/trunk Developers: westram

Login name:
westram
Total Commits:
43,713 (87.3%)
Lines of Code:
1,207,436 (48.1%)
Most Recent Commit:
2025-04-17 19:09
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Activity in Directories

Directory Changes Lines of Code Lines per Change
Totals 43713 (100.0%) 1207436 (100.0%) 27.6
ARBDB/ 3999 (9.1%) 120757 (10.0%) 30.1
lib/nas/ 30 (0.1%) 66561 (5.5%) 2218.7
GDE/PHYLIP/ 196 (0.4%) 57426 (4.8%) 292.9
WINDOW/ 2662 (6.1%) 55943 (4.6%) 21.0
AWT/ 2230 (5.1%) 49066 (4.1%) 22.0
NTREE/ 2553 (5.8%) 48561 (4.0%) 19.0
UNIT_TESTER/run/display/ 204 (0.5%) 46531 (3.9%) 228.0
EDIT4/ 2476 (5.7%) 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/ 463 (1.1%) 29090 (2.4%) 62.8
TOOLS/ 735 (1.7%) 23559 (2.0%) 32.0
GDE/PHYLIP/doc/ 42 (0.1%) 21478 (1.8%) 511.3
GENOM_IMPORT/ 389 (0.9%) 19995 (1.7%) 51.4
PARSIMONY/ 752 (1.7%) 19035 (1.6%) 25.3
PROBE/ 706 (1.6%) 18996 (1.6%) 26.9
DIST/ 757 (1.7%) 17561 (1.5%) 23.1
SOURCE_TOOLS/ 824 (1.9%) 16036 (1.3%) 19.4
/ 1092 (2.5%) 15441 (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 (1.4%) 11758 (1.0%) 19.7
CORE/ 574 (1.3%) 11124 (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/ 333 (0.8%) 9632 (0.8%) 28.9
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/ 418 (1.0%) 8701 (0.7%) 20.8
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
GDE/AxML/ 21 (0.0%) 6023 (0.5%) 286.8
CONSENSUS_TREE/ 328 (0.8%) 5967 (0.5%) 18.1
lib/import/ 211 (0.5%) 5908 (0.5%) 28.0
HELP_SOURCE/ 234 (0.5%) 5720 (0.5%) 24.4
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 (0.3%) 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
SH/ 190 (0.4%) 3377 (0.3%) 17.7
GDEHELP/MENUS/ 261 (0.6%) 3324 (0.3%) 12.7
SL/DB_QUERY/ 179 (0.4%) 3025 (0.3%) 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/ 232 (0.5%) 2549 (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 (0.4%) 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/ 72 (0.2%) 1069 (0.1%) 14.8
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
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/ 28 (0.1%) 637 (0.1%) 22.7
lib/pixmaps/edit/ 72 (0.2%) 632 (0.1%) 8.7
HELP_SOURCE/source/ 56 (0.1%) 606 (0.1%) 10.8
UNIT_TESTER/run/help/ 11 (0.0%) 600 (0.0%) 54.5
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
PROBE_WEB/SERVER/ 43 (0.1%) 523 (0.0%) 12.1
UNIT_TESTER/run/xsub/ 5 (0.0%) 511 (0.0%) 102.2
SL/MACROS/ 81 (0.2%) 508 (0.0%) 6.2
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
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
HELP_SOURCE/genhelp/ 24 (0.1%) 272 (0.0%) 11.3
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
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 (0.1%) 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 2025-04-17 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)
westram 2024-10-01 18:45 Rev.: 19499


* implements #863
* add new ACI command "dupidx" (active in group search).
* update group-enumeration presets: use '~' instead of '_'. use new ACI command 'dupidx'.

72 lines of code changed in 5 files:

  • HELP_SOURCE/source: group_rename.hlp (new)
  • NTREE: NT_group_search.cxx (+6 -6), NT_tree_cmp.cxx (+5 -5)
  • SL/GROUP_SEARCH: group_search.cxx (+52 -7)
westram 2024-04-09 14:39 Rev.: 19495


* rename {{{aw_file_selection}}} -> {{{aw_modal_file_selection}}} to emphasize that it will break macro-capability.
* use non-modal fileprompter to select reference database for sina.

35 lines of code changed in 5 files:

  • AWT: AWT_config_manager.cxx (+2 -2)
  • EDIT4: graph_aligner_gui.cxx (+27 -15)
  • WINDOW: AW_cb_struct.cxx (+1 -1), AW_modal.cxx (+4 -2), aw_root.hxx (+1 -1)
westram 2024-02-05 12:50 Rev.: 19494


* collection of sysinfo terminated with error
- caused by undefined environment variable
- relevant info (like available memory) was not collected

2 lines of code changed in 1 file:

  • SH: arb_launcher (+2 -2)
westram 2023-12-07 19:22 Rev.: 19493


* homebrew build looked for wrong lib-suffix. patch from jan. thx :)
* fixed a typo in {{{warn_undefined_symbols.pl}}}

4 lines of code changed in 2 files:

  • PERL2ARB: Makefile.main (+3 -1), warn_undefined_symbols.pl (+1 -1)
westram 2023-11-23 12:44 Rev.: 19492


* mention {{{libgomp1}}} (required by FastTreeMP)

2 lines of code changed in 2 files:

  • arb_INSTALL.txt (+1)
  • SH: arb_installubuntu4arb.sh (+1)
westram 2023-11-18 10:15 Rev.: 19491


* after detecting perl/macro-incompatibility, show OS-specific advice.

10 lines of code changed in 1 file:

  • SH: arb_macro_compatibility.sh (+10)
westram 2023-09-13 18:33 Rev.: 19489


* reintegrates 'macros' into 'trunk'
* implements #856
* adds: log:branches/macros@19482:19488

277 lines of code changed in 16 files:

  • HELP_SOURCE/source: macro.hlp (+14 -13), macro_interruption.hlp (new 58)
  • PERL2ARB: ARB.pm (+17)
  • SL/MACROS: Makefile (+3), macro_gui.cxx (+65 -3), macros_local.hxx (+1), recmac.cxx (+21 -3), recmac.hxx (+2), trackers.cxx (+5), trackers.hxx (+2)
  • WETC: Makefile (+1), WETC_main.cxx (+58 -11)
  • WINDOW: aw_window.hxx (+5)
  • lib/pictures: macro_interruption.fig (new 19), macro_select.fig (+6 -5)
westram 2023-08-11 13:40 Rev.: 19480


* reintegrates 'gde' into 'trunk'
* adds: log:branches/gde@19460:19479

2421 lines of code changed in 138 files:

  • GDE: Makefile (+7 -14)
  • GDE/AxML: axml.c (+9 -11), axml.h (+4 -4)
  • GDE/CLUSTAL: amenu.c (+48 -51), clustalv.c (+1 -1), myers.c (+3 -3), sequence.c (+17 -17), showpair.c (+3 -3), trees.c (+8 -11), upgma.c (+1 -1), util.c (+12 -12)
  • GDE/CLUSTALW: amenu.c (+27 -25), calcgapcoeff.c (+4 -4), calctree.c (+42 -36), clustalw.c (+2 -2), clustalw.h (+12 -12), interface.c (+72 -99), malign.c (-1), matrices.h (+2 -2), param.h (+19 -19), readmat.c (+18 -12), sequence.c (+103 -66), trees.c (+2 -4), util.c (+5 -5)
  • GDE/FASTDNAML: fastDNAml.c (+4 -4), fastDNAml.h (+4 -4)
  • GDE/MAFFT: Makefile (+1 -1)
  • GDE/MAFFT/mafft-7.055-with-extensions/core: Makefile (+40 -40), io.c (+74 -68), rna.c (+45 -33)
  • GDE/MAFFT/mafft-7.055-with-extensions/extensions: Makefile (+2 -1)
  • GDE/MAFFT/mafft-7.055-with-extensions/extensions/mxscarna_src: BPPMatrix.hpp (+9 -2)
  • GDE/MrBAYES/mrbayes_3.2.1: Makefile (-1), sumt.c (+2 -2)
  • GDE/PHYLIP: Makefile (+1 -36), clique.c (+44 -44), cons.c (+28 -26), cons.h (+1 -1), consense.c (+5 -5), contml.c (+10 -10), contrast.c (+12 -8), disc.c (+17 -17), discrete.c (+79 -81), dnacomp.c (+55 -50), dnaml.c (+48 -44), dnamlk.c (+53 -48), dnamove.c (+36 -31), dnapars.c (+29 -24), dnapenny.c (+1 -1), dollop.c (+36 -31), dolmove.c (+22 -17), dolpenny.c (+4 -4), draw.c (+105 -113), draw.h (+2 -3), draw2.c (+41 -52), drawgram.c (+35 -34), drawtree.c (+23 -27), factor.c (+24 -24), fitch.c (+17 -18), hermite.c (del), interface.c (del), interface.h (del), io.h (del), kitsch.c (+1 -1), macface.c (del), macface.h (del), mix.c (+23 -23), move.c (+31 -27), moves.c (+30 -30), neighbor.c (+5 -5), pars.c (+33 -25), penny.c (+2 -2), phylip.c (+43 -39), phylip.h (+2 -2), proml.c (+61 -56), promlk.c (+74 -73), protdist.c (+54 -54), protpars.c (+37 -37), restdist.c (+3 -8), restml.c (+20 -20), retree.c (+59 -60), seq.c (+80 -80), seqboot.c (+3 -1)
  • GDE/PHYML: eigen.c (+1 -2), free.c (-35), free.h (-3), lk.c (+1 -4), lk.h (+1 -1), main.c (+3 -5), models.c (+8 -16), models.h (-1), optimiz.c (+7 -106), optimiz.h (-2), options.c (+24 -12), simu.c (+19 -27), simu.h (+2 -2), utilities.c (+16 -39), utilities.h (+4 -5)
  • GDE/PHYML20130708/phyml/src: models.c (+7 -2), simu.c (+1 -1), spr.c (+1 -1)
  • GDE/PROBCONS: Makefile (+2 -2)
  • GDE/PROBCONS/probcons: Main.cc (+4 -4), Makefile (+2 -2), ProbabilisticModel.h (+2 -2)
  • GDE/RAxML: axml.c (+84 -90), axml.h (+2 -2), bipartitionList.c (+2), classify.c (+5 -6), evaluateGenericSpecial.c (+21 -3), evaluatePartialGenericSpecial.c (+1), fastDNAparsimony.c (+15 -19), globalVariables.h (+3 -3), leaveDropping.c (+15 -14), models.c (+12 -15), multiple.c (+7 -8), newviewGenericSpecial.c (+17 -3), searchAlgo.c (+2 -2), treeIO.c (+10 -14)
  • GDE/RAxML8: Makefile (+6 -5)
  • GDE/SUPPORT: Flatio.c (+15 -44), Restriction.c (+9 -22), Zuk_to_gen.c (+7 -8), count.c (+18 -21), findall.c (+14 -14), lsadt.c (+45 -78), sho_helix.c (+4 -5), varpos.c (+5 -5)
  • GDE/TREEPUZZLE/src: ml.h (+1 -1), ml1.c (+9 -9), ml2.c (+13 -13), model1.c (+1 -1), ppuzzle.c (+7 -7), ppuzzle.h (+4 -4), puzzle.h (+3 -4), puzzle1.c (+27 -64), puzzle2.c (+38 -42), sched.c (+3 -3)
westram 2023-08-05 14:43 Rev.: 19459


* activate warnings (reverts parts of r15483).

3 lines of code changed in 1 file:

  • GDE/PHYML20130708/phyml: configure.fallback (+3 -3)
westram 2023-08-05 14:41 Rev.: 19458


* do NOT suppress warnings in MrBAYES => {{{-Werror-implicit-function-declaration}}} now active. No error reported.

1 lines of code changed in 1 file:

  • GDE/MrBAYES/mrbayes_3.2.1: Makefile (+1 -1)
westram 2023-08-05 14:38 Rev.: 19457


* pass down {{{onlyC_flags}}}.
* use onlyC_flags in all Makefiles (inject using seq).
* patch SATIVA raxml code in tarball (one missing prototype).

7 lines of code changed in 2 files:

  • GDE/SATIVA: Makefile (+7 -6), sativa-RAxML-8.2.3-patched.tar.gz (changed)
westram 2023-08-05 14:34 Rev.: 19456


* fix builds of AxML, FASTDNAML + SUPPORT
- mostly fixed by add missing includes.
- had to change code order to avoid otherwise required definition of protytypes in SUPPORT.

455 lines of code changed in 10 files:

  • GDE/AxML: axml.c (+6 -3)
  • GDE/FASTDNAML: fastDNAml.c (+2), fastDNAml.h (+3 -6)
  • GDE/SUPPORT: Flatio.c (+3), Restriction.c (+109 -109), Zuk_to_gen.c (+39 -36), count.c (+200 -197), findall.c (+25 -25), lsadt.c (+35 -30), sho_helix.c (+33 -33)
westram 2023-08-05 14:22 Rev.: 19455


* keep {{{-W -Wall}}} everywhere in GDE => activates -Werror-implicit-function-declaration.
- Note: (re)build of GDE tools fails.

1 lines of code changed in 1 file:

  • GDE: Makefile (+1 -1)
westram 2023-08-05 14:19 Rev.: 19454


* hide message from autoreconf (misinterpreted by emacs).

4 lines of code changed in 1 file:

  • GDE/SINA: Makefile (+4 -2)
westram 2023-08-05 14:17 Rev.: 19453


* use {{{-W -Wall}}} in FASTTREE + fix warnings.

15 lines of code changed in 2 files:

  • GDE/FASTTREE: FastTree.c (+13 -8), Makefile (+2 -2)

(8968 more)

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