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 b4ebef1a64cc94c260f36fbf072a212e50f895ce Ian Holmes yam@static-169-229-195-136.qb3.berkeley.edu http://github.com/ihh/dart/commit/d4fe6aa5f777f74aece7c89bd6ec3f187d8cdead d4fe6aa5f777f74aece7c89bd6ec3f187d8cdead

2009-11-23T15:03:15-08:00

Limited xrate grammar syntax checking 9b443c3a6ba829b5d659098ab9355a11c93f4266 Ian Holmes yam@static-169-229-195-136.qb3.berkeley.edu ad905f849e93383572e665c2ec840bce8d6bca61 Ian Holmes yam@static-169-229-195-136.qb3.berkeley.edu http://github.com/ihh/dart/commit/b4ebef1a64cc94c260f36fbf072a212e50f895ce b4ebef1a64cc94c260f36fbf072a212e50f895ce

2009-11-23T12:07:35-08:00

SExpr validator... still untested but compiles OK 127f851120251fb6b146c8e27d0bbe3415666201 Ian Holmes yam@static-169-229-195-136.qb3.berkeley.edu 3afda0149a9c3f03afba21cb673d67ad918cac1c Ian Holmes yam@emin.local http://github.com/ihh/dart/commit/ad905f849e93383572e665c2ec840bce8d6bca61 ad905f849e93383572e665c2ec840bce8d6bca61

2009-11-23T10:31:50-08:00

untested SExpr validation code 02529b83bcfc1e81d056d853c9a7416560c0d826 Ian Holmes yam@emin.local f87142643427885ddfb93de436b18a155d6e49ac Ian Holmes yam@static-169-229-195-136.qb3.berkeley.edu http://github.com/ihh/dart/commit/3afda0149a9c3f03afba21cb673d67ad918cac1c 3afda0149a9c3f03afba21cb673d67ad918cac1c

2009-11-20T16:06:13-08:00

fixed bug where hybrid-chains weren't being copied correctly in ECFG_matrix_set copy constructor & so were missing from training log (-tlog) 54030804e61c30c03b89094e1c2cf5306e9655f8 Ian Holmes yam@static-169-229-195-136.qb3.berkeley.edu 01864ea3c6fcd8de622692a90d98df87ae4a9158 Ian Holmes yam@static-169-229-195-136.qb3.berkeley.edu http://github.com/ihh/dart/commit/f87142643427885ddfb93de436b18a155d6e49ac f87142643427885ddfb93de436b18a155d6e49ac

2009-11-20T14:19:53-08:00

fixed vector overflow bug 6920bde517a008683b7aa31105c6a9aa24b5e0f8 Ian Holmes yam@static-169-229-195-136.qb3.berkeley.edu 0bf6c71800651ff8b8631c0615547ded1c1850db Ian Holmes yam@static-169-229-195-136.qb3.berkeley.edu http://github.com/ihh/dart/commit/01864ea3c6fcd8de622692a90d98df87ae4a9158 01864ea3c6fcd8de622692a90d98df87ae4a9158

2009-11-18T14:41:43-08:00

fixed emit_ll bug d27b7774334d006ca5a385720847496b01f6959c Ian Holmes yam@static-169-229-195-136.qb3.berkeley.edu 0e50fad2bd4bfcebb7e12b029d1911c03f5b3cef Ian Holmes yam@static-169-229-195-136.qb3.berkeley.edu http://github.com/ihh/dart/commit/0bf6c71800651ff8b8631c0615547ded1c1850db 0bf6c71800651ff8b8631c0615547ded1c1850db

2009-11-18T13:13:38-08:00

fixed compile bug in ecfg.cc 17eeaf5a208a6325b38636f6f37575c49881c412 Ian Holmes yam@static-169-229-195-136.qb3.berkeley.edu d5d08fd2a1f03c8a861b66d4d65be594ff576315 Ian Holmes yam@emin.local http://github.com/ihh/dart/commit/0e50fad2bd4bfcebb7e12b029d1911c03f5b3cef 0e50fad2bd4bfcebb7e12b029d1911c03f5b3cef

2009-11-15T16:06:11-08:00

probabilistic annotation labels 71a6edd6cf5238249ea95efca50ebcc513e80b05 Ian Holmes yam@emin.local cb34618aec3a6d9be391cda7069c99df5af2e1a3 Ian Holmes yam@smith.local http://github.com/ihh/dart/commit/d5d08fd2a1f03c8a861b66d4d65be594ff576315 d5d08fd2a1f03c8a861b66d4d65be594ff576315

2009-11-13T11:31:55-08:00

added some comments/critique to PHYLIP_tree definition 52ecdb0bc58da767da0117e54967c6f3c10678d3 Ian Holmes yam@smith.local c14669102c63718720be04d9832571c50c11f84b Ian Holmes yam@smith.local http://github.com/ihh/dart/commit/cb34618aec3a6d9be391cda7069c99df5af2e1a3 cb34618aec3a6d9be391cda7069c99df5af2e1a3

2009-11-13T11:10:25-08:00

xrate-validate-grammar, xrate-validate-stockholm-grammar f54df8c14508b07aa6c523f32893124bdcaac659 Ian Holmes yam@smith.local a9cfae9a7d43283173f62ff58cc842228a84e96c Ian Holmes yam@emin.local http://github.com/ihh/dart/commit/c14669102c63718720be04d9832571c50c11f84b c14669102c63718720be04d9832571c50c11f84b

2009-11-12T20:31:22-08:00

newick-tree and stockholm-alignment primitives, to convert smobs into Scheme data structures b045a46c27e47c6e1883df6cdcea68adc9be38e5 Ian Holmes yam@emin.local c90cd850e0fc26417ad76cea684f1a9cbb8b06da Ian Holmes yam@emin.local http://github.com/ihh/dart/commit/a9cfae9a7d43283173f62ff58cc842228a84e96c a9cfae9a7d43283173f62ff58cc842228a84e96c

2009-11-12T20:30:32-08:00

newick-tree and stockholm-alignment primitives, to convert smobs into Scheme data structures 9042f9a98199c58c1cc97f5ec8b5a974e9d20fed Ian Holmes yam@emin.local 808a865637adfad71678815feb908b1454d47274 Ian Holmes yam@emin.local http://github.com/ihh/dart/commit/c90cd850e0fc26417ad76cea684f1a9cbb8b06da c90cd850e0fc26417ad76cea684f1a9cbb8b06da

2009-11-12T20:28:21-08:00

newick-tree and stockholm-alignment primitives, to convert smobs into Scheme data structures b35596b2ea38bb6609671afbf4e0e7097f91f734 Ian Holmes yam@emin.local