/trunk Developers: westram

Login name:
westram
Total Commits:
45,242 (87.2%)
Lines of Code:
1,221,047 (48.5%)
Most Recent Commit:
2026-03-10 19:56
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Activity in Directories

Directory Changes Lines of Code Lines per Change
Totals 45242 (100.0%) 1221047 (100.0%) 26.9
ARBDB/ 4016 (8.9%) 120884 (9.9%) 30.1
lib/nas/ 30 (0.1%) 66561 (5.5%) 2218.7
GDE/PHYLIP/ 196 (0.4%) 57426 (4.7%) 292.9
WINDOW/ 2687 (5.9%) 56252 (4.6%) 20.9
NTREE/ 2619 (5.8%) 49135 (4.0%) 18.7
AWT/ 2270 (5.0%) 48309 (4.0%) 21.2
UNIT_TESTER/run/display/ 204 (0.5%) 46531 (3.8%) 228.0
EDIT4/ 2501 (5.5%) 45297 (3.7%) 18.1
UNIT_TESTER/run/ 133 (0.3%) 30642 (2.5%) 230.3
HELP_SOURCE/oldhelp/ 2246 (5.0%) 30060 (2.5%) 13.3
CONVERTALN/ 464 (1.0%) 29093 (2.4%) 62.7
TOOLS/ 737 (1.6%) 23737 (1.9%) 32.2
GDE/PHYLIP/doc/ 42 (0.1%) 21478 (1.8%) 511.3
GENOM_IMPORT/ 389 (0.9%) 19995 (1.6%) 51.4
PARSIMONY/ 762 (1.7%) 19071 (1.6%) 25.0
PROBE/ 707 (1.6%) 18997 (1.6%) 26.8
DIST/ 767 (1.7%) 17594 (1.4%) 22.9
SOURCE_TOOLS/ 850 (1.9%) 16268 (1.3%) 19.1
/ 1106 (2.4%) 15580 (1.3%) 14.0
GDE/PHYML/ 48 (0.1%) 15276 (1.3%) 318.2
GENOM/ 902 (2.0%) 14345 (1.2%) 15.9
MERGE/ 760 (1.7%) 14340 (1.2%) 18.8
SECEDIT/ 607 (1.3%) 13646 (1.1%) 22.4
GDE/PHYML20130708/phyml/ 10 (0.0%) 13413 (1.1%) 1341.3
SL/FAST_ALIGNER/ 321 (0.7%) 12523 (1.0%) 39.0
lib/ 60 (0.1%) 12302 (1.0%) 205.0
ARB_GDE/ 601 (1.3%) 11809 (1.0%) 19.6
CORE/ 579 (1.3%) 11207 (0.9%) 19.3
PROBE_DESIGN/ 510 (1.1%) 11060 (0.9%) 21.6
SL/TREEDISP/ 521 (1.2%) 10520 (0.9%) 20.1
TEMPLATES/ 335 (0.7%) 9647 (0.8%) 28.7
MULTI_PROBE/ 563 (1.2%) 9447 (0.8%) 16.7
UNIT_TESTER/ 550 (1.2%) 9431 (0.8%) 17.1
NALIGNER/ 361 (0.8%) 9256 (0.8%) 25.6
lib/pictures/ 423 (0.9%) 8744 (0.7%) 20.6
ptpan/ 128 (0.3%) 8692 (0.7%) 67.9
PROBE_WEB/CLIENT/ 267 (0.6%) 8512 (0.7%) 31.8
GDE/FASTDNAML/ 45 (0.1%) 8305 (0.7%) 184.5
AWTI/ 390 (0.9%) 8024 (0.7%) 20.5
EISPACK/ 21 (0.0%) 7295 (0.6%) 347.3
AWTC/ 360 (0.8%) 7026 (0.6%) 19.5
PRIMER_DESIGN/ 294 (0.6%) 6919 (0.6%) 23.5
AISC/ 208 (0.5%) 6893 (0.6%) 33.1
GDE/RAxML/ 76 (0.2%) 6847 (0.6%) 90.0
GDE/CLUSTALW/ 66 (0.1%) 6471 (0.5%) 98.0
HELP_SOURCE/ 248 (0.5%) 6378 (0.5%) 25.7
GDE/AxML/ 23 (0.1%) 6038 (0.5%) 262.5
CONSENSUS_TREE/ 329 (0.7%) 5968 (0.5%) 18.1
lib/import/ 211 (0.5%) 5908 (0.5%) 28.0
PHYLO/ 413 (0.9%) 4824 (0.4%) 11.6
HELP_SOURCE/source/ 983 (2.2%) 4775 (0.4%) 4.8
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/ 282 (0.6%) 3892 (0.3%) 13.8
ISLAND_HOPPING/ 140 (0.3%) 3829 (0.3%) 27.3
lib/pixmaps/ 302 (0.7%) 3582 (0.3%) 11.8
AISC_MKPTPS/ 111 (0.2%) 3574 (0.3%) 32.1
AISC_COM/AISC/ 112 (0.2%) 3501 (0.3%) 31.2
RNA3D/ 312 (0.7%) 3497 (0.3%) 11.2
SH/ 194 (0.4%) 3406 (0.3%) 17.5
GDEHELP/MENUS/ 262 (0.6%) 3324 (0.3%) 12.6
SL/DB_QUERY/ 185 (0.4%) 3162 (0.3%) 17.0
ARBDBPP/ 72 (0.2%) 2998 (0.2%) 41.6
lib/addlibs/ 13 (0.0%) 2859 (0.2%) 219.9
SEQ_QUALITY/ 260 (0.6%) 2857 (0.2%) 10.9
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/ 167 (0.4%) 2413 (0.2%) 14.4
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/ 157 (0.3%) 2312 (0.2%) 14.7
RNACMA/ 85 (0.2%) 2286 (0.2%) 26.8
ALEIO/ 53 (0.1%) 2265 (0.2%) 42.7
SL/DB_SCANNER/ 139 (0.3%) 2257 (0.2%) 16.2
PROBE_SERVER/PROBE_GROUP_DESIGN/ 46 (0.1%) 2253 (0.2%) 48.9
SL/PRONUC/ 130 (0.3%) 2227 (0.2%) 17.1
GL/glAW/ 76 (0.2%) 2112 (0.2%) 27.7
SL/ALILINK/ 46 (0.1%) 2109 (0.2%) 45.8
NAMES/ 125 (0.3%) 2069 (0.2%) 16.5
READSEQ/ 45 (0.1%) 2059 (0.2%) 45.7
SL/GUI_ALIVIEW/ 185 (0.4%) 2047 (0.2%) 11.0
SL/TREE_READ/ 99 (0.2%) 2006 (0.2%) 20.2
SL/AW_NAME/ 185 (0.4%) 2001 (0.2%) 10.8
lib/pixmaps/unused/ 147 (0.3%) 1993 (0.2%) 13.5
PROBE_SERVER/ 85 (0.2%) 1809 (0.1%) 21.2
SL/HELIX/ 116 (0.3%) 1799 (0.1%) 15.5
SL/ITEMS/ 133 (0.3%) 1754 (0.1%) 13.1
SL/DB_UI/ 136 (0.3%) 1721 (0.1%) 12.6
lib/pictures/consensus/ 13 (0.0%) 1667 (0.1%) 128.2
SL/SEQIO/ 82 (0.2%) 1641 (0.1%) 20.0
ORS_CGI/ 55 (0.1%) 1633 (0.1%) 29.6
GL/glpng/ 39 (0.1%) 1555 (0.1%) 39.8
SERVERCNTRL/ 134 (0.3%) 1525 (0.1%) 11.3
UNIT_TESTER/run/consense/2/ 13 (0.0%) 1468 (0.1%) 112.9
PROBE_SERVER/WORKER/ 33 (0.1%) 1432 (0.1%) 43.3
SL/NDS/ 94 (0.2%) 1371 (0.1%) 14.5
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/ 49 (0.1%) 1291 (0.1%) 26.3
TRS/ 37 (0.1%) 1279 (0.1%) 34.5
GDEHELP/ 149 (0.3%) 1252 (0.1%) 8.4
lib/pictures/merge/ 50 (0.1%) 1230 (0.1%) 24.6
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
SL/MACROS/ 105 (0.2%) 1153 (0.1%) 10.9
PERL_SCRIPTS/SPECIES/ 30 (0.1%) 1149 (0.1%) 38.3
SEER/ 41 (0.1%) 1115 (0.1%) 27.1
SL/TREE_WRITE/ 97 (0.2%) 1085 (0.1%) 11.1
XML/ 76 (0.2%) 1084 (0.1%) 14.2
GDE/SUPPORT/ 44 (0.1%) 1063 (0.1%) 24.1
SL/SEQUENCE/ 144 (0.3%) 1016 (0.1%) 7.0
PROBE_COM/ 99 (0.2%) 913 (0.1%) 9.2
TREE_COMPRESS/ 9 (0.0%) 909 (0.1%) 101.0
SL/AW_HELIX/ 89 (0.2%) 908 (0.1%) 10.2
ARBDBS/ 29 (0.1%) 850 (0.1%) 29.3
SL/GROUP_SEARCH/ 29 (0.1%) 847 (0.1%) 29.2
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/ 30 (0.1%) 755 (0.1%) 25.1
PERL_SCRIPTS/DB/ 3 (0.0%) 719 (0.1%) 239.6
TREEGEN/ 128 (0.3%) 708 (0.1%) 5.5
DBSERVER/ 72 (0.2%) 702 (0.1%) 9.7
SL/FILTER/ 73 (0.2%) 699 (0.1%) 9.5
lib/macros/.checks/ 3 (0.0%) 675 (0.1%) 225.0
lib/pixmaps/icons/unused/ 32 (0.1%) 662 (0.1%) 20.6
UNIT_TESTER/run/help/ 14 (0.0%) 659 (0.1%) 47.0
GDEHELP/HELP_WRITTEN/ 33 (0.1%) 643 (0.1%) 19.4
lib/macros/ 34 (0.1%) 640 (0.1%) 18.8
lib/pixmaps/edit/ 72 (0.2%) 632 (0.1%) 8.7
UNIT_TESTER/run/pars/ 52 (0.1%) 597 (0.0%) 11.4
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
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
SL/REGEXPR/ 53 (0.1%) 479 (0.0%) 9.0
PERL_SCRIPTS/GENOME/ 16 (0.0%) 479 (0.0%) 29.9
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
SL/TREE_ADMIN/ 44 (0.1%) 439 (0.0%) 9.9
lib/inputMasks/ 25 (0.1%) 436 (0.0%) 17.4
GDE/HGL_SRC/ 27 (0.1%) 418 (0.0%) 15.4
SL/ARB_TREE/ 89 (0.2%) 416 (0.0%) 4.6
SL/NEIGHBOURJOIN/ 69 (0.2%) 393 (0.0%) 5.6
GDEHELP/HELP_PLAIN/ 13 (0.0%) 382 (0.0%) 29.3
SL/MATRIX/ 60 (0.1%) 371 (0.0%) 6.1
lib/pictures/faligner/ 16 (0.0%) 369 (0.0%) 23.0
lib/pictures/query/ 18 (0.0%) 368 (0.0%) 20.4
bin/ 33 (0.1%) 362 (0.0%) 10.9
SL/ROOTED_TREE/ 17 (0.0%) 350 (0.0%) 20.5
lib/pictures/pars/ 7 (0.0%) 335 (0.0%) 47.8
SL/PTCLEAN/ 43 (0.1%) 331 (0.0%) 7.6
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
SL/GUI_TK/ 8 (0.0%) 306 (0.0%) 38.2
CAT/ 20 (0.0%) 300 (0.0%) 15.0
lib/pixmaps/merge/ 7 (0.0%) 295 (0.0%) 42.1
GDE/ 51 (0.1%) 288 (0.0%) 5.6
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
WETC/ 63 (0.1%) 238 (0.0%) 3.7
SL/ 43 (0.1%) 238 (0.0%) 5.5
PERL_SCRIPTS/ARBTOOLS/IFTHELP/ 16 (0.0%) 237 (0.0%) 14.8
SL/CONSENSUS/ 18 (0.0%) 226 (0.0%) 12.5
SL/REFENTRIES/ 50 (0.1%) 225 (0.0%) 4.5
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
SL/INSDEL/ 45 (0.1%) 213 (0.0%) 4.7
HEADERLIBS/ 12 (0.0%) 213 (0.0%) 17.7
GDE/MrBAYES/mrbayes_3.2.1/ 14 (0.0%) 207 (0.0%) 14.7
PERLTOOLS/ 49 (0.1%) 191 (0.0%) 3.8
BINDEP/ 46 (0.1%) 191 (0.0%) 4.1
SL/ITEM_SHADER/ 46 (0.1%) 185 (0.0%) 4.0
SL/TRANSLATE/ 45 (0.1%) 183 (0.0%) 4.0
AISC_COM/ 10 (0.0%) 183 (0.0%) 18.3
UNIT_TESTER/valgrind/ 5 (0.0%) 182 (0.0%) 36.4
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
SL/XFERGUI/ 15 (0.0%) 151 (0.0%) 10.0
lib/export/ 43 (0.1%) 145 (0.0%) 3.3
lib/pictures/cpro/ 6 (0.0%) 143 (0.0%) 23.8
lib/sellists/ 29 (0.1%) 142 (0.0%) 4.8
lib/pixmaps/print/unused/ 8 (0.0%) 138 (0.0%) 17.2
SL/APP/ 10 (0.0%) 137 (0.0%) 13.7
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/ 19 (0.0%) 98 (0.0%) 5.1
SL/QUERY/ 19 (0.0%) 89 (0.0%) 4.6
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
GDE/PHYML20130708/ 12 (0.0%) 75 (0.0%) 6.2
lib/BUGS/ 5 (0.0%) 71 (0.0%) 14.2
SL/ALIVIEW/ 36 (0.1%) 71 (0.0%) 1.9
ORS_COM/ 23 (0.1%) 66 (0.0%) 2.8
UNIT_TESTER/run/consense/4/ 6 (0.0%) 61 (0.0%) 10.1
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
SL/XFERSET/ 14 (0.0%) 42 (0.0%) 3.0
UNIT_TESTER/run/pvp/ 8 (0.0%) 41 (0.0%) 5.1
lib/arb_default/ 19 (0.0%) 40 (0.0%) 2.1
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
SL/SAICALC/ 21 (0.0%) 35 (0.0%) 1.6
SL/PVP/ 12 (0.0%) 33 (0.0%) 2.7
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
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/MASKS/ 8 (0.0%) 20 (0.0%) 2.5
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
SL/HEADERTESTS/ 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 2026-03-10 19:56 Rev.: 19731


* reintegrates 'species' into 'trunk'
- provides species selections in mergetool (#868)
* adds: log:branches/species@19693:19730

568 lines of code changed in 54 files:

  • Makefile (+3), arb_CHANGES.txt (+2)
  • ARBDB: ad_config.cxx (+1), gb_cb.h (+1 -1)
  • ARB_GDE: GDE.cxx (+1 -1)
  • DIST: DI_view_matrix.cxx (+4 -4)
  • GENOM: EXP_interface.cxx (-2), GEN_interface.cxx (-2)
  • GL/glAW: AW_window_ogl.cxx (+1 -2)
  • HELP_SOURCE/source: mg_species.hlp (+17), mg_species_configs.hlp (+14 -11), nt_tree_select.hlp (+2 -2), species_configs.hlp (+28 -19), species_configs_highlight.hlp (+14 -9), species_configs_saveload.hlp (+1 -1), syncscroll.hlp (+2 -2)
  • MERGE: MG_configs.cxx (+86 -85), MG_main.cxx (+2 -2), MG_species.cxx (+6 -4), Makefile (+3), merge.hxx (+4 -1), needs_libs (+1 -2)
  • NTREE: Makefile (+14 -5), NT_branchAnalysis.cxx (+1 -1), NT_cb.cxx (+10 -6), NT_edconf.cxx (+44 -1036), NT_extern.cxx (+23 -55), NT_local_proto.h (+2 -3), NT_sort.cxx (+2 -1), NT_sync_scroll.cxx (+3 -5), ad_trees.cxx (+3 -3), needs_libs (+1)
  • PHYLO: PH_display.cxx (+4 -4)
  • SL/APP: app.cxx (+1 -1)
  • SL/DB_QUERY: db_query.cxx (+32 -45), db_query.h (-2)
  • SL/DB_UI: ui_species.cxx (-2)
  • SL/MACROS: macro_gui.cxx (+1 -1)
  • SL/TREEDISP: TreeDisplay.cxx (+19 -3), TreeDisplay.hxx (+16 -5)
  • SOURCE_TOOLS: dep.4dummy (+3 -2), dep.alltargets (+1), dep.libtargets (+1), generate_all_links.sh (+1)
  • WINDOW: AW_button.cxx (+1 -1), AW_root.cxx (+39), AW_window.cxx (+106 -120), aw_awar_defs.hxx (-1), aw_root.hxx (+1), aw_window.hxx (+15 -13)
  • lib/pictures: ad_query.fig (-2), mark_configs.fig (+15 -15)
  • lib/pictures/merge: configs.fig (+12 -12), species.fig (+4 -4)
westram 2026-03-10 12:11 Rev.: 19708


* update doc+gui:
- avoid terms "ARB_NT" (=former name of main arb window), "ARB_NTREE" and similar
* instead talk about "ARB main window"
- correct refs to 'ARB/Probes/PT_SERVER Admin'.
- update 'What are marked species?'.
- update protection level documentation (parts already done with previous commit).

469 lines of code changed in 230 files:

  • arb_CHANGES.txt (+8 -8), arb_README.txt (+1 -1), arb_install.sh (+1 -1)
  • ARBDB: adali.cxx (+1 -1)
  • EDIT4: ED4_main.cxx (+1 -1)
  • HELP_SOURCE/source: FORM.hlp (+1 -1), Protection.hlp (+3 -3), aci.hlp (+2 -4), acisrt.hlp (+1 -1), ad_align.hlp (+1 -1), ad_extended.hlp (+1 -1), alignment.hlp (+10 -10), arb_commands.hlp (+5 -6), arb_db.hlp (+1 -1), arb_edit4.hlp (+4 -4), arb_export.hlp (+1 -1), arb_export_nds.hlp (+1 -1), arb_import.hlp (+2 -2), arb_intro.hlp (+1 -2), arb_merge.hlp (+2 -2), arb_merge_into.hlp (+2 -2), arb_merge_outof.hlp (+2 -2), arb_merge_workflow.hlp (+6 -6), arb_ntree.hlp (+8 -5), arb_pars.hlp (+4 -4), arb_pars_init.hlp (+1 -1), asciiprint.hlp (+1 -1), awt_csp.hlp (+1 -1), bonds.hlp (+2 -2), branch_analysis.hlp (+2 -2), chimera_check.hlp (+1 -1), color_loadsave.hlp (+4 -4), color_props.hlp (+1 -1), color_ranges.hlp (+1 -1), colorize.hlp (+4 -4), compare_taxonomy.hlp (+1 -1), compare_topo.hlp (+1 -1), consense_algo.hlp (+2 -2), consense_tree.hlp (+1 -1), consensus.hlp (+1 -1), consensus_def.hlp (+1 -1), console.hlp (+2 -2), count_chars.hlp (+1 -1), csp_2_gnuplot.hlp (+1 -1), del_list.hlp (+7 -8), di_clusters.hlp (+1 -1), displayField.hlp (+1 -1), dist.hlp (+3 -3), e4.hlp (+2 -1), e4_block.hlp (+1 -1), experiment_info.hlp (+2 -2), experiment_search.hlp (+2 -2), export_format.hlp (+2 -2), export_test.hlp (+1 -1), field_shader.hlp (+1 -1), gen_create.hlp (+2 -2), gen_jump.hlp (+1 -1), gene_extract.hlp (+2 -2), gene_hide.hlp (+1 -1), gene_info.hlp (+3 -3), gene_map.hlp (+2 -2), gene_mark.hlp (+1 -1), gene_search.hlp (+4 -4), gene_species_field_transfer.hlp (+1 -1), gene_species_mark.hlp (+1 -1), group_rename.hlp (+1 -1), group_search.hlp (+1 -1), group_trees.hlp (+1 -1), helix.hlp (+4 -4), import_test.hlp (+1 -1), importift.hlp (+1 -1), input_mask.hlp (+3 -1), insdel.hlp (+1 -1), insdel_sai.hlp (+1 -1), iupac-codes.hlp (+1 -1), macro.hlp (+1 -1), macro_interruption.hlp (+1 -1), manage_test.hlp (+2 -2), mark.hlp (+23 -27), mark_duplicates.hlp (+1 -1), mark_list.hlp (+3 -3), markbyref.hlp (+1 -1), max_freq.hlp (+1 -1), merge_species.hlp (+2 -2), mod_field_list.hlp (+3 -3), mode.hlp (+2 -2), mode_group.hlp (+2 -2), mode_info.hlp (+2 -2), mode_length.hlp (+2 -2), mode_lzoom.hlp (+3 -3), mode_mark.hlp (+1 -1), mode_move.hlp (+1 -1), mode_pzoom.hlp (+3 -3), mode_rotate.hlp (+2 -2), mode_select.hlp (+1 -1), mode_setroot.hlp (+2 -2), mode_spread.hlp (+3 -3), mode_swap.hlp (+2 -2), mode_width.hlp (+2 -2), mode_www.hlp (+2 -2), move_groups.hlp (+1 -1), multifurcate.hlp (+1 -1), namesadmin.hlp (+1 -1), newwindow.hlp (+8 -7), next_neighbours.hlp (+1 -1), next_neighbours_common.hlp (+2 -2), next_neighbours_listed.hlp (+1 -1), no_tree.hlp (+5 -5), nt_align_select.hlp (+10 -10), nt_keys.hlp (+1 -1), nt_tree_marker_settings.hlp (+1 -1), nt_tree_select.hlp (+1 -1), nt_tree_settings.hlp (+1 -1), nt_tree_settings_bootstrap.hlp (+1 -1), nt_tree_settings_expert.hlp (+1 -1), optimize.hlp (+1 -2), organism_mark.hlp (+1 -1), pa_quick.hlp (+1 -1), pars.hlp (+2 -2), pd_match_iupac.hlp (+1 -1), pd_spec_param.hlp (+1 -1), pfold.hlp (+5 -5), pfold_sai.hlp (+1 -1), ph_export_markerline.hlp (+2 -2), phylo.hlp (+1 -1), pm_spec_param.hlp (+1 -1), pos_var_pars.hlp (+1 -1), primer.hlp (+1 -1), primer_new.hlp (+2 -2), primer_result.hlp (+1 -1), probe_param.hlp (+1 -1), probeadmin.hlp (+1 -1), probedesign.hlp (+1 -1), probedesignresult.hlp (+1 -1), probematch.hlp (+1 -1), probespec.hlp (+5 -4), props_nds.hlp (+3 -3), props_www.hlp (+3 -3), pt_server.hlp (+5 -5), quit.hlp (+3 -2), realign_dna.hlp (+1 -1), rename.hlp (+1 -1), rerepair.hlp (+2 -2), resortbyother.hlp (+1 -1), resorttree.hlp (+2 -2), rst_log_zoom.hlp (+4 -5), rst_phys_zoom.hlp (+1 -1), saiProbe.hlp (+1 -1), saicalc.hlp (+1 -1), save.hlp (+6 -6), savedef.hlp (+2 -1), search_duplicates.hlp (+2 -2), searching.hlp (+3 -3), sel_box.hlp (+1 -1), sel_fil.hlp (+5 -4), selected.hlp (+4 -6), selected_gene.hlp (+3 -3), seq_quality.hlp (+1 -1), set_color_of_listed.hlp (+3 -3), set_protection.hlp (+1 -1), sina_main.hlp (+1 -1), sp_IDs.hlp (+1 -1), sp_del_mrkd.hlp (+6 -5), sp_info.hlp (+4 -4), sp_info_locked.hlp (+1 -1), sp_mark.hlp (+5 -4), sp_search.hlp (+2 -3), sp_sort_fld.hlp (+1 -1), sp_sort_phyl.hlp (+2 -2), sp_sp_2_ext.hlp (+1 -1), spa_copy.hlp (+4 -4), spa_create.hlp (+1 -1), spa_delete.hlp (+5 -6), spa_rename.hlp (+4 -4), spaf_convert.hlp (+1 -1), spaf_delete.hlp (+3 -2), species_configs.hlp (+1 -1), species_configs_highlight.hlp (+1 -1), species_join.hlp (+2 -2), split.hlp (+1 -1), st_ml.hlp (+1 -1), submission.hlp (+1 -1), syncroots.hlp (+1 -1), syncscroll.hlp (+1 -1), tags.hlp (+1 -1), tbl_boot2len.hlp (+1 -1), tbl_justify.hlp (+1 -1), tbl_reset.hlp (+1 -1), tbl_scale.hlp (+1 -1), ted_boot.hlp (+1 -1), tkeep_mrkd.hlp (+1 -1), topology_shader.hlp (+1 -1), tr_export.hlp (+1 -1), tr_import.hlp (+1 -1), tr_jump.hlp (+5 -5), tr_type_dendro.hlp (+1 -1), tr_type_irs.hlp (+1 -1), tr_type_nds.hlp (+2 -2), tr_type_radial.hlp (+1 -1), track_ali_changes.hlp (+1 -1), translate_dna_2_pro.hlp (+1 -1), tree2file.hlp (+1 -1), tree2prt.hlp (+3 -3), tree_group.hlp (+1 -1), tree_pseudo.hlp (+1 -1), tree_shading.hlp (+1 -1), treeadm.hlp (+4 -4), trees.hlp (+2 -3), trm_boot.hlp (+1 -1), trm_del.hlp (+1 -1), trm_mrkd.hlp (+1 -1), undo.hlp (+1 -1), unmark_list.hlp (+3 -3), vn_delete.hlp (+1 -1), vn_import.hlp (+1 -1), vn_search.hlp (+1 -1), vn_suggest.hlp (+1 -1), write_field_list.hlp (+7 -8), xferset.hlp (+2 -2), xterm.hlp (+1 -1)
  • MERGE: MG_main.cxx (+1 -1), MG_species.cxx (+2 -2)
  • NTREE: NT_extern.cxx (+1 -1)
  • PERL2ARB: ARB.pm (+1 -1)
  • SERVERCNTRL: servercntrl.cxx (+2 -2)
  • SH: arb (+1 -1), example_batch_probe_match.sh (+1 -1)
  • SL/APP: db_browser.cxx (+1 -1)
  • SL/TREE_READ: TreeRead.cxx (+1 -1)
  • WINDOW: AW_help.cxx (+1 -1)
westram 2026-03-10 12:00 Rev.: 19707


* update doc
- improve doc of global protection level.
- eliminate references to 'Protection' menu (pre-svn)

28 lines of code changed in 6 files:

  • HELP_SOURCE/source: Protection.hlp (+6 -3), del_list.hlp (+5 -5), gene_info.hlp (+4 -4), security.hlp (+5 -4), sp_info.hlp (+3 -4), write_field_list.hlp (+5 -5)
westram 2026-03-10 11:56 Rev.: 19706


* update doc+gui:
- mention focus strategies.
- use term 'SAI admin'.
- arb introduction (updated + linked missing modules).

73 lines of code changed in 6 files:

  • HELP_SOURCE/source: arb.hlp (+51 -9), nt_keys.hlp (+11), pt_server.hlp (+8 -5)
  • NTREE: NT_extern.cxx (+1 -1), ad_ext.cxx (+1 -1)
  • SL/SAICALC: saicalc.cxx (+1 -1)
westram 2026-02-12 17:58 Rev.: 19691


* reintegrates 'macros' into 'trunk'
- fixes macro IDs for mergetool (completing #870).
* most common problem:
- several modules were reused (twice) for items of same type, but in different databases.
- auto-generated IDs were identical.
* adds: log:branches/macros@19667:19690

660 lines of code changed in 28 files:

  • GENOM: EXP_interface.cxx (+3 -3), GEN_interface.cxx (+41 -53)
  • HELP_SOURCE/source: color_loadsave.hlp (+1 -1), colorize.hlp (+1 -1)
  • MERGE: MG_preserves.cxx (+46 -43), MG_species.cxx (+9 -2), MG_trees.cxx (+3 -3), Makefile (+2)
  • NTREE: Makefile (+3), NT_edconf.cxx (+65 -59), NT_main.cxx (+3), ad_trees.cxx (+1 -1)
  • SL/DB_QUERY: db_query.cxx (+98 -118)
  • SL/DB_UI: ui_species.cxx (+82 -102)
  • SL/GUI_TK: config_manager.cxx (+90 -12), config_manager.hxx (+2)
  • SL/ITEMS: Makefile (+7), items.h (+11 -7), itemtools.cxx (+113 -15), species.cxx (+2 -1)
  • SL/TREE_ADMIN: Makefile (+1), TreeAdmin.cxx (+15 -2), TreeAdmin.h (+1 -1)
  • WINDOW: AW_preset.cxx (+16 -12), AW_root.cxx (+16 -2), AW_root_debug.cxx (+11), AW_window.cxx (+16 -7), Makefile (+1)
westram 2026-02-12 11:58 Rev.: 19666


* add support to rename/merge existing managed configs
* merge all existing "modify fields of listed" managers.

216 lines of code changed in 7 files:

  • SL/DB_QUERY: db_query.cxx (+2 -3)
  • SL/GUI_TK: Makefile (new), config_manager.cxx (+211 -9), config_manager.hxx (new)
westram 2026-02-12 11:53 Rev.: 19665


* fix string splitting
- add test showing that splitting an empty string with mode {{{SPLIT_DROPEMPTY}}} results in an empty array.
- document effect of 'mode' on empty arrays / empty elements.
- check + fix all callers:
* explicitly drop empty tokens where they are expected not to occur.
* {{{parse_helix_list}}}: accept adding "" to helix list for empty list => raise error if no helices specified.
* {{{gb_hierarchy_location}}}: explicitly accept EMPTY path elements. used correctly to encode absolute vs relative paths.

23 lines of code changed in 9 files:

  • ARBDB: ad_cb.cxx (+1 -1), ad_colorset.cxx (+1 -1)
  • CORE: arb_strarray.cxx (+12 -1)
  • EDIT4: ED4_detect_bad_ali.cxx (+2 -1)
  • SL/SAICALC: saicalc.cxx (+1 -1)
  • SL/XFERGUI: xfergui.cxx (+2 -2)
  • SL/XFERSET: xferset.cxx (+2 -2)
  • WINDOW: AW_modal.cxx (+1), AW_preset.cxx (+1)
westram 2026-02-12 11:40 Rev.: 19664


* modify {{{GBT_join_strings}}}:
- converting an array containing one empty string is an idiom. optimize for that.
* add {{{TEST_GBT_join_strings}}}.

27 lines of code changed in 1 file:

  • CORE: arb_strarray.cxx (+27 -1)
westram 2026-01-27 14:54 Rev.: 19662


* reintegrates 'macros' into 'trunk'
- implements #870
* provide macro playback from CLI for merge tool
* adds: log:branches/macros@19656:19661

121 lines of code changed in 14 files:

  • HELP_SOURCE/source: arb_merge.hlp (+1 -1), arb_merge_outof.hlp (+1 -1)
  • MERGE: MG_main.cxx (+19 -13)
  • NTREE: NT_extern.cxx (+4 -4), NT_main.cxx (+16 -12)
  • SL/APP: app.hxx (+1 -1)
  • SL/MACROS: MacroExitor.hxx (+1 -1), macro_gui.cxx (+2 -3), recmac.cxx (+2 -1), trackers.cxx (+1 -1)
  • WINDOW: AW_window.cxx (+18 -6), aw_root.hxx (+1 -1)
  • lib/macros: _dolog.amc (+4 -2), _dolog_merge.amc (new 50)
westram 2026-01-23 15:40 Rev.: 19654


* reintegrates 'macros' into 'trunk'
- improves program termination (#867)
* introduces {{{MacroExitor}}} classes
- handles confirmation (to quit)
- waits for macros to finish, then exits w/o confirmation
- provides specialized termination for different programs via derived classes
* has been implemented for "normal" arb and merge-tool.
* introduces {{{ARB_disconnect_from_db}}}
- generalizes code to terminate all interconnections between GUI, database and macro-ability
- allow to install atdisconnect-callbacks
* usable by modules operating on a database; allow to inform module that database will vanish.
- now used by all arb applications to disconnect from all their database(s), except the properties.
- fixes some broken behavior
* merge-tool
- crashed when quitting via macro
- wrong restarts, if originally started with arguments,
* importer
- failed to record/playback macros
- crashed in modules operating on the temporary import database
* database browser
- crashed on disappearing database
* adds: log:branches/macros@19620:19653

560 lines of code changed in 49 files:

  • Makefile (+1)
  • ARBDB: adindex.cxx (+1 -1), adsocket.cxx (+1 -1), gb_undo.h (+1 -1)
  • AWTI: AWTI_import.cxx (+10 -8), awti_import.hxx (+2 -3), needs_libs (-1)
  • DIST: DI_matr.cxx (+1 -6)
  • EDIT4: ED4_base.cxx (+4 -2), ED4_main.cxx (+1 -2), ED4_no_class.cxx (+13 -22), ed4_class.hxx (+1)
  • MERGE: MG_main.cxx (+53 -33), Makefile (+2), mg_merge.hxx (+1 -1)
  • NTREE: Makefile (+1), NT_extern.cxx (+53 -136), NT_import.cxx (+1 -1), NT_local_proto.h (+4 -3), NT_main.cxx (+14 -8)
  • PARSIMONY: PARS_main.cxx (+7 -10), ap_main_type.hxx (+1 -1)
  • PHYLO: PH_main.cxx (+5 -12), phylo.hxx (+3)
  • SL/APP: Makefile (+31), app.cxx (new 72), app.hxx (new), db_browser.cxx (new)
  • SL/DB_SCANNER: db_scanner.cxx (+4 -2)
  • SL/MACROS: MacroExitor.hxx (new 182), macro_gui.cxx (+18 -11), macros.hxx (+2 -2), trackers.cxx (+8 -2), trackers.hxx (+5 -1)
  • SL/MASKS: Makefile (new), input_mask.cxx (new), input_mask.hxx (-1), needs_libs (+1)
  • SL/XFERGUI: xfergui.cxx (+2 -2)
  • SOURCE_TOOLS: dep.4dummy (+2 -2), generate_all_links.sh (+1)
  • WINDOW: AW_root.cxx (+1)
westram 2025-12-23 15:30 Rev.: 19619


* support to show any number of inheritants / dependencies (previously only inf and 1 were supported)

95 lines of code changed in 2 files:

  • SOURCE_TOOLS: dependency_graphs.pl (+7 -4), needed_libs.pl (+88 -36)
westram 2025-12-19 17:32 Rev.: 19618


* link untested units for anybody (not only4me).
* fix interference between erasing directories + running find. delay erasing directories.

3 lines of code changed in 2 files:

  • Makefile (+1 -1)
  • UNIT_TESTER: Makefile.test (+2 -10)
westram 2025-12-19 17:24 Rev.: 19617


* remove now unneeded hack (added with [19613])

4 lines of code changed in 13 files:

  • SL/ALIVIEW: AliView.cxx (-12)
  • SL/AP_TREE: AP_Tree.cxx (-12)
  • SL/ARB_TREE: ARB_Tree.cxx (-14)
  • SL/DB_UI: ui_species.cxx (-12)
  • SL/HELIX: BI_helix.cxx (-12)
  • SL/QUERY: query_expr.cxx (-12)
  • SL/REFENTRIES: refentries.cxx (-12)
  • SL/SEQUENCE: AP_seq_dna.cxx (-12)
  • SL/TREE_ADMIN: TreeAdmin.cxx (-12)
  • UNIT_TESTER: Makefile.test (+1), forward_decl.hxx (del), sym2testcode.pl (+3 -48)
  • XML: xml.cxx (-13)
westram 2025-12-19 17:18 Rev.: 19616


* activate whole-unit linking
- causes several units to fail linking (caused by undefined symbols)
- add missing libraries to dependency definitions (fixing the above failures)

10 lines of code changed in 6 files:

  • MERGE: needs_libs (+2 -1)
  • SL/ALILINK: needs_libs (+1 -2)
  • SL/GUI_ALIVIEW: needs_libs (+1 -2)
  • SL/SAICALC: needs_libs (+1 -1)
  • SOURCE_TOOLS: dep.4dummy (+4 -4), needed_libs.pl (+1 -1)
westram 2025-12-19 17:08 Rev.: 19615


* prepare force linking of top unit as whole
- deactivated (because it fails atm)
- applied in testable units (tested + untested)
- any referenced symbol has to be satisfied by the specified libraries

54 lines of code changed in 3 files:

  • SOURCE_TOOLS: needed_libs.pl (+44 -3)
  • UNIT_TESTER: Makefile.test (+9 -4), sym2testcode.pl (+1)
westram 2025-12-16 17:09 Rev.: 19613


* reintegrates 'lib' into 'trunk'
- replace dynamic library {{{AWT}}} by several static libraries: APP, ARB_SPEC, MASKS, CANVAS, MAPKEY, GUI_TK
- now also check wrong library dependencies for untested units (only4me)
* adds: log:branches/lib@19578:19612

1468 lines of code changed in 330 files:

  • Makefile (+42 -12)
  • ARBDB: Makefile (+1 -1)
  • ARB_GDE: GDE.cxx (+3 -3), GDE_event.cxx (+1 -1), Makefile (+5 -5)
  • AWT: .cvsignore (del), AWT_TreeAwars.cxx (del), AWT_advice.cxx (del), AWT_asciiprint.cxx (del), AWT_attributes.cxx (del), AWT_automata.cxx (del), AWT_canio.cxx (del), AWT_canvas.cxx (del), AWT_changekey.cxx (del), AWT_codon_table.cxx (del), AWT_config_manager.cxx (del), AWT_csp.cxx (del), AWT_db_browser.cxx (del), AWT_dtree.cxx (del), AWT_file_selection.cxx (del), AWT_filter.cxx (del), AWT_hexdump.cxx (del), AWT_hotkeys.cxx (del), AWT_imp_exp.cxx (del), AWT_input_mask.cxx (del), AWT_irstree.cxx (del), AWT_item_sel_list.cxx (del), AWT_iupac.cxx (del), AWT_macro.cxx (del), AWT_map_key.cxx (del), AWT_misc.cxx (del), AWT_modules.cxx (del), AWT_nds.cxx (del), AWT_nei.cxx (del), AWT_pro_a_nucs.cxx (del), AWT_prompt.cxx (del), AWT_query_and_functions.cxx (del), AWT_sel_boxes.cxx (del), AWT_seq_colors.cxx (del), AWT_seq_dna.cxx (del), AWT_seq_protein.cxx (del), AWT_seq_simple_pro.cxx (del), AWT_species_sel_box.cxx (del), AWT_tables.cxx (del), AWT_tools.cxx (del), AWT_translate.cxx (del), AWT_tree.cxx (del), AWT_tree_cb.cxx (del), AWT_tree_cmp.cxx (del), AWT_www.cxx (del), BI_helix.cxx (del), BI_helix.hxx (del), Makefile (del), awt.hxx (del), awt_TreeAwars.hxx (del), awt_advice.hxx (del), awt_asciiprint.hxx (del), awt_assert.hxx (del), awt_attributes.hxx (del), awt_automata.hxx (del), awt_canvas.hxx (del), awt_changekey.hxx (del), awt_codon_table.hxx (del), awt_config_manager.hxx (del), awt_csp.hxx (del), awt_dtree.hxx (del), awt_hexdump.hxx (del), awt_hotkeys.hxx (del), awt_imp_exp.hxx (del), awt_input_mask.hxx (del), awt_input_mask_internal.hxx (del), awt_irstree.hxx (del), awt_item_sel_list.hxx (del), awt_iupac.hxx (del), awt_macro.hxx (del), awt_map_key.hxx (del), awt_misc.hxx (del), awt_modules.hxx (del), awt_nds.hxx (del), awt_nei.hxx (del), awt_parsimony_defaults.hxx (del), awt_preset.hxx (del), awt_pro_a_nucs.hxx (del), awt_prompt.hxx (del), awt_sel_boxes.hxx (del), awt_seq_colors.hxx (del), awt_seq_dna.hxx (del), awt_seq_protein.hxx (del), awt_seq_simple_pro.hxx (del), awt_translate.hxx (del), awt_tree.hxx (del), awt_tree_cb.hxx (del), awt_tree_cmp.hxx (del), awt_www.hxx (del), awtfilter.hxx (del), awtlocal.hxx (del), needs_libs.libAWT_so (del), newick_doc.html (del), refentries.cxx (del), refentries.h (del)
  • AWTC: Makefile (+1 -1)
  • AWTI: AWTI_edit.cxx (+1 -1), AWTI_import.cxx (+1 -1), Makefile (+6 -6), awti_edit.hxx (+2 -2), needs_libs (+1 -1)
  • CONSENSUS_TREE: Makefile (+1 -1)
  • CORE: Makefile (+1 -1)
  • DBSERVER: Makefile (+1 -1)
  • DIST: DI_clusters.cxx (+1 -1), DI_main.cxx (+5 -5), DI_matr.cxx (+5 -5), DI_view_matrix.cxx (+3 -3), Makefile (+10 -10), di_matr.hxx (+1 -1), di_view_matrix.hxx (+1), needs_libs (+2 -2)
  • EDIT4: ED4_block.cxx (+1 -1), ED4_dots.cxx (+2 -2), ED4_edit_string.cxx (+1 -1), ED4_flags.cxx (+1 -1), ED4_main.cxx (+2 -2), ED4_naligner.cxx (+1 -1), ED4_no_class.cxx (+4 -4), ED4_protein_2nd_structure.cxx (+1 -1), ED4_root.cxx (+2 -2), ED4_search.cxx (+2 -2), ED4_visualizeSAI.cxx (+3 -3), Makefile (+22 -22), ed4_search.hxx (+1 -1), graph_aligner_gui.cxx (+2 -2), needs_libs (+3 -1)
  • EISPACK: Makefile (+1 -1)
  • GENOM: EXP_interface.cxx (+2 -2), EXP_main.cxx (+1 -2), GEN_graphic.hxx (+2 -2), GEN_interface.cxx (+2 -2), GEN_map.cxx (+2 -3), GEN_nds.cxx (+1 -1), Makefile (+11 -13), needs_libs (+2)
  • GL/glAW: Makefile (+1 -1)
  • GL/glpng: Makefile (+1 -1)
  • ISLAND_HOPPING: Makefile (+1 -1)
  • MERGE: MG_alignment.cxx (+1 -1), MG_configs.cxx (+2 -2), MG_extendeds.cxx (+2 -2), MG_gene_species.cxx (+1 -1), MG_main.cxx (+2 -2), MG_trees.cxx (+1 -1), Makefile (+10 -10), needs_libs (+1 -1)
  • MULTI_PROBE: MP_Window.cxx (+2 -2), MP_main.cxx (-1), Makefile (+5 -5)
  • NALIGNER: Makefile (+1 -1)
  • NAMES: Makefile (+1 -1), needs_libs (-1)
  • NTREE: AP_consensus.cxx (+3 -3), AP_pos_var_pars.cxx (+2 -2), ColumnStat_2_gnuplot.cxx (+2 -2), Makefile (+52 -53), NT_branchAnalysis.cxx (+1 -2), NT_cb.cxx (+1 -2), NT_concatenate.cxx (+2 -2), NT_edconf.cxx (+3 -3), NT_extern.cxx (+6 -6), NT_group_search.cxx (+2 -2), NT_import.cxx (+1 -2), NT_ins_col.cxx (+2 -2), NT_join.cxx (+1 -1), NT_main.cxx (+3 -3), NT_shadeTree.cxx (-2), NT_sync_scroll.h (+2 -2), NT_syncroot.cxx (+1 -1), NT_taxonomy.cxx (+1 -1), NT_trackAliChanges.cxx (+1 -1), NT_validNames.cxx (+1 -1), ScrollSynchronizer.cxx (-1), ad_ext.cxx (+1 -1), ad_spec.cxx (+1 -2), ad_transpro.cxx (+1 -1), ad_trees.cxx (+4 -4)
  • PARSIMONY: Makefile (+13 -13), PARS_dtree.cxx (+4 -3), PARS_main.cxx (+5 -5), needs_libs (+1 -1), pars_dtree.hxx (+2 -1), pars_main.hxx (+1 -1)
  • PHYLO: Makefile (+4 -4), PH_filt.cxx (+1 -1), PH_main.cxx (+2 -2), needs_libs (+2 -4)
  • PRIMER_DESIGN: Makefile (+3 -3), needs_libs (+1 -1), primer_design.cxx (+2 -2)
  • PROBE: Makefile (+1 -1)
  • PROBE_DESIGN: Makefile (+8 -8), SaiProbeVisualization.cxx (+2 -2), SaiProbeVisualization.hxx (+2 -2), needs_libs (+1), probe_design.cxx (+3 -3)
  • RNA3D: Makefile (+7 -7), RNA3D_Graphics.hxx (+2 -2), RNA3D_OpenGLGraphics.cxx (+1 -1), needs_libs (+1 -1)
  • RNACMA: Makefile (+1 -1)
  • SECEDIT: Makefile (+7 -7), SEC_graphic.hxx (+2 -2), SEC_main.cxx (+1 -1), needs_libs (+2 -2)
  • SEQ_QUALITY: Makefile (+4 -4), SQ_main.cxx (+3 -3)
  • SERVERCNTRL: Makefile (+1 -1)
  • SL: README (+11 -8)
  • SL/ALILINK: AdminGui.cxx (+2 -2), Makefile (+3 -3), needs_libs (+2 -1)
  • SL/ALIVIEW: AliView.cxx (+12), Makefile (+1 -1)
  • SL/AP_TREE: AP_Tree.cxx (+12), Makefile (+1 -1), needs_libs (+1 -1)
  • SL/ARB_TREE: ARB_Tree.cxx (+14), Makefile (+1 -1)
  • SL/AW_HELIX: AW_helix.cxx (+1 -1), Makefile (+2 -2), needs_libs (+1 -1)
  • SL/AW_NAME: AW_names_admin.cxx (+1 -1), Makefile (+2 -2), needs_libs (+1 -1)
  • SL/CB: Makefile (+1 -1), cb.h (+1 -1)
  • SL/CONSENSUS: Makefile (+1 -1)
  • SL/DB_QUERY: Makefile (+3 -3), db_query.cxx (+2 -2)
  • SL/DB_SCANNER: Makefile (+1 -1)
  • SL/DB_UI: Makefile (+4 -4), ui_species.cxx (+14 -3)
  • SL/FAST_ALIGNER: Makefile (+3 -3), fast_aligner.cxx (+2 -2), needs_libs (+1 -1)
  • SL/FILTER: AP_filter.cxx (+1 -1), AP_filter.hxx (+1 -1), Makefile (+1 -1)
  • SL/FILTSEQEXP: Makefile (+1 -1)
  • SL/GROUP_SEARCH: Makefile (+1 -1)
  • SL/GUI_ALIVIEW: AWT_filter.cxx (del), ColumnStat.cxx (+1 -1), GUI_aliview.cxx (+2 -2), Makefile (+45 -45), ali_filter.cxx (new 483), ali_filter.hxx (new 64), awt_filter.hxx (del), gui_aliview.hxx (+1 -1), needs_libs (+1 -2)
  • SL/HEADERTESTS: Makefile (+1 -1)
  • SL/HELIX: BI_helix.cxx (+12), Makefile (+1 -1)
  • SL/INSDEL: Makefile (+1 -1)
  • SL/ITEMS: Makefile (+2 -2), item_sel_list.cxx (+1 -1), needs_libs (+1 -1)
  • SL/ITEM_SHADER: Makefile (+3 -3), field_shader.cxx (+1 -1), item_shader.cxx (+1 -1)
  • SL/LOCATION: Makefile (+1 -1)
  • SL/MACROS: Makefile (+1 -1)
  • SL/MATRIX: Makefile (+1 -1)
  • SL/NDS: Makefile (+3 -3), nds.cxx (+4 -4)
  • SL/NEIGHBOURJOIN: Makefile (+1 -1)
  • SL/PRONUC: Makefile (+1 -1)
  • SL/PTCLEAN: Makefile (+1 -1), needs_libs (-1)
  • SL/PVP: Makefile (+1 -1)
  • SL/QUERY: Makefile (+1 -1), query_expr.cxx (+12)
  • SL/REFENTRIES: Makefile (+2 -2), needs_libs (+2 -1), refentries.cxx (+13 -1)
  • SL/REGEXPR: Makefile (+1 -1)
  • SL/SAICALC: Makefile (+3 -3), needs_libs (+2 -1), saicalc.cxx (+2 -2)
  • SL/SEQIO: Makefile (+1 -1)
  • SL/SEQUENCE: AP_seq_dna.cxx (+12), Makefile (+1 -1)
  • SL/TRANSLATE: Makefile (+1 -1)
  • SL/TREEDISP: Makefile (+5 -5), TreeDisplay.cxx (+3 -3), TreeDisplay.hxx (+3 -3), needs_libs (+1)
  • SL/TREE_ADMIN: Makefile (+2 -2), TreeAdmin.cxx (+13 -1), needs_libs (+1 -2)
  • SL/TREE_READ: Makefile (+1 -1)
  • SL/TREE_WRITE: Makefile (+1 -1), needs_libs (+1)
  • SL/XFERGUI: Makefile (+2 -2), needs_libs (+1 -1), xfergui.cxx (+1 -1)
  • SL/XFERSET: Makefile (+1 -1)
  • SOURCE_TOOLS: dep.4dummy (+31 -26), dep.alltargets (+6 -1), dep.libtargets (+6 -1), dependency_graphs.pl (+4 -2), generate_all_links.sh (+13 -14), needed_libs.pl (+5 -1)
  • STAT: Makefile (+3 -3), ST_window.cxx (+2 -2)
  • TREEGEN: Makefile (+1 -1)
  • UNIT_TESTER: Makefile (+2 -1), Makefile.suite (+10 -3), Makefile.test (+25 -5), forward_decl.hxx (new 27), reporter.pl (+16 -2), sym2testcode.pl (+77 -23)
  • WETC: Makefile (+3 -2), WETC_main.cxx (+6 -2), needs_libs (+2 -2)
  • WINDOW: AW_device_click.cxx (+1 -1), Makefile (+1 -1), aw_def.hxx (-5), aw_system.hxx (+1 -1)
  • XML: Makefile (+1 -1), xml.cxx (+12)
westram 2025-12-05 11:10 Rev.: 19581


* fix assertion failure in shutdown code
- by avoiding to create {{{GB_shell}}} and {{{AW_root}}} in error cases.

3 lines of code changed in 1 file:

  • WETC: WETC_main.cxx (+3 -3)
westram 2025-11-15 13:21 Rev.: 19577


* (completely) updated changelog

29 lines of code changed in 1 file:

  • arb_CHANGES.txt (+29 -7)
westram 2025-11-13 12:44 Rev.: 19575


* reintegrates 'help' into 'trunk'
- preformatted text gets checked for width now (to enforce it fits into the arb help window).
- fixed help following these checks, using the following steps:
* ignore problems in foreign documentation.
* increase default help window width.
* introduce control comments to
- accept oversized preformatted sections.
- enforce preformatted style for whole sections.
- simply define single-line preformatted sections\\Used intensive for definition of internal script languages.
- fixed several non-related problems found in documentation.
- minor layout changes for HTML version of arb help (more compacted; highlight anchored/all sections).
- refactor system interface (GUI version) and use it from help module.
* adds: log:branches/help@19532:19574

4812 lines of code changed in 63 files:

  • Makefile (+7), arb_CHANGES.txt (+4), arb_LICENSE.txt (+25 -28)
  • AWT: AWT_db_browser.cxx (+2 -2), AWT_misc.cxx (+1 -9), Makefile (+1 -3), awt_misc.hxx (-17)
  • GDE/AxML: AxML.doc (del), AxML.txt (new 15)
  • GDE/CLUSTALW: clustalv.doc (del), clustalv.txt (new 1978), clustalw.doc (del), clustalw.txt (new 765)
  • GDE/FASTDNAML: arb_help_prefix.txt (del), fastDNAml.doc (del), fastDNAml.txt (new 899)
  • GDEHELP: Makefile (+1 -1), Makefile.helpfiles (+11 -11)
  • GDEHELP/HELP_PLAIN: DNAml_rates.help (+10 -10)
  • GDEHELP/MENUS: phylip_help.menu (del)
  • HELP_SOURCE: Makefile (+17 -4), arb_help.dtd (+1), arb_help2xml.cxx (+87 -6), help.readme (+16 -2), postxslt.pl (new 87), to_help.xsl (+54 -7), to_html.xsl (+14 -18)
  • HELP_SOURCE/source: aci.hlp (+103 -51), arb_db.hlp (+186 -184), arb_merge.hlp (+3 -1), arb_ntree.hlp (+95 -66), compare_taxonomy.hlp (+2 -1), dssp_ift.hlp (+8 -4), e4_options.hlp (+4 -4), ed4_nds.hlp (+6 -1), group_rename.hlp (+2), help.hlp (+15 -15), input_mask_format.hlp (+51 -38), macro.hlp (+14 -7), next_neighbours_common.hlp (+2 -1), primer_new.hlp (+3 -1), props_nds.hlp (+1 -1), reg.hlp (+20 -9), save.hlp (+3 -3), searching.hlp (+5 -3), species_configs.hlp (+2 -2), srt.hlp (+134 -39), track_ali_changes.hlp (+16 -11)
  • NTREE: Makefile (+3 -2), NT_edconf.cxx (+2 -2), NT_extern.cxx (+8 -7), NT_main.cxx (+2 -2)
  • SL/AW_NAME: AW_names_admin.cxx (+2 -2), Makefile (+1 -1)
  • SL/MACROS: xcmd.hxx (+1 -1)
  • SOURCE_TOOLS: export2sub (+2), generate_all_links.sh (+1)
  • UNIT_TESTER/run/help: unittest.hlp (+37 -43), unittest.html (+21 -22)
  • WINDOW: AW_help.cxx (+29 -14), Makefile (+2), aw_system.hxx (new 29)
  • lib/pictures: help.fig (+2 -2)
westram 2025-10-29 16:15 Rev.: 19551


* add missing dependency: PROBE_DESIGN->SL/MACROS.

2 lines of code changed in 2 files:

  • PROBE_DESIGN: needs_libs (+1 -3)
  • SOURCE_TOOLS: dep.4dummy (+1 -1)

(9002 more)

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