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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

Added an item.

github.com/BioJulia/ragel - f6cb3687594dcca3a4ebd46354936f54b9bf33d3 authored almost 18 years ago
The code generators now exit immediately if the language is not correct. Write

statements are no longer interpreted in rlgen-dot. Since they have no meaning
in this generator, ...

github.com/BioJulia/ragel - 965e8db56cdbc4997b11327c061cdd1eaaa7d9e4 authored almost 18 years ago
Updated the help and version information in the backend programs. Also updated

the option processing. Renamed and updated the man page for the backend. Added
man pages for the ...

github.com/BioJulia/ragel - 14283e2fd9ab2f28a4316e823aac5f46cb664c3e authored almost 18 years ago
The rlcodegen executable was changed to rlgen-cd.

github.com/BioJulia/ragel - ca1d12b0fde5f477d5f00bfc697e1e4fcef04a3c authored almost 18 years ago
Moved rlcodegen to rlgen-cd.

github.com/BioJulia/ragel - c98a2e8e38fa93d6308d897cf2ff20fa70378ed4 authored almost 18 years ago
Split dotfile generation out into its own executable.

github.com/BioJulia/ragel - 43f2c3266ce9962915991f455897d61c3ff71e2c authored almost 18 years ago
Fixed error in ruby code generation which crept in during the last change.

Updated the machine name and alphtype in atoi3 to reflect the fact that it is a
ruby test.

github.com/BioJulia/ragel - 5521c775da1cd5d49eeeaa0f45872a7b7e3c0d76 authored almost 18 years ago
Same patch as previous revision, except for Ruby: KEY() should be returning a

string, allowing it to be interpreted. ARRAY_ITEM() now accepts a string.

github.com/BioJulia/ragel - 44863d3e7c8321ea5a563a23b21c779a6aa41060 authored almost 18 years ago
KEY() should be returning a string, allowing it to be interpreted. ARRAY_ITEM()

now accepts a string.

github.com/BioJulia/ragel - 3f7ba043438b9c20804c636ff82e70fe889f8a02 authored almost 18 years ago
We have gone back to supporting all alphtypes. We don't need to force the byte

alphabet type anymore.

github.com/BioJulia/ragel - 322d220ed1459f45685e0c20bdcf4493d49b9866 authored almost 18 years ago
Use a single function for both the active flag (now called ignoreSection) and

the parser exists test. The initialization of ignoreSection was flipped to fix
a bug which inhibi...

github.com/BioJulia/ragel - b7312add77c0b3f9bd7d322947715036808a598d authored almost 18 years ago
The parserExists function should be called before active is checked.

github.com/BioJulia/ragel - c50cea5fdd2a5e5a89055fe31d517d8e0112542c authored almost 18 years ago
When displaying printables in graphviz output, print 32 as SP.

github.com/BioJulia/ragel - dbe28d5ca0771ad4c17c674f131b48b9b6d25398 authored almost 18 years ago
New array generation for Java. For a single array a series of initialization

functions are created, with each function only handling a max number of
elements. This compiles t...

github.com/BioJulia/ragel - 4295997f473deabb42886350c55b86bc9b246d5c authored almost 18 years ago
Fixed the segfault which occured when a machine reference failed.

github.com/BioJulia/ragel - 3eba666c8bb7702951b335d477081a29a4e5d407 authored almost 18 years ago
Added a couple items.

github.com/BioJulia/ragel - cb26ad3a439ac44351a5fd0b69a4995a5b2a6689 authored almost 18 years ago
Fixed the null dereference and consequential segfault which occurred when

trying to create empty machines with [] and // and /a[]b/.

github.com/BioJulia/ragel - 08aa5af9b2a22c9613f8ef663ebb6653d24bd4cc authored almost 18 years ago
Make control codes with escape sequences into printable characters. From Arne

Goedeke.

github.com/BioJulia/ragel - a6fda53d8b900914d384c78a44d923e72cd7368a authored almost 18 years ago
Removed a completed item.

github.com/BioJulia/ragel - 003d3fb7bec5630dc1e1071b421416a0b8e5be3f authored almost 18 years ago
Updated to the latest aapl. This completely eliminates the shallowCopy

function. With that, a definite memory leak is fixed.

github.com/BioJulia/ragel - 796271ec4a3e07a304be345374481f4b409d92b6 authored almost 18 years ago
Updated an item.

github.com/BioJulia/ragel - 866750a91ee29a9f956daa0893aebc2db2437de4 authored almost 18 years ago
Added missing write init.

github.com/BioJulia/ragel - 8194b62b5f22df7c5e574b9dbbe5db1f5a669d61 authored almost 18 years ago
Added an item.

github.com/BioJulia/ragel - a5d1e087dcaf6d45905c12669bb23710488b3cc8 authored almost 18 years ago
Added a ruby test: atoi3.rl and adapted the test harness to build and run ruby

tests.

github.com/BioJulia/ragel - 03eb3fb9bf2cdedd046b1ff33fe9dee48104c5af authored almost 18 years ago
Added an item.

github.com/BioJulia/ragel - ca204655497230fbb60db118faeb4f332024d219 authored almost 18 years ago
Updated Victor's email address. The frontend parameter check must accept -R.

The genLineDirective function in rlcodegen must guard against graphviz dotfile
generation.

If th...

github.com/BioJulia/ragel - de43274325585033443e3c4013b178993ef44812 authored almost 18 years ago
Some fixes and cleanup. Some basic tests appear to work.

github.com/BioJulia/ragel - b932e04936fee5bb32ebd4946c4b05223c97d0c1 authored almost 18 years ago
Some documentation updates for 5.18. The recursive rules in the makefile can

use hidden commands.

github.com/BioJulia/ragel - 57de5fb340781e27e2fe4c7d617c4678dfb3b863 authored almost 18 years ago
The reference to the act variable in the scanner switch was not done with

ACT(). Now fixed.

github.com/BioJulia/ragel - 2e9d82636b375908d28c3d143a74fecdf90a6473 authored almost 18 years ago
Now that static data is also const, there is no need to eliminate the error and

first final states from the write data statement in order to avoid a gcc
compiler warnings. For a...

github.com/BioJulia/ragel - 51c266abcac9e032414a8d295d9f92da1291a4f7 authored almost 18 years ago
The writeStatement function is now part of CodeGenData.

Leading code which is common to all finishRagelDef() functions has been moved
to the parser clas...

github.com/BioJulia/ragel - 86710e012fc7c380a7eb74b4ebecedde5835e1f5 authored almost 18 years ago
The conversion from the string language type which comes in from the XML file

to the hostLangType and hostLang variables is now handled by the redfsm.a
library. The code gener...

github.com/BioJulia/ragel - 4e4314fbb48936ee8425fb5a78cd3317fe0af621 authored almost 18 years ago
Some cleanup of code. These functions are not needed in Java and Ruby code

generation.

github.com/BioJulia/ragel - 9f7716b8f47fbf2dcf67512853199f6c20ae91d9 authored almost 18 years ago
Movement of common classes and code to common.a.

github.com/BioJulia/ragel - 7f39dcc949699b7166065dbe60ed3af4d2fecd05 authored almost 18 years ago
Disabled the setting of state ids in the backend to go live with the equivalent

work done in the frontend.

github.com/BioJulia/ragel - a6a182124c6da5ace4c8c7c63e9e0a53aa2049ff authored almost 18 years ago
Complete transition list building must be avoided for the error state.

github.com/BioJulia/ragel - 3e863b44507421de99dd74fe184aae5496104fed authored almost 18 years ago
The frontend is now responsible for creating the error state, if needed. The

error state id is passed using the <error_state> tag.

github.com/BioJulia/ragel - 50b093f3d680cce92164046633e1f6037b517d2f authored almost 18 years ago
Java and Ruby code generators don't need to switch on the language to choose a

default extension.

github.com/BioJulia/ragel - a2af7885539303a36818e90a8084db0cb890bdf8 authored almost 18 years ago
Fixed error from last commit: The frontend should emit states with numbers

starting at 0. The state numbers in the XML file are now read and used to set
the state id. They ...

github.com/BioJulia/ragel - 770468c5d26b36be66e4e53f70793bed9a455b08 authored almost 18 years ago
The frontend now does a depth first ordering of states and then sorts states

based on final state status before assigning ids.

github.com/BioJulia/ragel - 174ca7231615d6643c462bbda6d688727d2fb1b2 authored about 18 years ago
Enabled rlgen-ruby in the top-level makefile. Merged the remaining parts of the

patch from Victor.

github.com/BioJulia/ragel - bc74b74eeeb0349794dc1f3bfef3b27834cdd7f7 authored about 18 years ago
Merged in Ruby code generator from Victor Hugo Borja. Started with a copy of

the Java code generator written in the framework, then merged in the code
generation that Victor ...

github.com/BioJulia/ragel - dd47f279ae1d8a68341cede864ffb3d8c54dca7a authored about 18 years ago
Updated version information in the both backend programs. Removed outputFormat

and codeStyle options from the java code generator.

github.com/BioJulia/ragel - 9804340d1975227abc19b17072b4f6590809f031 authored about 18 years ago
CR characters need to be treated as whitespace.

github.com/BioJulia/ragel - 407d236e86339f8d870a65fb286ccd6abb7c9241 authored about 18 years ago
Merged the FsmCodeGen, TabCodeGen and JavaTabCodeGen classes. Updated the

runtests script to use the new filename for the java code generator.

github.com/BioJulia/ragel - a11f5b3ec692e5fc99fbd015a31e7b1231c37fb1 authored about 18 years ago
Shortened the name of the Java code generation executable.

github.com/BioJulia/ragel - e592d9b647f10bcf02f5eb8df28a36d66755f97e authored about 18 years ago
Updated svn:ignore in common, now that objects and an archive are created.

github.com/BioJulia/ragel - f772ccadb81b3aa36cdd57cee29307df23df9b84 authored about 18 years ago
Improvements to the examples build following the merge.

github.com/BioJulia/ragel - 29f1c2a7225478e7557d341b3f31fcbec95be416 authored about 18 years ago
Removed last example directory.

github.com/BioJulia/ragel - 0c0e9c1d95fd267a2231a886196ada5e6138acba authored about 18 years ago
Eliminated per-example private directories.

github.com/BioJulia/ragel - e019f72d44b9815c730028586bd36f3a2643e670 authored about 18 years ago
The common code is now a library (no more #include "common.cpp"). Improvements

to the recurisve calls to make. Now using phony targets instead of shell script
code which iterat...

github.com/BioJulia/ragel - 7cb9364687f76fa4e76ec56d060666d2b58736a4 authored about 18 years ago
Removed Java code generation from rlcodegen. Added the cd javagen && make to

the top level makefile (not covered by SUBDIRS variable).

github.com/BioJulia/ragel - b10b8684d35525ac7405e49dfb74fcf5701b389b authored about 18 years ago
Updated SUBDIRS in the top-level makefile and the clean target in javagen.

github.com/BioJulia/ragel - dc7bb43db1eaf68fab1f69501fbf6aa47b91cd7f authored about 18 years ago
Removed inactive code originating from the split out of rlcodegen.

github.com/BioJulia/ragel - e7a81afe4320794dff0a6b11affb33df68ee30c3 authored about 18 years ago
Applied java data array encoding patch from Colin Fleming. Only works with byte

and short alphabet types. The transformation to java in the test suite sets the
byte alphabet typ...

github.com/BioJulia/ragel - ecc351f7c5e122292b8189be2b97f547fb64ea8a authored about 18 years ago
Java code generation split out into its own executable. Still needs to be

removed from rlcodegen.

github.com/BioJulia/ragel - 190afdfe0c297402c8b87127ec24c8563a5587b6 authored about 18 years ago
GraphvizDotGen is now a subclass of CodeGenData.

github.com/BioJulia/ragel - 848097b7f7a4529fff31c872342cc74398bbbf62 authored about 18 years ago
Split the XML parsing, reduced fsm, and the code generation data structures out

of rlcodegen.

github.com/BioJulia/ragel - 69f8f9eba1efb5fb5ddbbebd3244604443f0186e authored about 18 years ago
More separation between the XML reading and data collection classes, and the

code generation classes. The rlcodegen.h include was removed from the files
which will go into th...

github.com/BioJulia/ragel - 1c81a54cdacc897bf1d39d86170515b09a938fb9 authored about 18 years ago
Added an item. Resulted from discussion with MenTaLguY.

github.com/BioJulia/ragel - c9b829a8007169c25a4f749f7ee6d5c73550fcbc authored about 18 years ago
Improvements to the handling of write statements in the backend.

github.com/BioJulia/ragel - d92b6c7349404dc6fb1806414a0d8adeca78cd3a authored about 18 years ago
Machine preparation and code generation is now handled by two virtual functions

in FsmCodeGen: finishRagelDef and writeStatement. All interpretation of the
write statement will ...

github.com/BioJulia/ragel - 3328676f9ad79fa697f791135f70bb5d5bccf7a2 authored about 18 years ago
Write statements are no longer in ragel_def elements. They appear on their own

next to host elements. The ragel_def tag is now used exclusively for defining a
machine.

github.com/BioJulia/ragel - 2dddd0ec562935bfec462a716fd9152a10e26f31 authored about 18 years ago
Moved code dependent on the output type and code style from CodeGenData to

FsmCodeGen.

github.com/BioJulia/ragel - f4d8c81f0f72d0485397033e9a88656b7e256d58 authored about 18 years ago
Eliminated the pointer from the subclass FsmCodeGen up to the superclass

CodeGenData.

github.com/BioJulia/ragel - e01aaca58e109b392a6fabaa76a505d717b43290 authored about 18 years ago
This transformation makes CodeGenData a superclass of FsmCodeGen. The existing

pointer structure still works fine. They just now point to superclass and
subclass of one another...

github.com/BioJulia/ragel - 59ec784a2778b26d34e652c665c1575cf7f51c6c authored about 18 years ago
More organizational changes. The codeGen structure is now created in the

CodeGenData constructor.

github.com/BioJulia/ragel - d5a5ee4b5d6f0c5710b7b6f7de87489fdf12c55a authored about 18 years ago
Eliminated the cgd global.

github.com/BioJulia/ragel - d2eb7113a3e547bd41b6cef53ce1e276d46a91e3 authored about 18 years ago
Added an item.

github.com/BioJulia/ragel - c2c9337219708c1fa0d6c1411505dc00920f58e7 authored about 18 years ago
Did some more reorganization in support of separating out a redfsm.a library

from code generation. The makeCodeGen function is now a callback which will be
executed by the re...

github.com/BioJulia/ragel - 2849290a7e68fe02c348e14db68ffa668686d71c authored about 18 years ago
Moved the value limits which are collected during machine analysis time from

CodeGenData to RedFsm.

github.com/BioJulia/ragel - 93447f722f4e2d239c7b2fc3d2f458b19e669b26 authored about 18 years ago
Added item.

github.com/BioJulia/ragel - 5d93161748b26c1073141952c9056aa7180e878c authored about 18 years ago
The spelling of Erich's name has changed. Now updated throughout.

github.com/BioJulia/ragel - 935485f8d093ce9cfde64f6834058210f00a4116 authored about 18 years ago
Moved more analysis code from FsmCodeGen into CodeGenData. Eliminated the

fsmName variable from FsmCodeGen.

github.com/BioJulia/ragel - 62da7113af5f233c5b9993e32875360b47af7c1b authored about 18 years ago
Moved analysis code from FsmCodeGen into CodeGenData.

github.com/BioJulia/ragel - d6e8be1ab8b9b024419ca9ae00e1fe180444653d authored about 18 years ago
Removed output-related globals. Fixed and error in splitcodegen which tested

the wrong output_filter for open failure.

github.com/BioJulia/ragel - 54f6370cf7e412f291c8c8bb3cb0ac674db1cb16 authored about 18 years ago
Added an item.

github.com/BioJulia/ragel - 318ac90e619af6b115291b8d649b8525cca98c6c authored about 18 years ago
Updates to the scanner section. Gave the semantic condition figures bounding

boxes.

github.com/BioJulia/ragel - 458e3579b51d4b348a66c6fbe3141da3a4937ac4 authored about 18 years ago
Minor update to CREDITS file.

github.com/BioJulia/ragel - 79f8ed28b440f9d92dd17fb253453a181fa5e8ec authored about 18 years ago
This can go.

github.com/BioJulia/ragel - 0f118cbe9e6fe4144488e2639fdb48b4e5ffedb5 authored about 18 years ago
More content added. Did a smallish reorganization. Needs a lot of cleanup

still.

github.com/BioJulia/ragel - ace5a170c97c845c009b6869d982fbb6c57b6574 authored about 18 years ago
Updates to the guarded operator section.

github.com/BioJulia/ragel - ce7dfc9ab4c484647438d6151b38192afd703532 authored about 18 years ago
Expanded the Introductions to chapters 3 and 4 (actions and controlling

non-determinism).

github.com/BioJulia/ragel - 940d73f72db5cede017c39f33fbfdd69021c2865 authored about 18 years ago
added an item

github.com/BioJulia/ragel - c1aec7d77a7039ce878b644a77f1bbdf2694c9a2 authored about 18 years ago
Documented 5.17 release. Updated the homepage in various places. Updated the

README.

github.com/BioJulia/ragel - 6f4a03da908e4e7d801ccdc77f1c9af5bef4d4ed authored about 18 years ago
Some rewording of things in the Introduction chapter.

github.com/BioJulia/ragel - 3f01150ce66120dcecee5238898ee9a2a7c90278 authored about 18 years ago
Added bounding boxes to the figures that had text cut off. Reduced the line

weight in the figures describing the operations.

github.com/BioJulia/ragel - 9c0a9fee62044a727b80003ba2185b575a71ca3f authored about 18 years ago
Adjusted formatting: 11pt font, margins, don't use titlesec or pslatex.

github.com/BioJulia/ragel - ca94f1f052f3dad499b73af4bdb948c0257c4bca authored about 18 years ago
Finished replacement of manually drawn figures with graphviz drawn figures.

These need bounding box fixes at the very least.

github.com/BioJulia/ragel - e2c401371a9db146b5b579093748ca3acbf4b2ba authored about 18 years ago
Began replacement of manually drawn figures with graphviz drawn figures.

github.com/BioJulia/ragel - a24c8b53e5b2fea63a68c2256292393fb8a31ecc authored about 18 years ago
Fixed an unintentional concatenation of two patterns due to a missing

semi-colon. The error was not covered by the (meagre) test input.

github.com/BioJulia/ragel - fd5e66eb0654cbb82eff7d17ce88bf6e5d960a43 authored about 18 years ago
added an item

github.com/BioJulia/ragel - d5e56b606d62aa159ef7b263740e0b1bfaade861 authored about 18 years ago
The range keyword has been disabled for the parser rewrite of 5.17 so that the

ragel language matches 5.16 exactly. Can revert these changes to the test to
make diffing against...

github.com/BioJulia/ragel - 9d09798288362cfb01fdf03dd4de43f1f3f7ed37 authored about 18 years ago
Cleanup and removal of globals.

github.com/BioJulia/ragel - c79257ef2ead031c47d1b086716ac143e5827b34 authored about 18 years ago
Converted to single-line parser specifications where appropriate.

github.com/BioJulia/ragel - 80151e4083d13d38dd3e2f5805433dc29b070915 authored about 18 years ago
Switched to the latest kelbt syntax. Like Ragel, this syntax is based on write

statements embedded in the host code which explicitly specify which portions of
the machine to wr...

github.com/BioJulia/ragel - 43318982bd1da5fbcc354721db92ba04985b9838 authored about 18 years ago
Improved the sync patterns.

github.com/BioJulia/ragel - 5628c10a2a2b4cd3e47a360184fac9a3d3bea21f authored about 18 years ago
Enabled the location printing in the warning function.

github.com/BioJulia/ragel - d97a5d6e8128e810b9cd4fcd6217f6ef2a1c103b authored about 18 years ago
A fix from Matt Mower.

github.com/BioJulia/ragel - 1860b2567f6c5ad2edc203b7c33944e2599b0531 authored about 18 years ago
Some cleanup of comments and error messages.

github.com/BioJulia/ragel - f7eccf2ccaaed78752d9625c0a02c4bdbf40510a authored about 18 years ago