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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

using cerr for the condition-related errors

github.com/BioJulia/ragel - 58feea11c05f54a48fcb809d01bc1c6cd7a9cce6 authored almost 12 years ago by Adrian Thurston <[email protected]>
traverse condition lists in the stop-final reachability marking

github.com/BioJulia/ragel - 6202a614ece78cc0d947a3692142c6e375372420 authored almost 12 years ago by Adrian Thurston <[email protected]>
fix for GenBase::appendTrans, need to traverse cond list to test targs/actions

github.com/BioJulia/ragel - d685465d3978ee15032fd9636d3442ce8d5290e9 authored almost 12 years ago by Adrian Thurston <[email protected]>
removed the / and & operators from the key data structures

github.com/BioJulia/ragel - b254b396770a6a632a12cc1ff1734501973c6d9c authored almost 12 years ago by Adrian Thurston <[email protected]>
removed +=, -= and |= operators from the key structs

github.com/BioJulia/ragel - 03ea258cdbc939053703a979f9ddc746a953dda1 authored almost 12 years ago by Adrian Thurston <[email protected]>
fill gaps in condition lists

This causes error actions/transtions to work correctly when conditions fail,
and not just the ke...

github.com/BioJulia/ragel - 3ec5fd37f4dc318fe229aa89ad7f082582ae74da authored almost 12 years ago by Adrian Thurston <[email protected]>
can remove the catch for FSM construct fail

This was for the exhaustion of key space used up by conditions. This can still
happen, but it is...

github.com/BioJulia/ragel - ef2d4f9c7e02151e7997ca38f8263c3ed04295b0 authored almost 12 years ago by Adrian Thurston <[email protected]>
removed lastCondKey from cond data

github.com/BioJulia/ragel - e3ac94a796ac3fc5de55efc73981046913d7fa56 authored almost 12 years ago by Adrian Thurston <[email protected]>
eliminated baseKey from CondSpace

The notion of a base key was from the original condition implementation. Also
removed some some ...

github.com/BioJulia/ragel - e90c0459333baebf4f166e3c83280f2b99021d4c authored almost 12 years ago by Adrian Thurston <[email protected]>
stop compiling the origin DOT code generator

github.com/BioJulia/ragel - 3e536c7a191be25a9b5acd84615ae5999451b9c5 authored almost 12 years ago by Adrian Thurston <[email protected]>
more removal of old condition code

github.com/BioJulia/ragel - c79f75b0b2ef839c0b6d04ac784c06d523d4e585 authored almost 12 years ago by Adrian Thurston <[email protected]>
more removal of original condition implementation

github.com/BioJulia/ragel - 6cdb645fbc9fb416c4b873fa0161e41fbee751e5 authored almost 12 years ago by Adrian Thurston <[email protected]>
elimnated PTR_CONST, was from the C/D code generator

github.com/BioJulia/ragel - 2fa38319373f7c9ce0e8ac7476c399ea2a5e2e97 authored almost 12 years ago by Adrian Thurston <[email protected]>
removed a couple relics of the C/D code genertor

github.com/BioJulia/ragel - a36388ab32ae6d067a9592ca95095efda9f9ca2e authored almost 12 years ago by Adrian Thurston <[email protected]>
removal of the wide key functions in the C codegen

also uppercased gen functions that were in camel case

github.com/BioJulia/ragel - 436b7ef6a2358849c603e25435fa5990a36642cf authored almost 12 years ago by Adrian Thurston <[email protected]>
removed more of the orignal conditions implementation

github.com/BioJulia/ragel - 1e32dc1b210897fbd39d0b2a7dc0b1058c704116 authored almost 12 years ago by Adrian Thurston <[email protected]>
eliminated PTR_CONST_END()

github.com/BioJulia/ragel - 40de1a27c7d87369b13596aae4c2101c8e1de85d authored almost 12 years ago by Adrian Thurston <[email protected]>
eliminated WIDE_ALPH_TYPE from the C code generator

github.com/BioJulia/ragel - 56f1d073559fdf817a427c05f8d29f6c6b98ca22 authored almost 12 years ago by Adrian Thurston <[email protected]>
deleted more of the original condition implementation

github.com/BioJulia/ragel - 5832e79f9f3b0ceb47832a835f6d2bb26be4112e authored almost 12 years ago by Adrian Thurston <[email protected]>
removing original condition implementation

github.com/BioJulia/ragel - 897d7b7a34fa79bcc9a5b978bb8a269cad4e3688 authored almost 12 years ago by Adrian Thurston <[email protected]>
the TRANS_ACTION function can be removed

github.com/BioJulia/ragel - 640b5dd992b57125d461501402ac2108249ce30f authored almost 12 years ago by Adrian Thurston <[email protected]>
converted the TRANS_TARGS functions into setTransPos

github.com/BioJulia/ragel - 0dfcd3eff40d7870110586eed112c94af2b254fa authored almost 12 years ago by Adrian Thurston <[email protected]>
eliminated code generation from TRANS_TARGS

Can't yet eliminate the function entirely becuase there was an important side
effect of setting ...

github.com/BioJulia/ragel - 04d7bf089d2c1162e070d2547f70db73f71e0da8 authored almost 12 years ago by Adrian Thurston <[email protected]>
disabled the split codegen

github.com/BioJulia/ragel - f216a9b718f090e97493eadf80962e657d365fd6 authored almost 12 years ago by Adrian Thurston <[email protected]>
don't recurse into the non C/XML/DOT code gen dirs

github.com/BioJulia/ragel - e5b3f12c0d8907cd3bb435fb0f9bf5d3f54ca82a authored almost 12 years ago by Adrian Thurston <[email protected]>
disabled all code generators except C

Will now eliminate the data structure support for the original condition
implementation. Will al...

github.com/BioJulia/ragel - f1119469fb924f7bf4eacac04b8e4353a72fe48f authored almost 12 years ago by Adrian Thurston <[email protected]>
split up the allocation C/D/D2 code generators into distinct functions

github.com/BioJulia/ragel - e84130a75d0b77877343517b504ea1e448ad0cef authored almost 12 years ago by Adrian Thurston <[email protected]>
final update for goto loop and expand, G0 and G1 tests now pass

github.com/BioJulia/ragel - bdb636abfe0bafe4c6a42f919150c4653246cc5f authored almost 12 years ago by Adrian Thurston <[email protected]>
made flat expanded work with inner conditions, -F1 tests pass

github.com/BioJulia/ragel - 2324b05db81c5ecdb4f1ab0576e075377fdbfeb6 authored almost 12 years ago by Adrian Thurston <[email protected]>
upgrade FlatLooped to work with inner conditions, -F0 tests pass

github.com/BioJulia/ragel - c0a3ac60cd7522b4bcb207a712c331b72ff47d42 authored almost 12 years ago by Adrian Thurston <[email protected]>
made BinaryExpanded work with the inner conditions, T1 tests pass

github.com/BioJulia/ragel - e8897a612e92cdcd8f336214ed5c4a6480652a0e authored almost 12 years ago by Adrian Thurston <[email protected]>
force indicies off and forced char type for cond keys

Makes all tests pass under -l -T0 options.

github.com/BioJulia/ragel - 98817a4c4a9e332164fb3c47d8578fa8548f85ea authored almost 12 years ago by Adrian Thurston <[email protected]>
always need the again label (temporary)

This is due to the error transition failing cond lookups. Need a proper error
transition here.

github.com/BioJulia/ragel - fdaf5a7e039d58f58a3b2709ea01ec07557875e5 authored almost 12 years ago by Adrian Thurston <[email protected]>
_match2 label renamed to _match_cond

github.com/BioJulia/ragel - ce408954835ab863620d17a88af73a44813b126e authored almost 12 years ago by Adrian Thurston <[email protected]>
need to set _cond before jumping to the error transition

github.com/BioJulia/ragel - c596e2091b4a69774ad2e40346117880cf1351bf authored almost 12 years ago by Adrian Thurston <[email protected]>
using the generic table array for three more array

github.com/BioJulia/ragel - d9ec4703a58026b87b567d4d38aeeb0dd8c824be authored almost 12 years ago by Adrian Thurston <[email protected]>
using the generic table array for actions

github.com/BioJulia/ragel - 89431e2a6e4ea5a57a77ec7399bef924d05c341e authored almost 12 years ago by Adrian Thurston <[email protected]>
pass FsmCodeGen ref into TableArray

github.com/BioJulia/ragel - 57d9b2a50b1da5b427c2468b5f11ef59dcf6fb76 authored almost 12 years ago by Adrian Thurston <[email protected]>
type computation and code generation for the table array

github.com/BioJulia/ragel - bd7de71f5b99a5c4b2f0062ad2ae386605f3e872 authored almost 12 years ago by Adrian Thurston <[email protected]>
set up the table arrays for the binary looped code generator

github.com/BioJulia/ragel - c8741d8d724ef4a68c73a835408816b061a2d50c authored almost 12 years ago by Adrian Thurston <[email protected]>
array size calculation was moved

Moved the calcArray size from binary, into binary looped class. There is one
for the looped and ...

github.com/BioJulia/ragel - 10c28e64e36ba98b8cb00d736f997a33c89d8e14 authored almost 12 years ago by Adrian Thurston <[email protected]>
started on the table-array abstraction

The TableArray class will be used to collect information on tables, then to
generate them. We wi...

github.com/BioJulia/ragel - b604d3193ca9ca10d6a4fd9d82bbd4b84b9fc05c authored almost 12 years ago by Adrian Thurston <[email protected]>
a couple array type changes (hacks to make it work)

github.com/BioJulia/ragel - 088379423be29016f2def86fc304e100766ecd0a authored almost 12 years ago by Adrian Thurston <[email protected]>
additional tables and driver for executing conditions in T0 mode

The cond2 test now works, many other tests are broken however, as these changes
affect all state...

github.com/BioJulia/ragel - 51c61a0733410c21889073a3e701e0952192ca05 authored almost 12 years ago by Adrian Thurston <[email protected]>
move the old condition codegen funcs aside, use names for the new one

github.com/BioJulia/ragel - ea2b40dfd2fddbe4cbd27436899bb3d0ae690c86 authored almost 12 years ago by Adrian Thurston <[email protected]>
condition key, targ, action arrays for C/Binary

github.com/BioJulia/ragel - 825f46154eebf91272bcabf2a95b554775ee2d8a authored almost 12 years ago by Adrian Thurston <[email protected]>
moved condition bsearch into goto class and added COND_GOTO

The condition tests now work for GotoLooped and GotoExpanded.

github.com/BioJulia/ragel - 1b1102c96b5d58c17522bde3271ceb6e7e55d4cc authored almost 12 years ago by Adrian Thurston <[email protected]>
generate condition transitions after the original trans conditions

github.com/BioJulia/ragel - 78730f3befb7cce2087eb2870764dd99174c5c8e authored almost 12 years ago by Adrian Thurston <[email protected]>
include references from conditions when computing action refs

github.com/BioJulia/ragel - 088cd2ce68109632aecafe9e9d381d7dcf7fba37 authored almost 12 years ago by Adrian Thurston <[email protected]>
renaming C goto code gen files to match classes

github.com/BioJulia/ragel - 1282d80016431bc61eb826b82de1b4425efc67a2 authored almost 12 years ago by Adrian Thurston <[email protected]>
renaming the C flat code generator to reflect class names

github.com/BioJulia/ragel - 28283a43a3d8ad968fccd03b96fb2930bf611f08 authored almost 12 years ago by Adrian Thurston <[email protected]>
file renaming to reflect class names

github.com/BioJulia/ragel - c42ccc950d86ba798dbae18ab759e2157dff58d8 authored almost 12 years ago by Adrian Thurston <[email protected]>
a class renaming around styles of transition and action

github.com/BioJulia/ragel - 90cf4b06d7f251c2062bbfa241c92bb79dff73ec authored almost 12 years ago by Adrian Thurston <[email protected]>
now have lang subdirs, taking target language out of file names

github.com/BioJulia/ragel - dc5e887ac76985d669040243989d441314699695 authored almost 12 years ago by Adrian Thurston <[email protected]>
removed the language prefix from the filenames in the D code generator

github.com/BioJulia/ragel - 2bb974dcc4968e909f5fb54e8cc581bbf496d1e1 authored almost 12 years ago by Adrian Thurston <[email protected]>
added classes for the plain tab, flat and goto code gens, moved code over

Restructuring the class hierarchy. Rather than having code generators inherit
from other code ge...

github.com/BioJulia/ragel - d2c5d2886d9771c343dddbef8932da921b81a2df authored almost 12 years ago by Adrian Thurston <[email protected]>
no longer need virtual inheritance of FsmCodeGen

This was used as the base to the code style and the language and allowed
combining the two disti...

github.com/BioJulia/ragel - dce19c5f42f6153b42ec7c2458b3dfc654055794 authored almost 12 years ago by Adrian Thurston <[email protected]>
removed the C-specific code generators from the C library

Since breaking apart the C and D code generators these classes are no longer necessary.

github.com/BioJulia/ragel - d3aad46bec30aa1b250dcfc37356643048bee6ca authored almost 12 years ago by Adrian Thurston <[email protected]>
took 'cd' off the file names in the C code generator

github.com/BioJulia/ragel - b7a52bd074e84211e38af0cfde092844e9fe0dac authored almost 12 years ago by Adrian Thurston <[email protected]>
iterate the condition list when removing dups

github.com/BioJulia/ragel - b68cb9ebc18c7825e990346138575ad86eb88641 authored almost 12 years ago by Adrian Thurston <[email protected]>
some more wrapping of TRANS_GOTO in {}.

github.com/BioJulia/ragel - 36bc14d005df5594e4a793a2950550ced47a138a authored almost 12 years ago by Adrian Thurston <[email protected]>
fixed the test for no conditions in transition code generation (G2)

github.com/BioJulia/ragel - 196ecbc2d1ff17c477d977fe0772ca92e592915d authored almost 12 years ago by Adrian Thurston <[email protected]>
logging and dead code cleanup

github.com/BioJulia/ragel - bd1199944a0b17180d8afc2075e9ca60e4c9fd20 authored almost 12 years ago by Adrian Thurston <[email protected]>
attach the duplicate source conditions before expansion

We are now attaching all of the expansions and detaching afterwards. Was
neglecting to attach th...

github.com/BioJulia/ragel - e92a5b1f3d065edee035b6bd0dc3fb84afad3eb6 authored almost 12 years ago by Adrian Thurston <[email protected]>
make the check for the error trans work with conditions

github.com/BioJulia/ragel - 8dcc8efdca6952ffa24551fbb0555ba2586c4b32 authored almost 12 years ago by Adrian Thurston <[email protected]>
need to attach expanded copy of source transitions in merge

The expanded copy of the source transitions need to be attached otherwise they
are not meaningfu...

github.com/BioJulia/ragel - 38df02a93e1185a7a143047ff6a2503f69b1dd7c authored almost 12 years ago by Adrian Thurston <[email protected]>
added error condition trans to reduced trans

This is the error transition taken when no condition transition matches.

github.com/BioJulia/ragel - a6d0590892585dc2d543ed9a32dae96307ba221a authored almost 12 years ago by Adrian Thurston <[email protected]>
upref actions from the whole condition list

github.com/BioJulia/ragel - 57f34614739a989e2f3b3576dc6bbce86cf923ea authored almost 12 years ago by Adrian Thurston <[email protected]>
removed a couple debug messages

github.com/BioJulia/ragel - 537d3b9ce0bb6073d4f85e1362ec8d9cd12bb320 authored almost 12 years ago by Adrian Thurston <[email protected]>
unified reducedgen and gendata files, added allocgen

github.com/BioJulia/ragel - dc902fd899ab72222e10dc02a7bc900e843876ca authored almost 12 years ago by Adrian Thurston <[email protected]>
unified ReducedGen and CodeGenData

github.com/BioJulia/ragel - 602132fdf525a40f72b63ee2f1c33cff83f8b0c2 authored almost 12 years ago by Adrian Thurston <[email protected]>
no longer need makeCodeGen2 wrapper

github.com/BioJulia/ragel - e39908b7ebb5bf2fb23a080bd9f0c89a231f4912 authored almost 12 years ago by Adrian Thurston <[email protected]>
reduce action tables for all condition transitions

github.com/BioJulia/ragel - 3d5e03dc7493e56c9656610201c0d4701a39a5bf authored almost 12 years ago by Adrian Thurston <[email protected]>
depth-first ordering needs to use condition lists

github.com/BioJulia/ragel - 98dc6f20cccc685dd5f58a3533950cd22f78b032 authored almost 12 years ago by Adrian Thurston <[email protected]>
consider cond transitions when computing labels needed

github.com/BioJulia/ragel - 34df0030fa5e33bc1edd09b5c538a39cec14fdb8 authored almost 12 years ago by Adrian Thurston <[email protected]>
TRANS_GOTO can now be a statement list, wrap in {}

github.com/BioJulia/ragel - 6031a486e294ca3def3b64255937a8d4eec099f1 authored almost 12 years ago by Adrian Thurston <[email protected]>
added a binary search for condition values

github.com/BioJulia/ragel - 6a3f7c25ae6025c815b6a65a87b8a79f6073bdb1 authored almost 12 years ago by Adrian Thurston <[email protected]>
put a pointer to the cond space in RedTransEl

Added uprefs on condition actions in transitions. Testing condition block
calls, no jumps yet.

github.com/BioJulia/ragel - e23b6b20c73e712c88b8ab4e29055e6bc7c7ec5a authored almost 12 years ago by Adrian Thurston <[email protected]>
eliminated CCodeGen from C code generator

This generator is now generating only C so we don't need the base class that
provides the C-Spec...

github.com/BioJulia/ragel - 8110cdc7b78250ca3f59936530a8e490b75ae882 authored about 12 years ago by Adrian Thurston <[email protected]>
copy move STATE_GOTOS from Goto into IpGoto

github.com/BioJulia/ragel - 55e625027dcf42ee0f3854ee3d356fc8cc632e45 authored about 12 years ago by Adrian Thurston <[email protected]>
switched over to the cond transitions entirely in the IpGoto generator

github.com/BioJulia/ragel - 0a3c78796c4d65c67e682500787d8481829eeaec authored about 12 years ago by Adrian Thurston <[email protected]>
reverted the GT2 patch, will reapply to a fork of IpGoto

github.com/BioJulia/ragel - c56ad5fe67cedb730a34a57bcb121b162aa60617 authored about 12 years ago by Adrian Thurston <[email protected]>
generate cond in-transitions and call them in ipgoto

github.com/BioJulia/ragel - f0b83887e08e06dd724f493e92bb75c73e99fc39 authored about 12 years ago by Adrian Thurston <[email protected]>
removed some the D code generation from the c codegen files

github.com/BioJulia/ragel - 9bef44694d6ff7685f64b01afcc7b87a8cc89cbd authored about 12 years ago by Adrian Thurston <[email protected]>
forked the C/D code generator into C and D code generators

github.com/BioJulia/ragel - 31d8f024fe2efd44bc7ce3d6aadba8da4df2b763 authored about 12 years ago by Adrian Thurston <[email protected]>
put remaining code generators except xml and dot into namespaces

github.com/BioJulia/ragel - 9584f8091f34f7c20a9fc66c7116b68c7a36a4bb authored about 12 years ago by Adrian Thurston <[email protected]>
put the C code generator in a namespace

will do the same with the rest

github.com/BioJulia/ragel - aff16e1137236f3f2fcd8877642b80d9fbfe5f14 authored about 12 years ago by Adrian Thurston <[email protected]>
don't need to include the code generators from gendata.cc

github.com/BioJulia/ragel - be3c8983bdd6913fb0b66b5913226fdc5483ed0b authored about 12 years ago by Adrian Thurston <[email protected]>
moved remaining code generators to their subdirs

github.com/BioJulia/ragel - a84f60424c9b241b0d2a59968a85fa19e2d633c5 authored about 12 years ago by Adrian Thurston <[email protected]>
moved the c-sharp code generator to its subdir

github.com/BioJulia/ragel - 0cfb45c1e404eab5f1f07257798734b1d8713c18 authored about 12 years ago by Adrian Thurston <[email protected]>
moved the crack code generator files into crack/

github.com/BioJulia/ragel - 1009cd1079d2a3a6ade207e902c5943d07a9aee9 authored about 12 years ago by Adrian Thurston <[email protected]>
moved the C code generator into its subdir

github.com/BioJulia/ragel - 56a5fb59dd38cb55277edd4d318da2b6452520b1 authored about 12 years ago by Adrian Thurston <[email protected]>
moving code generators into subdirs, added the tree, files not moved

github.com/BioJulia/ragel - 55ab4069c3de7f99a78d19330b00d345ea0db0a2 authored about 12 years ago by Adrian Thurston <[email protected]>
ignore a file used to store the currently valid tests in light of internal changes

github.com/BioJulia/ragel - 92b2823f374620837a8e24784515ae6e6538afad authored about 12 years ago by Adrian Thurston <[email protected]>
create in-conds along side in-trans

github.com/BioJulia/ragel - 2854621a24492d89e4f5236d61975d95c24a1f4f authored about 12 years ago by Adrian Thurston <[email protected]>
create all reduced transitions in the cond list

github.com/BioJulia/ragel - c8290d34a3831490e158a2db01faad0fdbe154ee authored about 12 years ago by Adrian Thurston <[email protected]>
some work on constructing the condition list inside a transition

github.com/BioJulia/ragel - 9ddf551cdd689fab8bfd9e85c051e5428ad45732 authored about 12 years ago by Adrian Thurston <[email protected]>
include the outConds in the comparison of RedTransAp

github.com/BioJulia/ragel - d4401402f7e9fd51953a9df13675e4a8ce2581ce authored about 12 years ago by Adrian Thurston <[email protected]>
added reduce cond set, the condition equivalent of the reduced trans set

github.com/BioJulia/ragel - 125ff2ec84df7c67944fe25e420b261797b90f08 authored about 12 years ago by Adrian Thurston <[email protected]>
when expanding the source list we can't attach

github.com/BioJulia/ragel - 51bd76b7f43a93e30beea6d03a69eb3d6c0bcb46 authored about 12 years ago by Adrian Thurston <[email protected]>