authored almost 12 years ago by Adrian Thurston <[email protected]>
renamed keyOps and condData

Will move keyOps and condData into a context data structure so they are not
global. Prefixed wit...

github.com/BioJulia/ragel - 42f24248eb80ba40b2caeba35bc29d9da7462da5 authored almost 12 years ago by Adrian Thurston <[email protected]>
warning fixes

github.com/BioJulia/ragel - 96eeba274bb601a0bc8a158df2d3fdc22a59d720 authored almost 12 years ago by Adrian Thurston <[email protected]>
Can omit the act variable. Init stack to avoid warnings.

github.com/BioJulia/ragel - d3fac59771a575d63992a8f7c2d105ad1b016dfc authored almost 12 years ago by Adrian Thurston <[email protected]>
determine if act is necessary before initializing it

If the 'act' variable is not used anywhere then don't initialize it in the init
section. The use...

github.com/BioJulia/ragel - 101db349d57acac44f6f6b9e753d95a0c52d5b4e authored almost 12 years ago by Adrian Thurston <[email protected]>
fixed warning in mailbox2.rl test case

github.com/BioJulia/ragel - 9dda7ed745e6c3e9e90e32d9c3dfd996aafba0d6 authored almost 12 years ago by Adrian Thurston <[email protected]>
newer colm syntax (less curlies)

github.com/BioJulia/ragel - 3b9788926e9916513383ee5e2ccb861d2943c0e9 authored almost 12 years ago by Adrian Thurston <[email protected]>
more of the ragel parser, added gitignore

Filled in more of the ragel test case parser. Now parsing all of the language
independent test c...

github.com/BioJulia/ragel - 80918094780a9b3d5683841ed115a57819ee11c6 authored almost 12 years ago by Adrian Thurston <[email protected]>
some more work on the ragel grammar, two lang indep tests pass

github.com/BioJulia/ragel - 2dfaa2f1034b6efdd77cb0766a781f04c2c53da9 authored almost 12 years ago by Adrian Thurston <[email protected]>
started on a colm program for processing the language-independent tests

github.com/BioJulia/ragel - 3c6ccead5388147bd18f5328fa6a1084e628ca7b authored almost 12 years ago by Adrian Thurston <[email protected]>
use uppercase funcs for the array type and ref

github.com/BioJulia/ragel - 70b29e96cc7ad10a9de58777d59ee4e388d98bd7 authored almost 12 years ago by Adrian Thurston <[email protected]>
cleanup of the genAnalysis step, which is now in the leaf generators

github.com/BioJulia/ragel - c131df6b0777197eb99d67c01e98a6a3558e1faa authored almost 12 years ago by Adrian Thurston <[email protected]>
use the ref() call on table arrays to get the names

github.com/BioJulia/ragel - 6c89ec7c97dbf45cea1df6b5ef7ea63eb6da5471 authored almost 12 years ago by Adrian Thurston <[email protected]>
moved the setTableState( Generate ) to the end of analysis

github.com/BioJulia/ragel - c5bc68baffd7f0db8afe12d0de15d7ebe0850c6f authored almost 12 years ago by Adrian Thurston <[email protected]>
the genAnalysis function was moved into the leaf code generators

It is now part of the generator API. Will now remove some of the more obscure
functions.

github.com/BioJulia/ragel - f55a3d1428eb97af91a138fdaa815b70ea4f47f2 authored almost 12 years ago by Adrian Thurston <[email protected]>
minor comment improvements

github.com/BioJulia/ragel - 0bf6aaafbe9bd2e60207e970435540879aaa0b51 authored almost 12 years ago by Adrian Thurston <[email protected]>
function renaming for gen-specific analysis step

github.com/BioJulia/ragel - 139116bb648b00db70c6a57930ac005b5c46efb1 authored almost 12 years ago by Adrian Thurston <[email protected]>
cleanup around reduced machine making

github.com/BioJulia/ragel - 74d8a6abc3a28c655f47d5ba4d105ad170272de7 authored almost 12 years ago by Adrian Thurston <[email protected]>
moved the setTableState functions up one level in the heirarchy

github.com/BioJulia/ragel - 109a4151cc71434d4034a109c160da61ff099e05 authored almost 12 years ago by Adrian Thurston <[email protected]>
more use of TableArray.type

github.com/BioJulia/ragel - 0b3c8ce9e99e478a1f2dd8671c088851560fc09b authored almost 12 years ago by Adrian Thurston <[email protected]>
more use of TableArray.type, some other code movement

github.com/BioJulia/ragel - bd152ca4149a3998682c4daa33f453e37b93601b authored almost 12 years ago by Adrian Thurston <[email protected]>
eliminated remaining language-specific functions

removed OPEN_ARRAY, CLOSE_ARRAY, STATIC_VAR, UINT, CAST.

github.com/BioJulia/ragel - 273e2d51502ef4d668446f9dbd8c5a68da36e7b0 authored almost 12 years ago by Adrian Thurston <[email protected]>
using TableArray.type for referencing the type of the actions array

github.com/BioJulia/ragel - f3715120a1130807d0f11504fa5b5eaf66394099 authored almost 12 years ago by Adrian Thurston <[email protected]>
removed the switch default and control flow funcs

Neither of these had any effect in C code, they were there for D.

github.com/BioJulia/ragel - 063ac60a144f1faf7c096c6a402b6e7b3c318ad0 authored almost 12 years ago by Adrian Thurston <[email protected]>
removed ARR_OFF as it is no longer a point of variation

github.com/BioJulia/ragel - 27545ea99ee523cd150cf9aed8be40a7664b186b authored almost 12 years ago by Adrian Thurston <[email protected]>
updated ignore for common testing file

github.com/BioJulia/ragel - 11e1c8376d639819b750f4f9ad9a54ddd75e03fe authored almost 12 years ago by Adrian Thurston <[email protected]>
warning elimination

github.com/BioJulia/ragel - 8e1268d3bed9868499d403dafd3104cd2c17f88f authored almost 12 years ago by Adrian Thurston <[email protected]>
adjusted conderr.rl expected output following bug fix in parent commit

github.com/BioJulia/ragel - 827852789d3b1d51accb6e9ce292b4343992b40e authored almost 12 years ago by Adrian Thurston <[email protected]>
fixed for reduced transition

This bug led to incorrect actions/targets getting set in conditions two and on.

github.com/BioJulia/ragel - a9c28b2295fd344b906a82860080de5c37711f39 authored almost 12 years ago by Adrian Thurston <[email protected]>
removed targ and action from the reduced trans allocation funcs

github.com/BioJulia/ragel - 50657a1dd5e64fba1a57b8060ac85dc855658d4f authored almost 12 years ago by Adrian Thurston <[email protected]>
targ and action now come out of RedTrans

github.com/BioJulia/ragel - d8c7890b0b769ca18ba1d1aed663759452887df4 authored almost 12 years ago by Adrian Thurston <[email protected]>
traverse condition lists when computing actionn references

github.com/BioJulia/ragel - 57371d930798aca9a0491388eebb5db7589700c0 authored almost 12 years ago by Adrian Thurston <[email protected]>
don't add action refs for transitions

github.com/BioJulia/ragel - 4143eddc0a5621bb3cfebb5e5854cf7f6c05c6aa authored almost 12 years ago by Adrian Thurston <[email protected]>
use condition targets and not trans targets when finding default transitions

github.com/BioJulia/ragel - a628440aefab0e48f05e0eef087df48a9db1eb6b authored almost 12 years ago by Adrian Thurston <[email protected]>
don't use trans targ when performing the depth-first ordering

github.com/BioJulia/ragel - 09bbdfa40478da6c3644cb9747c074f9a2d12db8 authored almost 12 years ago by Adrian Thurston <[email protected]>
don't use the trans set when finding labels-needed, conds only

github.com/BioJulia/ragel - f451363290fe414d07b250c095c368121f7fba4a authored almost 12 years ago by Adrian Thurston <[email protected]>
removed the in-trans array from reduced state, using in in-conds now

github.com/BioJulia/ragel - ce9561d2ae97e95b58938d07cad7e4e6b723ee59 authored almost 12 years ago by Adrian Thurston <[email protected]>
removed targ and action from the transition comparison

github.com/BioJulia/ragel - 40db54825dda3abe6e55f21776e7ccb61ba57f85 authored almost 12 years ago by Adrian Thurston <[email protected]>
converted the arrays in goto code gens to TableArray style

github.com/BioJulia/ragel - fde747c5f2a2d043b9224319a49f606c79a8390d authored almost 12 years ago by Adrian Thurston <[email protected]>
rest of the flat actions converted to table-array style

github.com/BioJulia/ragel - 3a53a15a391935178c8ce07d7bd1e7ead2a89b86 authored almost 12 years ago by Adrian Thurston <[email protected]>
a couple more conversions to table array in the flat code gen

github.com/BioJulia/ragel - b202337d41bdfd08a7cb891b04804774287a62ed authored almost 12 years ago by Adrian Thurston <[email protected]>
starting to convert arrays in the Flat code generator: keys and keySpans

github.com/BioJulia/ragel - 02b166b49319fe4ca62b74ef0fad29f23bed3198 authored almost 12 years ago by Adrian Thurston <[email protected]>
fix for the last checkin, need to call taCondKeys in the table-data pass

github.com/BioJulia/ragel - 6a1783f38aab4ce3e5bae45e508e435ae5f9dc7e authored almost 12 years ago by Adrian Thurston <[email protected]>
binary cond keys converted to table array, last for that code gen

github.com/BioJulia/ragel - f81be9a885c2226a116e9460f1d99f967229ec2f authored almost 12 years ago by Adrian Thurston <[email protected]>
more work on table array

converted keys and also moved the actions table array out of CodeGen

github.com/BioJulia/ragel - 0429f37273d8b6531ec2f2100652bf39ee496728 authored almost 12 years ago by Adrian Thurston <[email protected]>
more code distribution into children from the parent

github.com/BioJulia/ragel - 34b8cabdb3a02276ffad63ab405cb9d836ff9623 authored almost 12 years ago by Adrian Thurston <[email protected]>
renaming FsmCodeGen -> CodeGen

github.com/BioJulia/ragel - 81fae5246624027b05d37f8d09af1abc4101a6ff authored almost 12 years ago by Adrian Thurston <[email protected]>
distribute the action funcs to both child classes of Flat

Had code in parent and in one child.

github.com/BioJulia/ragel - 95c83c2b8ca04e5775ae1d74b87849e6eed57ccc authored almost 12 years ago by Adrian Thurston <[email protected]>
use virtual calcIndexSize like a gen-specific analysis call

will likely rename as such

github.com/BioJulia/ragel - 626d1a1dcea565873b8dc0916f283169ed85e141 authored almost 12 years ago by Adrian Thurston <[email protected]>
fixed taEofTrans start/finish calling

github.com/BioJulia/ragel - 7c2838d4e33b8bec2db2c77f54cc8d82f78189e6 authored almost 12 years ago by Adrian Thurston <[email protected]>
one more conversion to table array

The binary search code generators just have keys left to convert. This requires
specifying the t...

github.com/BioJulia/ragel - bd6fca3ba8b2eb76d02657e5f18df74d139825c2 authored almost 12 years ago by Adrian Thurston <[email protected]>
some more conversions to table array

github.com/BioJulia/ragel - 1edb226e4e2345cfd5b9139d95315a836cc3eb20 authored almost 12 years ago by Adrian Thurston <[email protected]>
a few more conversions to table array

github.com/BioJulia/ragel - c3cd5b794d1f6e9cbfc11567f91009c27d908b98 authored almost 12 years ago by Adrian Thurston <[email protected]>
more conversion to table array

github.com/BioJulia/ragel - efe90db915e629527708b26a2c81f86fcbd29bcf authored almost 12 years ago by Adrian Thurston <[email protected]>
converted trans_lengths_wi to the table array struct

github.com/BioJulia/ragel - fb71dd01715193cf507dc8b8ad14bcf61a8a04fb authored almost 12 years ago by Adrian Thurston <[email protected]>
a few more arrays converted to TableArray style

github.com/BioJulia/ragel - 320088fee27a2facd71972069ebbe64c2cf5d056 authored almost 12 years ago by Adrian Thurston <[email protected]>
more conversion to TableArray structures for writing state machine data

github.com/BioJulia/ragel - 6423009693b83b9ef36fdd4eee58d65120ba49a2 authored almost 12 years ago by Adrian Thurston <[email protected]>
use the table arrays structs for referencing data

github.com/BioJulia/ragel - e8f301c69f04c3d4713f4981c066ecdede697624 authored almost 12 years ago by Adrian Thurston <[email protected]>
functionally equivalent improvements to reduced gen

github.com/BioJulia/ragel - 9d98446be99e83c4265fc963d97741482a36abcd authored almost 12 years ago by Adrian Thurston <[email protected]>
more cleanup of condList.head usage

github.com/BioJulia/ragel - fbb3131693f16408ea7d9f1bff321753e8d4b90b authored almost 12 years ago by Adrian Thurston <[email protected]>
more dead condition code removal

github.com/BioJulia/ragel - a80d9b6ec05b8e32eb5d242f8fca2ba510dde463 authored almost 12 years ago by Adrian Thurston <[email protected]>
condition class and member renaming for consistency

CondTransList -> CondList
ctList -> condList

github.com/BioJulia/ragel - 25b7b2bb9d96e88c1821e7177f522af8114fcc19 authored almost 12 years ago by Adrian Thurston <[email protected]>
some cleanup WRT conds in checkErrTrans

github.com/BioJulia/ragel - 9ec44d6f70c27eaf6bcc8475b159a0a60f8755f5 authored almost 12 years ago by Adrian Thurston <[email protected]>
added fullSize to the cond space, returns max length of a cond list in the space

github.com/BioJulia/ragel - 5b63f8525464dbcd323c8db389bc3ab492507c71 authored almost 12 years ago by Adrian Thurston <[email protected]>
fix for the check for error conditions WRT new condition impl

github.com/BioJulia/ragel - 5ea371a7667392f93bd863f0bc0f2a6c846caf52 authored almost 12 years ago by Adrian Thurston <[email protected]>
cond error, not currently giving the right results

The error action is getting run on non-error transitions. The condition
implementation is not ye...

github.com/BioJulia/ragel - 58f983a7d45aa081d079fc1a8e9f33f320c5a084 authored almost 12 years ago by Adrian Thurston <[email protected]>
check the cond space pointer when finding candidate merges

The compress transitions was using the ctList length to check for a lack of
conditions, this isn...

github.com/BioJulia/ragel - 9aba2584d2c699dc124ff48768e61037a8329c84 authored almost 12 years ago by Adrian Thurston <[email protected]>
fixed unecessary pointer traversal in condition code

Resulted from series of transformations to introduce condition code.

github.com/BioJulia/ragel - dd502fe294f74b8f619e0db96db96b701ddd4367 authored almost 12 years ago by Adrian Thurston <[email protected]>
refactored the merge test in compressTransitions, functionally equivalent

It is somewhat easier to read now.

github.com/BioJulia/ragel - 0159884e158fb5a3e0582e10ac020220a7b5b615 authored almost 12 years ago by Adrian Thurston <[email protected]>