a6aca3a16855bd51350233c0945b566a73115caf Ian Holmes yam@smith.local http://github.com/ihh/dart/commit/86daa1dfeb65122b7813d231bed344be5f382774 86daa1dfeb65122b7813d231bed344be5f382774

2010-02-08T17:42:30-08:00

tidied up pseudoterm output 661e5402c528acc823222941a82073ef62c0a7cf Ian Holmes yam@smith.local cbf711651fcc4362d9713344d3997b924f0ecd18 Ian Holmes yam@smith.local http://github.com/ihh/dart/commit/a6aca3a16855bd51350233c0945b566a73115caf a6aca3a16855bd51350233c0945b566a73115caf

2010-02-08T17:35:35-08:00

fixed output bug in grammars with complemented pseudoterminal emissions c9a5041fd9d6c63dd06b17e0bdd1114249841884 Ian Holmes yam@smith.local d44ffa3cde4619cb0cbf3e18826eef07dbac4471 Ian Holmes yam@emin.local http://github.com/ihh/dart/commit/cbf711651fcc4362d9713344d3997b924f0ecd18 cbf711651fcc4362d9713344d3997b924f0ecd18

2009-12-22T01:30:24-08:00

OPTFLAGS 6ca9f64f3af09edd23d0d7057698f95b2eeb83a4 Ian Holmes yam@emin.local f1a15f8502681fc6c6fe232d4895d9a004ddbb97 7d4e7b9b90a8d30a26b5cf3f960f6de20dbb83dd Ian Holmes yam@emin.local http://github.com/ihh/dart/commit/d44ffa3cde4619cb0cbf3e18826eef07dbac4471 d44ffa3cde4619cb0cbf3e18826eef07dbac4471

2009-12-21T23:33:18-08:00

Merge branch 'master' of git@github.com:ihh/dart ecabc8ada3c7b80f2872a654fc9a0396e9c86ae7 Ian Holmes yam@emin.local f9342ff4693e2232ad2be10a95c601f6513e63f9 Ian Holmes yam@emin.local http://github.com/ihh/dart/commit/f1a15f8502681fc6c6fe232d4895d9a004ddbb97 f1a15f8502681fc6c6fe232d4895d9a004ddbb97

2009-12-21T23:32:26-08:00

added compile flag -ffast-math at the suggestion of Roger Sayle 3c027ccad43c17fbc911476f2230c7a9e92e1241 Ian Holmes yam@emin.local 0a0de262bef085144da472e54bb5847bff3ac1cf Ian Holmes yam@static-169-229-195-136.qb3.berkeley.edu http://github.com/ihh/dart/commit/7d4e7b9b90a8d30a26b5cf3f960f6de20dbb83dd 7d4e7b9b90a8d30a26b5cf3f960f6de20dbb83dd

2009-12-04T10:32:36-08:00

implemented get_partials in preparation for Beagle de630d677633338e04800a4a84d959636286fa21 Ian Holmes yam@static-169-229-195-136.qb3.berkeley.edu f83fa6bcebbd25ecd236b5bad2e9b0eb05f6ddb8 Ian Holmes yam@rosebud.local http://github.com/ihh/dart/commit/0a0de262bef085144da472e54bb5847bff3ac1cf 0a0de262bef085144da472e54bb5847bff3ac1cf

2009-12-03T17:16:16-08:00

added stubs for Beagle helpers d2581058e97be09a0236e3e45369eb03533fb364 Ian Holmes yam@rosebud.local 8f2f974f2967a4eab5b03cceab2ccaf1bae296f8 Ian Holmes yam@rosebud.local http://github.com/ihh/dart/commit/f83fa6bcebbd25ecd236b5bad2e9b0eb05f6ddb8 f83fa6bcebbd25ecd236b5bad2e9b0eb05f6ddb8

2009-12-03T17:13:57-08:00

added stubs for Beagle helpers 00b1612a9d260f083cd0d445c8a56529d47c3b69 Ian Holmes yam@rosebud.local 2fd3b3a96baaf64f8589dbc58bcea72e8c644990 Ian Holmes yam@rosebud.local http://github.com/ihh/dart/commit/8f2f974f2967a4eab5b03cceab2ccaf1bae296f8 8f2f974f2967a4eab5b03cceab2ccaf1bae296f8

2009-12-03T15:58:58-08:00

Tidied up ECFG log-likelihood code in prep for Beagle compatibility 6281d0ae07ce9c3f5494422db32a3dc5c7565679 Ian Holmes yam@rosebud.local a8acec0918333e8855c5ff194bf8f892a90a6c81 Ian Holmes yam@rosebud.local http://github.com/ihh/dart/commit/2fd3b3a96baaf64f8589dbc58bcea72e8c644990 2fd3b3a96baaf64f8589dbc58bcea72e8c644990

2009-12-03T15:36:40-08:00

Added stub main file for beagle version of xrate 126cd81d4d093c4ee8ba24e3ef51aa3b38bb6a95 Ian Holmes yam@rosebud.local f9342ff4693e2232ad2be10a95c601f6513e63f9 Ian Holmes yam@rosebud.local http://github.com/ihh/dart/commit/a8acec0918333e8855c5ff194bf8f892a90a6c81 a8acec0918333e8855c5ff194bf8f892a90a6c81

2009-12-03T15:35:22-08:00

Added stub for beagle version of xrate cdfd26c49269dceeff4c7cc0858e3f6a3d35195a Ian Holmes yam@rosebud.local 9865f7f54f43f9aa46b651292445d52a87be0d5c Ian Holmes yam@emin.local http://github.com/ihh/dart/commit/f9342ff4693e2232ad2be10a95c601f6513e63f9 f9342ff4693e2232ad2be10a95c601f6513e63f9

2009-11-30T09:39:18-08:00

tidying up in prep for beagle cfcc83060324b318c16a0bf2d18f3974bc8d3fcc Ian Holmes yam@emin.local a1e48c24fb1b23ac041ba06995beb1687556948b Ian Holmes yam@emin.local http://github.com/ihh/dart/commit/9865f7f54f43f9aa46b651292445d52a87be0d5c 9865f7f54f43f9aa46b651292445d52a87be0d5c

2009-11-30T09:35:22-08:00

tidying up in prep for beagle bc9895f8e43f8581ae7e06711de674a2acb148f3 Ian Holmes yam@emin.local 5328c357fff8c543be485c41e446cde4562c0091 Ian Holmes yam@smith.local http://github.com/ihh/dart/commit/a1e48c24fb1b23ac041ba06995beb1687556948b a1e48c24fb1b23ac041ba06995beb1687556948b

2009-11-25T15:26:42-08:00

tidied up function names bb8bc504d2666d69fd63814b8d815d1eac3c2d12 Ian Holmes yam@smith.local da6b0e00f23c581e4a47abdccfc23f542d4ab365 Ian Holmes yam@smith.local http://github.com/ihh/dart/commit/5328c357fff8c543be485c41e446cde4562c0091 5328c357fff8c543be485c41e446cde4562c0091

2009-11-25T15:16:32-08:00

changed 'stockholm-tree' to 'newick-from-stockholm' 32a7cda925306913d6a2aea861cbeaed3f485637 Ian Holmes yam@smith.local 822dd0eb7992af9a9327bf65e9990fe2f498b31f Ian Holmes yam@rosebud.local http://github.com/ihh/dart/commit/da6b0e00f23c581e4a47abdccfc23f542d4ab365 da6b0e00f23c581e4a47abdccfc23f542d4ab365

2009-11-25T14:55:11-08:00

Updated test script 6ce0915ecb2ba082d0744156dab474104b52d352 Ian Holmes yam@rosebud.local d1e92bb2da9df1a728a7ebf69a72f214e7d1a236 Ian Holmes yam@rosebud.local http://github.com/ihh/dart/commit/822dd0eb7992af9a9327bf65e9990fe2f498b31f 822dd0eb7992af9a9327bf65e9990fe2f498b31f

2009-11-25T14:50:02-08:00

comments re Scheme garbage collection 1ee04f79156e45f681bc8cc819f44655bcf9adad Ian Holmes yam@rosebud.local 0abc924d651f24ad3177790b0c423f677988406e Ian Holmes yam@rosebud.local http://github.com/ihh/dart/commit/d1e92bb2da9df1a728a7ebf69a72f214e7d1a236 d1e92bb2da9df1a728a7ebf69a72f214e7d1a236

2009-11-25T14:46:26-08:00

fixed Stockholm deep-copy, added comments 86fcc5fd134ce240fcfe22d443757635a92dc04f Ian Holmes yam@rosebud.local c7cd6e81c178714676aa3a30e210566a0e27ad57 Ian Holmes yam@rosebud.local http://github.com/ihh/dart/commit/0abc924d651f24ad3177790b0c423f677988406e 0abc924d651f24ad3177790b0c423f677988406e

2009-11-25T14:38:47-08:00

headed off a deep-copy problem in sketch of DPM type, by using pointers instead of members db6857df9d9c428c36447614d97cdcd0d9385c2a Ian Holmes yam@rosebud.local d52a1c722471f3c3fa839488ef921a8d487bf632 Ian Holmes yam@rosebud.local http://github.com/ihh/dart/commit/c7cd6e81c178714676aa3a30e210566a0e27ad57 c7cd6e81c178714676aa3a30e210566a0e27ad57

2009-11-25T14:36:25-08:00

started dpm-type.h; fixed a missing deep-copy bug 234b457507c820fc0be3e7623d59ca02d379d650 Ian Holmes yam@rosebud.local d06c68e0f6a7cf153f3ad64a133afc6bc070fbfc Ian Holmes yam@emin.local http://github.com/ihh/dart/commit/d52a1c722471f3c3fa839488ef921a8d487bf632 d52a1c722471f3c3fa839488ef921a8d487bf632

2009-11-24T14:25:58-08:00

Complete xrate-format syntax validator 91b19054d27a350392546e441d85f317fee5c0a5 Ian Holmes yam@emin.local 2838b21d2e8580fc150123732ce35491b1753eb8 Ian Holmes yam@emin.local http://github.com/ihh/dart/commit/d06c68e0f6a7cf153f3ad64a133afc6bc070fbfc d06c68e0f6a7cf153f3ad64a133afc6bc070fbfc

2009-11-24T12:20:31-08:00

fixed syntax validation of pseudocount blocks 047c5880ea72a01f2dc275d0233282711b3ca2a1 Ian Holmes yam@emin.local 73393d858e5d94689a67ff99cdb2d6bfb68d51b6 Ian Holmes yam@emin.local http://github.com/ihh/dart/commit/2838b21d2e8580fc150123732ce35491b1753eb8 2838b21d2e8580fc150123732ce35491b1753eb8

2009-11-24T11:26:01-08:00

Developing XrateFormat syntax validator d6628051ecdfc63419dc1349a3c9d21cb32c387b Ian Holmes yam@emin.local c123c43b2ac6de561d8f34aa6be8b2ac7cecb775 Ian Holmes yam@emin.local http://github.com/ihh/dart/commit/73393d858e5d94689a67ff99cdb2d6bfb68d51b6 73393d858e5d94689a67ff99cdb2d6bfb68d51b6

2009-11-23T22:29:03-08:00

more accurate syntax warnings 5b4cff2cc328ed7bd8eedcceee2e32ddd68101ba Ian Holmes yam@emin.local 99d6a91db4d6a1f1519d22f7a0df6af7002c0d0e Ian Holmes yam@emin.local http://github.com/ihh/dart/commit/c123c43b2ac6de561d8f34aa6be8b2ac7cecb775 c123c43b2ac6de561d8f34aa6be8b2ac7cecb775

2009-11-23T22:13:03-08:00

fixed minor syntax warning format glitches 4a5ef1ef8bc81e9ae93e2844e4e929b3505e1441 Ian Holmes yam@emin.local 35e27542bb955a67e32a9ac8514a451df8289edb Ian Holmes yam@emin.local http://github.com/ihh/dart/commit/99d6a91db4d6a1f1519d22f7a0df6af7002c0d0e 99d6a91db4d6a1f1519d22f7a0df6af7002c0d0e

2009-11-23T21:56:22-08:00

fixed syntax warning format glitch 6bae1a8bf583e75d178cb7eef0aebcafd4f5948f Ian Holmes yam@emin.local deca05632316de3928667f9819d354f9e3aa6bd8 Ian Holmes yam@emin.local http://github.com/ihh/dart/commit/35e27542bb955a67e32a9ac8514a451df8289edb 35e27542bb955a67e32a9ac8514a451df8289edb

2009-11-23T21:49:06-08:00

fixed segfault when matching () 69c55112b1db0ec7ec03b840977bef9dc55de967 Ian Holmes yam@emin.local f08fb8c3d39835ef459bbe3a79df3a32f5830831 Ian Holmes yam@emin.local http://github.com/ihh/dart/commit/deca05632316de3928667f9819d354f9e3aa6bd8 deca05632316de3928667f9819d354f9e3aa6bd8

2009-11-23T21:31:23-08:00

more efficient parsing of syntax grammar f6b03c03c3573d11da04d329df78e66908ed4897 Ian Holmes yam@emin.local 3abef5395e3c577a3885abb2e2fd78adda679ed1 Ian Holmes yam@emin.local http://github.com/ihh/dart/commit/f08fb8c3d39835ef459bbe3a79df3a32f5830831 f08fb8c3d39835ef459bbe3a79df3a32f5830831

2009-11-23T20:35:13-08:00

xrate syntax checking 78334f254a8f8ae5474ba43c60350d9721301e1b Ian Holmes yam@emin.local d4fe6aa5f777f74aece7c89bd6ec3f187d8cdead Ian Holmes yam@static-169-229-195-136.qb3.berkeley.edu http://github.com/ihh/dart/commit/3abef5395e3c577a3885abb2e2fd78adda679ed1 3abef5395e3c577a3885abb2e2fd78adda679ed1

2009-11-23T16:21:20-08:00

Added more to -log CYK_TRACEBACK 7709a4c416a24ac0410a07bf2a0086e2239cbd21 Ian Holmes yam@static-169-229-195-136.qb3.berkeley.edu