/trunk Developers: westram

Login name:
westram
Total Commits:
44,431 (87.0%)
Lines of Code:
1,211,771 (48.2%)
Most Recent Commit:
2025-09-11 13:43
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Activity in Directories

Directory Changes Lines of Code Lines per Change
Totals 44431 (100.0%) 1211771 (100.0%) 27.2
ARBDB/ 4001 (9.0%) 120761 (10.0%) 30.1
lib/nas/ 30 (0.1%) 66561 (5.5%) 2218.7
GDE/PHYLIP/ 196 (0.4%) 57426 (4.7%) 292.9
WINDOW/ 2662 (6.0%) 55943 (4.6%) 21.0
AWT/ 2230 (5.0%) 49066 (4.0%) 22.0
NTREE/ 2559 (5.8%) 48733 (4.0%) 19.0
UNIT_TESTER/run/display/ 204 (0.5%) 46531 (3.8%) 228.0
EDIT4/ 2476 (5.6%) 45224 (3.7%) 18.2
UNIT_TESTER/run/ 133 (0.3%) 30642 (2.5%) 230.3
HELP_SOURCE/oldhelp/ 2246 (5.1%) 30060 (2.5%) 13.3
CONVERTALN/ 464 (1.0%) 29093 (2.4%) 62.7
TOOLS/ 735 (1.7%) 23559 (1.9%) 32.0
GDE/PHYLIP/doc/ 42 (0.1%) 21478 (1.8%) 511.3
GENOM_IMPORT/ 389 (0.9%) 19995 (1.7%) 51.4
PARSIMONY/ 754 (1.7%) 19037 (1.6%) 25.2
PROBE/ 706 (1.6%) 18996 (1.6%) 26.9
DIST/ 757 (1.7%) 17561 (1.4%) 23.1
SOURCE_TOOLS/ 826 (1.9%) 16039 (1.3%) 19.4
/ 1094 (2.5%) 15456 (1.3%) 14.1
GDE/PHYML/ 48 (0.1%) 15276 (1.3%) 318.2
GENOM/ 890 (2.0%) 14278 (1.2%) 16.0
MERGE/ 735 (1.7%) 14078 (1.2%) 19.1
SECEDIT/ 603 (1.4%) 13634 (1.1%) 22.6
GDE/PHYML20130708/phyml/ 10 (0.0%) 13413 (1.1%) 1341.3
SL/FAST_ALIGNER/ 318 (0.7%) 12517 (1.0%) 39.3
lib/ 60 (0.1%) 12302 (1.0%) 205.0
ARB_GDE/ 594 (1.3%) 11758 (1.0%) 19.7
CORE/ 576 (1.3%) 11167 (0.9%) 19.3
PROBE_DESIGN/ 502 (1.1%) 11035 (0.9%) 21.9
SL/TREEDISP/ 515 (1.2%) 10473 (0.9%) 20.3
TEMPLATES/ 334 (0.8%) 9639 (0.8%) 28.8
MULTI_PROBE/ 560 (1.3%) 9440 (0.8%) 16.8
UNIT_TESTER/ 538 (1.2%) 9258 (0.8%) 17.2
NALIGNER/ 360 (0.8%) 9255 (0.8%) 25.7
lib/pictures/ 420 (0.9%) 8727 (0.7%) 20.7
ptpan/ 128 (0.3%) 8692 (0.7%) 67.9
PROBE_WEB/CLIENT/ 267 (0.6%) 8512 (0.7%) 31.8
AWTI/ 382 (0.9%) 8001 (0.7%) 20.9
GDE/FASTDNAML/ 42 (0.1%) 7406 (0.6%) 176.3
EISPACK/ 20 (0.0%) 7294 (0.6%) 364.7
AWTC/ 359 (0.8%) 7025 (0.6%) 19.5
PRIMER_DESIGN/ 291 (0.7%) 6913 (0.6%) 23.7
AISC/ 208 (0.5%) 6893 (0.6%) 33.1
GDE/RAxML/ 76 (0.2%) 6847 (0.6%) 90.0
HELP_SOURCE/ 241 (0.5%) 6102 (0.5%) 25.3
GDE/AxML/ 21 (0.0%) 6023 (0.5%) 286.8
CONSENSUS_TREE/ 328 (0.7%) 5967 (0.5%) 18.1
lib/import/ 211 (0.5%) 5908 (0.5%) 28.0
PHYLO/ 406 (0.9%) 4803 (0.4%) 11.8
ALIV3/ 174 (0.4%) 4669 (0.4%) 26.8
UNIT_TESTER/run/impexp/ 51 (0.1%) 4435 (0.4%) 86.9
PROBE_SERVER/PROBE_GROUP/ 91 (0.2%) 4351 (0.4%) 47.8
PROBE_SET/ 312 (0.7%) 4330 (0.4%) 13.8
AISC_COM/C/ 283 (0.6%) 4069 (0.3%) 14.3
STAT/ 280 (0.6%) 3887 (0.3%) 13.8
ISLAND_HOPPING/ 139 (0.3%) 3828 (0.3%) 27.5
GDE/CLUSTALW/ 62 (0.1%) 3728 (0.3%) 60.1
lib/pixmaps/ 302 (0.7%) 3582 (0.3%) 11.8
AISC_MKPTPS/ 111 (0.2%) 3574 (0.3%) 32.1
AISC_COM/AISC/ 112 (0.3%) 3501 (0.3%) 31.2
RNA3D/ 308 (0.7%) 3486 (0.3%) 11.3
HELP_SOURCE/source/ 726 (1.6%) 3468 (0.3%) 4.7
SH/ 191 (0.4%) 3386 (0.3%) 17.7
GDEHELP/MENUS/ 261 (0.6%) 3324 (0.3%) 12.7
SL/DB_QUERY/ 179 (0.4%) 3025 (0.2%) 16.8
ARBDBPP/ 72 (0.2%) 2998 (0.2%) 41.6
lib/addlibs/ 13 (0.0%) 2859 (0.2%) 219.9
SEQ_QUALITY/ 258 (0.6%) 2850 (0.2%) 11.0
EDIT/ 91 (0.2%) 2810 (0.2%) 30.8
util/ 233 (0.5%) 2550 (0.2%) 10.9
GDE/MOLPHY/ 105 (0.2%) 2531 (0.2%) 24.1
PGT/ 178 (0.4%) 2495 (0.2%) 14.0
PERL2ARB/ 166 (0.4%) 2412 (0.2%) 14.5
lib/import/nonformats/ 19 (0.0%) 2340 (0.2%) 123.1
UNIT_TESTER/run/consense/3/ 11 (0.0%) 2336 (0.2%) 212.3
lib/pictures/edit4/ 47 (0.1%) 2324 (0.2%) 49.4
SL/AP_TREE/ 153 (0.3%) 2298 (0.2%) 15.0
RNACMA/ 84 (0.2%) 2285 (0.2%) 27.2
ALEIO/ 53 (0.1%) 2265 (0.2%) 42.7
PROBE_SERVER/PROBE_GROUP_DESIGN/ 46 (0.1%) 2253 (0.2%) 48.9
SL/DB_SCANNER/ 137 (0.3%) 2252 (0.2%) 16.4
SL/PRONUC/ 129 (0.3%) 2226 (0.2%) 17.2
GL/glAW/ 74 (0.2%) 2110 (0.2%) 28.5
SL/ALILINK/ 42 (0.1%) 2101 (0.2%) 50.0
NAMES/ 123 (0.3%) 2068 (0.2%) 16.8
READSEQ/ 45 (0.1%) 2059 (0.2%) 45.7
SL/TREE_READ/ 97 (0.2%) 2004 (0.2%) 20.6
SL/AW_NAME/ 180 (0.4%) 1994 (0.2%) 11.0
lib/pixmaps/unused/ 147 (0.3%) 1993 (0.2%) 13.5
PROBE_SERVER/ 85 (0.2%) 1809 (0.1%) 21.2
SL/HELIX/ 113 (0.3%) 1786 (0.1%) 15.8
lib/pictures/consensus/ 13 (0.0%) 1667 (0.1%) 128.2
SL/SEQIO/ 81 (0.2%) 1640 (0.1%) 20.2
ORS_CGI/ 55 (0.1%) 1633 (0.1%) 29.6
SL/DB_UI/ 131 (0.3%) 1621 (0.1%) 12.3
SL/ITEMS/ 126 (0.3%) 1617 (0.1%) 12.8
GL/glpng/ 38 (0.1%) 1554 (0.1%) 40.8
SERVERCNTRL/ 132 (0.3%) 1522 (0.1%) 11.5
UNIT_TESTER/run/consense/2/ 13 (0.0%) 1468 (0.1%) 112.9
SL/GUI_ALIVIEW/ 175 (0.4%) 1449 (0.1%) 8.2
PROBE_SERVER/WORKER/ 33 (0.1%) 1432 (0.1%) 43.3
SL/NDS/ 92 (0.2%) 1364 (0.1%) 14.8
lib/pictures/awt/ 75 (0.2%) 1360 (0.1%) 18.1
TEST/ 40 (0.1%) 1327 (0.1%) 33.1
ARBDB2/ 29 (0.1%) 1309 (0.1%) 45.1
SL/CB/ 47 (0.1%) 1289 (0.1%) 27.4
TRS/ 37 (0.1%) 1279 (0.1%) 34.5
GDEHELP/ 147 (0.3%) 1240 (0.1%) 8.4
lib/pictures/merge/ 48 (0.1%) 1214 (0.1%) 25.2
lib/pixmaps/pgt/ 43 (0.1%) 1199 (0.1%) 27.8
ARBDB_COMPRESS/ 30 (0.1%) 1197 (0.1%) 39.9
GDE/CORE/ 94 (0.2%) 1193 (0.1%) 12.6
PERL_SCRIPTS/ARBTOOLS/ 20 (0.0%) 1160 (0.1%) 58.0
PERL_SCRIPTS/SPECIES/ 30 (0.1%) 1149 (0.1%) 38.3
SEER/ 41 (0.1%) 1115 (0.1%) 27.1
SL/TREE_WRITE/ 95 (0.2%) 1083 (0.1%) 11.4
XML/ 73 (0.2%) 1071 (0.1%) 14.6
GDE/SUPPORT/ 44 (0.1%) 1063 (0.1%) 24.1
SL/SEQUENCE/ 141 (0.3%) 1003 (0.1%) 7.1
PROBE_COM/ 99 (0.2%) 913 (0.1%) 9.2
TREE_COMPRESS/ 9 (0.0%) 909 (0.1%) 101.0
SL/AW_HELIX/ 86 (0.2%) 904 (0.1%) 10.5
ARBDBS/ 29 (0.1%) 850 (0.1%) 29.3
SL/GROUP_SEARCH/ 28 (0.1%) 846 (0.1%) 30.2
UNIT_TESTER/run/consense/1/ 17 (0.0%) 813 (0.1%) 47.8
GDE/MOLPHY/doc/ 4 (0.0%) 758 (0.1%) 189.5
SL/LOCATION/ 29 (0.1%) 754 (0.1%) 26.0
PERL_SCRIPTS/DB/ 3 (0.0%) 719 (0.1%) 239.6
TREEGEN/ 127 (0.3%) 707 (0.1%) 5.5
DBSERVER/ 71 (0.2%) 701 (0.1%) 9.8
SL/FILTER/ 70 (0.2%) 696 (0.1%) 9.9
lib/macros/.checks/ 3 (0.0%) 675 (0.1%) 225.0
lib/pixmaps/icons/unused/ 32 (0.1%) 662 (0.1%) 20.6
GDEHELP/HELP_WRITTEN/ 33 (0.1%) 643 (0.1%) 19.4
lib/pixmaps/edit/ 72 (0.2%) 632 (0.1%) 8.7
UNIT_TESTER/run/help/ 12 (0.0%) 601 (0.0%) 50.0
UNIT_TESTER/run/pars/ 52 (0.1%) 597 (0.0%) 11.4
lib/macros/ 32 (0.1%) 586 (0.0%) 18.3
ORS_SERVER/ 33 (0.1%) 580 (0.0%) 17.5
PROBE_SERVER/TREE_MERGE/ 14 (0.0%) 572 (0.0%) 40.8
SOURCE_TOOLS/release/ 18 (0.0%) 557 (0.0%) 30.9
PERL_SCRIPTS/MAUS/ 11 (0.0%) 549 (0.0%) 49.9
GDE/MUSCLE/src/unused/ 3 (0.0%) 548 (0.0%) 182.6
SL/MACROS/ 85 (0.2%) 530 (0.0%) 6.2
PROBE_WEB/SERVER/ 43 (0.1%) 523 (0.0%) 12.1
UNIT_TESTER/run/xsub/ 5 (0.0%) 511 (0.0%) 102.2
UNIT_TESTER/run/tools/ 44 (0.1%) 499 (0.0%) 11.3
GDE/RAxML8/ 16 (0.0%) 497 (0.0%) 31.0
SL/FILE_BUFFER/ 43 (0.1%) 495 (0.0%) 11.5
PERL_SCRIPTS/GENOME/ 16 (0.0%) 479 (0.0%) 29.9
SL/REGEXPR/ 52 (0.1%) 478 (0.0%) 9.1
lib/pixmaps/edit/unused/ 48 (0.1%) 469 (0.0%) 9.7
lib/pictures/unused/ 11 (0.0%) 462 (0.0%) 42.0
NAMES_COM/ 72 (0.2%) 460 (0.0%) 6.3
lib/submit/ 2 (0.0%) 446 (0.0%) 223.0
lib/inputMasks/ 25 (0.1%) 436 (0.0%) 17.4
GDE/HGL_SRC/ 27 (0.1%) 418 (0.0%) 15.4
SL/TREE_ADMIN/ 37 (0.1%) 406 (0.0%) 10.9
SL/ARB_TREE/ 86 (0.2%) 401 (0.0%) 4.6
SL/NEIGHBOURJOIN/ 68 (0.2%) 392 (0.0%) 5.7
GDEHELP/HELP_PLAIN/ 12 (0.0%) 372 (0.0%) 31.0
SL/MATRIX/ 59 (0.1%) 370 (0.0%) 6.2
lib/pictures/faligner/ 16 (0.0%) 369 (0.0%) 23.0
lib/pictures/query/ 18 (0.0%) 368 (0.0%) 20.4
bin/ 32 (0.1%) 361 (0.0%) 11.2
SL/ROOTED_TREE/ 17 (0.0%) 350 (0.0%) 20.5
lib/pictures/pars/ 7 (0.0%) 335 (0.0%) 47.8
SL/PTCLEAN/ 41 (0.1%) 330 (0.0%) 8.0
GDE/FASTTREE/ 13 (0.0%) 328 (0.0%) 25.2
lib/pictures/awtc/ 19 (0.0%) 327 (0.0%) 17.2
HELP_SOURCE/genhelp/ 27 (0.1%) 321 (0.0%) 11.8
TESTAWT/ 17 (0.0%) 317 (0.0%) 18.6
lib/pixmaps/icons/ 17 (0.0%) 310 (0.0%) 18.2
GDE/CLUSTAL/ 37 (0.1%) 309 (0.0%) 8.3
TESTVECTORFONT/ 15 (0.0%) 307 (0.0%) 20.4
CAT/ 20 (0.0%) 300 (0.0%) 15.0
lib/pixmaps/merge/ 7 (0.0%) 295 (0.0%) 42.1
GDE/ 50 (0.1%) 287 (0.0%) 5.7
lib/pixmaps/print/ 20 (0.0%) 281 (0.0%) 14.0
BUGEX/ 12 (0.0%) 251 (0.0%) 20.9
PERL_SCRIPTS/test/ 18 (0.0%) 239 (0.0%) 13.2
PERL_SCRIPTS/ARBTOOLS/IFTHELP/ 16 (0.0%) 237 (0.0%) 14.8
SL/ 42 (0.1%) 227 (0.0%) 5.4
SL/CONSENSUS/ 17 (0.0%) 225 (0.0%) 13.2
WETC/ 59 (0.1%) 224 (0.0%) 3.7
GDE/MAFFT/mafft-7.055-with-extensions/core/ 7 (0.0%) 224 (0.0%) 32.0
GDE/TREEPUZZLE/src/ 24 (0.1%) 219 (0.0%) 9.1
HEADERLIBS/ 12 (0.0%) 213 (0.0%) 17.7
SL/INSDEL/ 44 (0.1%) 212 (0.0%) 4.8
SL/REFENTRIES/ 46 (0.1%) 208 (0.0%) 4.5
GDE/MrBAYES/mrbayes_3.2.1/ 14 (0.0%) 207 (0.0%) 14.7
PERLTOOLS/ 49 (0.1%) 191 (0.0%) 3.8
BINDEP/ 45 (0.1%) 187 (0.0%) 4.1
AISC_COM/ 10 (0.0%) 183 (0.0%) 18.3
UNIT_TESTER/valgrind/ 5 (0.0%) 182 (0.0%) 36.4
SL/TRANSLATE/ 44 (0.1%) 182 (0.0%) 4.1
SL/ITEM_SHADER/ 43 (0.1%) 180 (0.0%) 4.1
PERL_SCRIPTS/SAI/ 5 (0.0%) 163 (0.0%) 32.6
CHIP/ 29 (0.1%) 160 (0.0%) 5.5
SOURCE_TOOLS/COMPILE_COMPAT/ 16 (0.0%) 157 (0.0%) 9.8
GDE/TREEPUZZLE/ 29 (0.1%) 155 (0.0%) 5.3
GDE/LOOPTOOL/ 26 (0.1%) 152 (0.0%) 5.8
lib/export/ 43 (0.1%) 145 (0.0%) 3.3
lib/pictures/cpro/ 6 (0.0%) 143 (0.0%) 23.8
SL/XFERGUI/ 9 (0.0%) 143 (0.0%) 15.8
lib/sellists/ 29 (0.1%) 142 (0.0%) 4.8
lib/pixmaps/print/unused/ 8 (0.0%) 138 (0.0%) 17.2
UNIT_TESTER/run/general/ 13 (0.0%) 136 (0.0%) 10.4
lib/macros/ARB/SEQ_DATA/ 4 (0.0%) 127 (0.0%) 31.7
PERL_SCRIPTS/BIOPERL/ 3 (0.0%) 123 (0.0%) 41.0
lib/pictures/phylo/ 9 (0.0%) 118 (0.0%) 13.1
GL/ 16 (0.0%) 114 (0.0%) 7.1
lib/dtd/ 8 (0.0%) 111 (0.0%) 13.8
AWDEMO/ 18 (0.0%) 107 (0.0%) 5.9
PERL_SCRIPTS/GENERAL/ 1 (0.0%) 99 (0.0%) 99.0
SL/FILTSEQEXP/ 18 (0.0%) 97 (0.0%) 5.3
ARBDB/EXAMPLES/ 19 (0.0%) 89 (0.0%) 4.6
PERL_SCRIPTS/lib/ 3 (0.0%) 81 (0.0%) 27.0
SOURCE_TOOLS/docs/ 1 (0.0%) 79 (0.0%) 79.0
PERL_SCRIPTS/ARBTOOLS/TESTS/ 2 (0.0%) 78 (0.0%) 39.0
SL/QUERY/ 16 (0.0%) 76 (0.0%) 4.7
GDE/PHYML20130708/ 12 (0.0%) 75 (0.0%) 6.2
lib/BUGS/ 5 (0.0%) 71 (0.0%) 14.2
ORS_COM/ 23 (0.1%) 66 (0.0%) 2.8
UNIT_TESTER/run/consense/4/ 6 (0.0%) 61 (0.0%) 10.1
SL/ALIVIEW/ 33 (0.1%) 58 (0.0%) 1.7
lib/motifHack/ 8 (0.0%) 56 (0.0%) 7.0
XML_IMPORT/IMP_TREE/ 36 (0.1%) 53 (0.0%) 1.4
XML_IMPORT/ 12 (0.0%) 47 (0.0%) 3.9
PROBE_WEB/ 4 (0.0%) 46 (0.0%) 11.5
lib/pictures/window/ 3 (0.0%) 45 (0.0%) 15.0
GDE/MAFFT/ 7 (0.0%) 44 (0.0%) 6.2
UNIT_TESTER/run/pvp/ 8 (0.0%) 41 (0.0%) 5.1
lib/arb_default/ 19 (0.0%) 40 (0.0%) 2.1
SL/XFERSET/ 12 (0.0%) 39 (0.0%) 3.2
etc/ 11 (0.0%) 38 (0.0%) 3.4
UNIT_TESTER/run/distance/ 11 (0.0%) 38 (0.0%) 3.4
GDE/MrBAYES/ 6 (0.0%) 38 (0.0%) 6.3
GDE/MUSCLE/ 6 (0.0%) 37 (0.0%) 6.1
BINDINGS/PERL/ 1 (0.0%) 37 (0.0%) 37.0
PERL_SCRIPTS/ARBTOOLS/DOCUMENTED/ 3 (0.0%) 33 (0.0%) 11.0
GDE/MAFFT/mafft-7.053-without-extensions/ 1 (0.0%) 33 (0.0%) 33.0
lib/gde/ 5 (0.0%) 32 (0.0%) 6.4
SL/PVP/ 11 (0.0%) 32 (0.0%) 2.9
RNA3D/Attic/OPENGL/ 14 (0.0%) 32 (0.0%) 2.2
HELP_SOURCE/oldhelp/prompt/ 3 (0.0%) 32 (0.0%) 10.6
PERL_SCRIPTS/ACI/ 1 (0.0%) 30 (0.0%) 30.0
HELP_SOURCE/oldhelp/seer/ 15 (0.0%) 30 (0.0%) 2.0
UNIT_TESTER/run/trees/ 1 (0.0%) 27 (0.0%) 27.0
GDE/SATIVA/ 14 (0.0%) 27 (0.0%) 1.9
UNIT_TESTER/run/consense/6/ 2 (0.0%) 26 (0.0%) 13.0
SL/SAICALC/ 14 (0.0%) 25 (0.0%) 1.7
GDE/PROBCONS/ 5 (0.0%) 20 (0.0%) 4.0
PERL_SCRIPTS/IFTHELP/ 10 (0.0%) 18 (0.0%) 1.8
GDE/PROBCONS/probcons/ 7 (0.0%) 18 (0.0%) 2.5
GDE/PHYML20130708/phyml/src/ 5 (0.0%) 13 (0.0%) 2.6
GDE/MAFFT/mafft-7.055-with-extensions/extensions/mxscarna_src/ 3 (0.0%) 13 (0.0%) 4.3
doc/ 2 (0.0%) 11 (0.0%) 5.5
GDE/TREEPUZZLE/doc/ 5 (0.0%) 9 (0.0%) 1.8
GDE/SINA/builddir/src/ 4 (0.0%) 9 (0.0%) 2.2
GDEHELP/DATA_FILES/ 2 (0.0%) 8 (0.0%) 4.0
BINDINGS/ 6 (0.0%) 8 (0.0%) 1.3
UNIT_TESTER/sockets/ 3 (0.0%) 7 (0.0%) 2.3
HELP_SOURCE/source/prompt/ 2 (0.0%) 7 (0.0%) 3.5
GDE/SINA/ 4 (0.0%) 6 (0.0%) 1.5
lib/pictures/unused/findcorr/ 27 (0.1%) 5 (0.0%) 0.1
fig2dev/dev/ 62 (0.1%) 4 (0.0%) 0.0
fig2dev/ 68 (0.2%) 4 (0.0%) 0.0
UNIT_TESTER/run/diff/ 8 (0.0%) 4 (0.0%) 0.5
GDE/MAFFT/mafft-7.055-with-extensions/extensions/ 3 (0.0%) 4 (0.0%) 1.3
GDE/MUSCLE/src/ 5 (0.0%) 3 (0.0%) 0.6
SOURCE_TOOLS/refactor/ 4 (0.0%) 2 (0.0%) 0.5
PERL_SCRIPTS/MACROS/ 4 (0.0%) 2 (0.0%) 0.5
GDE/MAFFT/mafft-7.055-with-extensions/ 3 (0.0%) 2 (0.0%) 0.6
lib/motifHack/pixmaps/ 3 (0.0%) 1 (0.0%) 0.3
UNIT_TESTER/run/homefake/.arb_prop/ 1 (0.0%) 1 (0.0%) 1.0
UNIT_TESTER/run/fakehome/ 2 (0.0%) 1 (0.0%) 0.5
UNIT_TESTER/flags/ 2 (0.0%) 1 (0.0%) 0.5
lib/rna3d/images/ 44 (0.1%) 0 (0.0%) 0.0
lib/rna3d/ 2 (0.0%) 0 (0.0%) 0.0
lib/pixmaps/seer/ 3 (0.0%) 0 (0.0%) 0.0
lib/pictures/unused/demo/ 27 (0.1%) 0 (0.0%) 0.0
lib/pictures/seer/ 5 (0.0%) 0 (0.0%) 0.0
lib/pictures/findcorr/ 20 (0.0%) 0 (0.0%) 0.0
lib/pictures/etc/ 1 (0.0%) 0 (0.0%) 0.0
lib/pictures/demo/ 27 (0.1%) 0 (0.0%) 0.0
lib/pictures/PARS/ 1 (0.0%) 0 (0.0%) 0.0
lib/icons/ 2 (0.0%) 0 (0.0%) 0.0
RNA3D/Attic/images/ 22 (0.0%) 0 (0.0%) 0.0
RNA3D/Attic/data/ 5 (0.0%) 0 (0.0%) 0.0
PGT/xslt/ 1 (0.0%) 0 (0.0%) 0.0
PERL_SCRIPTS/ 4 (0.0%) 0 (0.0%) 0.0
NIELS_F77/ 13 (0.0%) 0 (0.0%) 0.0
JAVALIB/ 1 (0.0%) 0 (0.0%) 0.0
GDEHELP/PHYLIP/ 42 (0.1%) 0 (0.0%) 0.0
GDE/TREEPUZZLE/data/ 5 (0.0%) 0 (0.0%) 0.0
GDE/SATIVA/sativa/epac/ 1 (0.0%) 0 (0.0%) 0.0
GDE/PHYML20130708/phyml/bin/ 2 (0.0%) 0 (0.0%) 0.0
GDE/MOLPHY/utl/ 42 (0.1%) 0 (0.0%) 0.0
DUMMYINC/ 1 (0.0%) 0 (0.0%) 0.0
BERGEY/ 1 (0.0%) 0 (0.0%) 0.0

Activity of westram

Most Recent Commits

westram 2025-09-11 13:43 Rev.: 19534


* tweaks {{{Track alignment changes}}}:
- automatically adds changekeys for generated fields.
- enhances documentation (recommended workflow; why to use unique IDs).
- uses {{{GBS_strstruct}}} to build reports and history entries.
- changes terminology (initials -> session ID).
- annotates errors with species name.
- improves report:
* always reports unchanged species.
* reverts order.
* changes format and horizontal padding.
- refactors (renames; size_t for counters; DRY)

123 lines of code changed in 4 files:

  • HELP_SOURCE/source: track_ali_changes.hlp (+38 -10)
  • NTREE: Makefile (+1), NT_trackAliChanges.cxx (+72 -33)
  • lib/pictures: trackali.fig (+12 -12)
westram 2025-08-13 10:25 Rev.: 19532


* reintegrates 'help' into 'trunk'
- tweak arb documentation:
* automatically link
- ticket references to arb bug tracker (only affects html version).
- found URLs.
* page titles
- warn about long titles.
- introduce {{{SUBTITLE}}}s (automatically triggered by multi-line titles in source files).
- increase allowed length (limited by subwindow width).
* cleanup header sections in all helpfiles.
* fix and/or update several help files.
* document syntax of help sources.
* build issues:
- when xml validation fails, next build no longer uses invalid xml => keeps failing.
- remove output files on error (including files below {{{ARBHOME/lib}}}).
- pipe output through logs to ensure proper wrapping in {{{Entering/Leaving}}} lines.
- moves {{{Tree admin}}} + {{{NDS}}} menu entries to top of menu
* adds: log:branches/help@18783:19531

3271 lines of code changed in 689 files:

  • arb_CHANGES.txt (+6 -2)
  • GDEHELP/HELP_WRITTEN: MrBayes.help (+1 -1), ProbCons.help (+1 -1), fasttree.help (+1 -1), muscle.help (+1 -1), raxml8.help (+2 -2)
  • HELP_SOURCE: Makefile (+14 -8), arb_help.dtd (+3 -2), arb_help2xml.cxx (+203 -35), generate_index.pl (+42 -18), help.readme (+49), to_help.xsl (+51 -18), to_html.xsl (+20 -6)
  • HELP_SOURCE/genhelp: Makefile (+4 -4), postprocess_genhelp.pl (+41 -8), standard.header (+4 -4)
  • HELP_SOURCE/source: FAQS.hlp (new), FORM.hlp (new), Protection.hlp (+7 -7), aaali.hlp (new), accessibility_sai.hlp (new), aci.hlp (+5 -5), acisrt.hlp (new), ad_align.hlp (+7 -7), ad_extended.hlp (+8 -8), advice.hlp (+7 -7), alignment.hlp (new), ap_stack.hlp (new), arb.hlp (+18 -18), arb_commands.hlp (+10 -10), arb_db.hlp (new), arb_edit4.hlp (new), arb_envar.hlp (+7 -7), arb_export.hlp (new), arb_export_nds.hlp (+8 -8), arb_gde.hlp (new), arb_import.hlp (new), arb_intro.hlp (+15 -13), arb_merge.hlp (new), arb_merge_into.hlp (new), arb_merge_outof.hlp (+9 -9), arb_merge_workflow.hlp (new), arb_ntree.hlp (new), arb_pars.hlp (new), arb_pars_init.hlp (+8 -8), arb_secedit.hlp (new), asciiprint.hlp (new), awt_csp.hlp (+7 -7), bonds.hlp (new), bootstrap.hlp (new), branch_analysis.hlp (new), bugtracker.hlp (new 30), checkfield.hlp (new), chimera_check.hlp (new), cluster_group.hlp (+8 -8), color.hlp (+11 -11), color_loadsave.hlp (new), color_props.hlp (new), color_props_groups.hlp (new), color_ranges.hlp (+7 -7), colorize.hlp (new), compare_taxonomy.hlp (+7 -7), compare_topo.hlp (new), concatenate.hlp (+6 -7), consense_algo.hlp (+4 -4), consense_tree.hlp (+8 -8), consensus.hlp (+10 -10), consensus_def.hlp (+4 -4), console.hlp (+5 -5), copyNpaste.hlp (new), count_chars.hlp (+7 -7), csp_2_gnuplot.hlp (+7 -7), del_list.hlp (new), di_clusters.hlp (new), displayField.hlp (new), dist.hlp (+18 -18), dssp_ift.hlp (+11 -11), e4.hlp (new), e4_background_priority.hlp (new), e4_block.hlp (new), e4_consensus.hlp (+7 -7), e4_defaults.hlp (new), e4_get_species.hlp (new), e4_mode.hlp (new), e4_modsai.hlp (+9 -9), e4_options.hlp (new), e4_replace.hlp (+6 -6), e4_search.hlp (+7 -7), ecoliref.hlp (new), ed4_flags.hlp (+6 -6), ed4_nds.hlp (new), exec_bug.hlp (new), experiment_info.hlp (new), experiment_search.hlp (+7 -7), export_format.hlp (new), export_test.hlp (+5 -5), extended.hlp (+8 -9), faligner.hlp (new), field_sel_new.hlp (+8 -8), field_shader.hlp (new), gde_flat_ift.hlp (+5 -5), gde_menus.hlp (new), gen_create.hlp (+9 -9), gen_disp_style.hlp (+7 -7), gen_jump.hlp (+8 -8), gen_mode.hlp (+5 -5), gen_new_view.hlp (new), gen_options.hlp (new), gene_extract.hlp (new), gene_hide.hlp (new), gene_info.hlp (+6 -6), gene_map.hlp (+8 -8), gene_mark.hlp (new), gene_mode.hlp (new), gene_search.hlp (new), gene_species.hlp (+10 -10), gene_species_field_transfer.hlp (new), gene_species_mark.hlp (new), genes.hlp (new), glossary.hlp (+13 -13), group_by_field.hlp (new), group_rename.hlp (+7 -7), group_search.hlp (+5 -5), group_trees.hlp (+5 -5), helix.hlp (new), helixsym.hlp (+10 -10), help.hlp (new), import_test.hlp (new), importift.hlp (+8 -8), input_mask.hlp (+8 -8), input_mask_format.hlp (+9 -9), input_mask_new.hlp (new), insdel.hlp (+9 -9), insdel_sai.hlp (new), islandhopping.hlp (+7 -7), iupac-codes.hlp (new), keeled_groups.hlp (+4 -4), kernlin.hlp (new), macro.hlp (+7 -7), man_arb_edit4.hlp (new), manage_test.hlp (new), manual.hlp (+5 -5), mark.hlp (new), mark_duplicates.hlp (new), mark_genes.hlp (new), mark_list.hlp (new), markbyref.hlp (+5 -5), matrix_settings.hlp (new), max_freq.hlp (new), merge_species.hlp (+7 -7), mergetaggedfield.hlp (new), mg_alignment.hlp (new), mg_extendeds.hlp (new), mg_names.hlp (+4 -4), mg_preserve.hlp (+10 -8), mg_species.hlp (+4 -4), mg_species_configs.hlp (+8 -8), mg_trees.hlp (new), mg_xfer_field_of_listed.hlp (+4 -4), mg_xfer_field_of_sel.hlp (new), missbase.hlp (new), mod_field_list.hlp (+10 -10), mode.hlp (new), mode_group.hlp (new), mode_info.hlp (new), mode_kernlin.hlp (+9 -9), mode_length.hlp (+7 -7), mode_lzoom.hlp (+8 -8), mode_mark.hlp (+5 -5), mode_move.hlp (+8 -8), mode_nni.hlp (+9 -9), mode_optimize.hlp (+10 -10), mode_pzoom.hlp (new), mode_rotate.hlp (new), mode_select.hlp (new), mode_setroot.hlp (+8 -8), mode_spread.hlp (+8 -8), mode_swap.hlp (+9 -9), mode_width.hlp (+8 -8), mode_www.hlp (+8 -8), move_groups.hlp (new), mp_params.hlp (+5 -5), multifurcate.hlp (new), multiprobe.hlp (+10 -10), multiproberesults.hlp (+5 -5), namesadmin.hlp (+6 -6), ne_align_seq.hlp (+9 -9), nekey_map.hlp (new), newwindow.hlp (new), next_neighbours.hlp (new), next_neighbours_common.hlp (new), next_neighbours_listed.hlp (new), nni.hlp (new), no_tree.hlp (+6 -10), nt_align_select.hlp (new), nt_keys.hlp (+7 -7), nt_tree_marker_settings.hlp (+5 -5), nt_tree_select.hlp (new), nt_tree_settings.hlp (+7 -7), nt_tree_settings_bootstrap.hlp (+6 -6), nt_tree_settings_expert.hlp (new), optimize.hlp (+5 -5), organism_mark.hlp (new), organisms.hlp (new), pa_add.hlp (+7 -7), pa_bootstrap.hlp (new), pa_branchlengths.hlp (new), pa_globopti.hlp (new), pa_kernlin.hlp (new), pa_locopti.hlp (new), pa_mixtree.hlp (new), pa_optimizer.hlp (new), pa_partial.hlp (new), pa_quick.hlp (new), pa_reset.hlp (new), pa_value.hlp (+20 -20), pars.hlp (+9 -10), partial_sequences.hlp (+7 -7), pd_match_iupac.hlp (+8 -8), pd_spec_param.hlp (+8 -8), pfold.hlp (+9 -9), pfold_props.hlp (new), pfold_sai.hlp (+13 -11), ph_export_markerline.hlp (+7 -7), phylo.hlp (+9 -9), pm_spec_param.hlp (+7 -7), pos_var_pars.hlp (+7 -7), primer.hlp (new), primer_new.hlp (+6 -6), primer_result.hlp (new), probe_param.hlp (new), probeadmin.hlp (+8 -8), probedesign.hlp (+9 -9), probedesignresult.hlp (+14 -14), probematch.hlp (+5 -5), probespec.hlp (+4 -4), prop_configs.hlp (new), prop_configs_edit.hlp (new), props_frame.hlp (+7 -7), props_nds.hlp (+11 -11), props_www.hlp (+7 -9), proteinViewer.hlp (+9 -9), pt_server.hlp (new), questions.hlp (+7 -7), quit.hlp (+7 -7), realign_dna.hlp (new), reg.hlp (new), rename.hlp (+5 -5), rerepair.hlp (+7 -7), reset_win_layout.hlp (+7 -7), resortbyother.hlp (+15 -15), resorttree.hlp (new), rna3d_changeMolecule.hlp (new), rna3d_dispBases.hlp (+9 -9), rna3d_dispHelices.hlp (+10 -10), rna3d_dispMolecule.hlp (new), rna3d_general.hlp (+12 -10), rna3d_mapSeqData.hlp (new), rst_log_zoom.hlp (+8 -8), rst_phys_zoom.hlp (new), saiProbe.hlp (+7 -7), saicalc.hlp (+6 -6), save.hlp (+4 -4), save_matrix.hlp (new), savedef.hlp (+7 -7), scandb.hlp (new), search_duplicates.hlp (new), search_equal_fields.hlp (+9 -9), searching.hlp (new), sec_bonddef.hlp (+5 -5), sec_display.hlp (+7 -7), sec_imexport.hlp (+7 -7), sec_keys.hlp (+7 -7), sec_main.hlp (+10 -10), sec_mode.hlp (+14 -14), sec_props.hlp (new), secedit_imexport.hlp (+9 -9), security.hlp (+8 -8), sel_box.hlp (new), sel_fil.hlp (new), selected.hlp (new), selected_gene.hlp (new), seq_quality.hlp (+7 -7), sequence_colors.hlp (new), set_color_of_listed.hlp (new), set_protection.hlp (new), sina_main.hlp (+6 -7), sp_IDs.hlp (+5 -5), sp_del_mrkd.hlp (+9 -9), sp_info.hlp (new), sp_info_locked.hlp (+6 -6), sp_mark.hlp (+8 -8), sp_search.hlp (new), sp_sort_fld.hlp (new), sp_sort_phyl.hlp (+8 -8), sp_sp_2_ext.hlp (new), spa_copy.hlp (+4 -4), spa_create.hlp (new), spa_delete.hlp (new), spa_rename.hlp (+4 -4), spaf_convert.hlp (+7 -7), spaf_create.hlp (new), spaf_delete.hlp (+8 -8), spaf_reorder.hlp (+8 -8), species.hlp (+4 -4), species_configs.hlp (+8 -8), species_configs_highlight.hlp (new), species_configs_saveload.hlp (+7 -7), species_join.hlp (+5 -5), srt.hlp (new), st_ml.hlp (+6 -6), submission.hlp (new), sync_colors.hlp (new), syncroots.hlp (+5 -5), syncscroll.hlp (+5 -5), tags.hlp (+10 -10), tbl_boot2len.hlp (new), tbl_justify.hlp (new), tbl_reset.hlp (new), tbl_scale.hlp (new), ted_boot.hlp (+5 -5), tkeep_mrkd.hlp (+7 -7), toggle_secinfo.hlp (new), topology_shader.hlp (+5 -5), tr_export.hlp (+6 -6), tr_import.hlp (new), tr_jump.hlp (+8 -8), tr_type_dendro.hlp (new 34), tr_type_irs.hlp (+16 -16), tr_type_list.hlp (del), tr_type_nds.hlp (new), tr_type_radial.hlp (+16 -21), track_ali_changes.hlp (+7 -7), trans_anal.hlp (new), transl_table.hlp (new), translate_dna_2_pro.hlp (+7 -7), tree2file.hlp (new), tree2prt.hlp (+6 -6), tree_group.hlp (+5 -5), tree_pseudo.hlp (new), tree_shading.hlp (new), treeadm.hlp (+7 -7), trees.hlp (new), trm_boot.hlp (new), trm_del.hlp (new), trm_mrkd.hlp (new), undo.hlp (+13 -13), unittest.hlp (+14 -14), universal_ift.hlp (new), unmark_list.hlp (new), user_matrix.hlp (+8 -8), version.hlp (+5 -5), viewdiff.hlp (+8 -8), visualizeSAI.hlp (+7 -7), vn_delete.hlp (+4 -4), vn_import.hlp (new), vn_search.hlp (new), vn_suggest.hlp (+8 -8), write_field_list.hlp (+5 -5), xferset.hlp (+5 -5), xterm.hlp (+7 -7)
  • HELP_SOURCE/source/prompt: format_alignments.hlp (new)
  • NTREE: NT_extern.cxx (+5 -10)
  • PARSIMONY: PARS_main.cxx (+1 -1)
  • SOURCE_TOOLS: check_resources.pl (+1)
  • UNIT_TESTER/run/help: unittest.xml (+1 -1)
  • XML: xml.cxx (+2 -1)
  • lib/pictures: help.fig (+14 -15)
  • util: arb_fig (+1 -1)
westram 2025-08-07 18:50 Rev.: 19517


* fix typo.

1 lines of code changed in 1 file:

  • HELP_SOURCE/source: macro.hlp (+1 -1)
westram 2025-08-07 18:30 Rev.: 19516


* document automation using macros.

20 lines of code changed in 2 files:

  • HELP_SOURCE/source: arb_envar.hlp (+3 -3), macro.hlp (+17 -4)
westram 2025-08-07 18:27 Rev.: 19515


* allow to reduce the time-to-wait on error, by defining {{{ARB_SCRIPTED_SECS_WAIT_ON_ERROR}}}.

16 lines of code changed in 3 files:

  • HELP_SOURCE/source: arb_envar.hlp (+7)
  • SH: arb_launcher (+9 -4)
westram 2025-08-07 18:24 Rev.: 19514


* do not ask (if sure to quit) while quitting from macro.

34 lines of code changed in 1 file:

  • NTREE: NT_extern.cxx (+34 -32)
westram 2025-08-02 15:00 Rev.: 19513


* fix part of #867:
- allow detection of macro running.
- {{{NT_exit()}}} waits for macro to terminate (up to 100 seconds).

82 lines of code changed in 6 files:

  • NTREE: Makefile (+1), NT_extern.cxx (+59 -2)
  • SL/MACROS: macro_gui.cxx (+9), macros.hxx (+1), trackers.cxx (+10 -2), trackers.hxx (+2)
westram 2025-08-01 16:29 Rev.: 19512


* fix wrong group counts (slighly too many for some DBs).

1 lines of code changed in 1 file:

  • PERL_SCRIPTS/DB: databaseReport.pl (+1 -1)
westram 2025-08-01 16:02 Rev.: 19511


* DRYed code to read entries
* simplified nested sort conditions

53 lines of code changed in 1 file:

  • PERL_SCRIPTS/DB: databaseReport.pl (+53 -56)
westram 2025-08-01 12:09 Rev.: 19510


* fix int overflow while calculating steps for parsimony quick add (#807)
- thx to jan for providing a log for huge insertions

1 lines of code changed in 1 file:

  • PARSIMONY: PARS_main.cxx (+1 -1)
westram 2025-07-29 11:17 Rev.: 19509


* script to analyze structure of different databases (generated reports are meant to be compared using diff viewers)

667 lines of code changed in 2 files:

  • ARBDB: ad_config.cxx (+2)
  • PERL_SCRIPTS/DB: databaseReport.pl (new 665)
westram 2025-07-19 12:32 Rev.: 19508


* fix {{{TEST_diff_files()}}} (failing under some conditions)
- pull-out {{{TEST_diff_behavior_using_binary_files()}}}.
- disabled test for public.
- commented (strange failure; purpose).
- remove duplicated assertion.
- run tests for different amounts of expected different lines.

41 lines of code changed in 1 file:

  • CORE: arb_diff.cxx (+41 -15)
westram 2025-07-19 11:55 Rev.: 19507


* avoid building arb as root:
- may cause test failures (permissions checks apparently succeed unexpectedly when called as root)

11 lines of code changed in 2 files:

  • Makefile (+9)
  • CORE: arb_file.cxx (+2)
westram 2025-07-19 11:48 Rev.: 19506


* fix gcc10.x vectorization checks:
- update {{{LOOP_VECTORIZED}}} comment: fix one vectorization for gcc 10.x series. Depends on UNIT_TEST=0|1.
- document vectorization count may depend on UNIT_TEST.

4 lines of code changed in 2 files:

  • ARBDB: adoptimize.cxx (+2 -2)
  • SOURCE_TOOLS: vectorize.README (+2)
westram 2025-06-03 11:40 Rev.: 19505


* fix constexpr issues for compilation under OSX 15

10 lines of code changed in 2 files:

  • CONVERTALN: global.h (+3 -1)
  • TEMPLATES: cxxforward.h (+7 -1)
westram 2025-04-17 19:09 Rev.: 19504


* also add buttons to experiment and genes search.

48 lines of code changed in 2 files:

  • GENOM: EXP_interface.cxx (+24 -22), GEN_interface.cxx (+24 -22)
westram 2025-04-17 19:00 Rev.: 19503


* add mark/unmark listed buttons to search+query.

84 lines of code changed in 4 files:

  • SL/DB_QUERY: db_query.cxx (+16), db_query.h (+5 -1)
  • SL/DB_UI: ui_species.cxx (+23 -21)
  • lib/pictures: ad_query.fig (+40 -36)
westram 2025-04-17 15:31 Rev.: 19502


* import from calc-sheet now interprets lines ending with ',' as empty cell

10 lines of code changed in 1 file:

  • PERL_SCRIPTS/ARBTOOLS: import_from_table.pl (+10 -9)
westram 2025-01-30 15:49 Rev.: 19501


* implements #865:
- allows to match species and table rows, using list entries (in cells and/or fields).

428 lines of code changed in 3 files:

  • GDEHELP/HELP_WRITTEN: import_calc.help (+58 -4)
  • GDEHELP/MENUS: import.menu (+21 -3)
  • PERL_SCRIPTS/ARBTOOLS: import_from_table.pl (+349 -142)
westram 2025-01-30 13:19 Rev.: 19500


* rename {{{GBT_create_alignment}}} -> {{{GBT_create_new_alignment}}}.
* restore old {{{GBT_create_alignment}}} flavor used before r19146 for binary compatibility.

25 lines of code changed in 12 files:

  • ARBDB: ad_t_prot.h (+2 -1), adali.cxx (+12 -2)
  • AWTI: AWTI_import.cxx (+1 -1)
  • EDIT4: ED4_ProteinViewer.cxx (+1 -1)
  • GDE/SINA/builddir/src: query_arb.cpp (+1 -1)
  • GENOM: GEN_map.cxx (+1 -1)
  • NTREE: AP_consensus.cxx (+1 -1), NT_concatenate.cxx (+1 -1), NT_split_ali.cxx (+2 -2)
  • SL/ALILINK: AdminGui.cxx (+1 -1), TranslateRealign.cxx (+1 -1)
  • TEMPLATES: arb_unit_test.h (+1 -1)

(8983 more)

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