/trunk Developers: westram

Login name:
westram
Total Commits:
44,836 (87.1%)
Lines of Code:
1,218,207 (48.5%)
Most Recent Commit:
2025-12-19 17:32
Tweet this:
Tweet this

Activity by Clock Time

Activity by Hour of Day for westram

Activity by Day of Week for westram

Activity in Directories

Directory Changes Lines of Code Lines per Change
Totals 44836 (100.0%) 1218207 (100.0%) 27.1
ARBDB/ 4008 (8.9%) 120876 (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/ 2670 (6.0%) 56007 (4.6%) 20.9
NTREE/ 2595 (5.8%) 48864 (4.0%) 18.8
AWT/ 2270 (5.1%) 48309 (4.0%) 21.2
UNIT_TESTER/run/display/ 204 (0.5%) 46531 (3.8%) 228.0
EDIT4/ 2495 (5.6%) 45275 (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/ 760 (1.7%) 19063 (1.6%) 25.0
PROBE/ 707 (1.6%) 18997 (1.6%) 26.8
DIST/ 765 (1.7%) 17589 (1.4%) 22.9
SOURCE_TOOLS/ 842 (1.9%) 16164 (1.3%) 19.1
/ 1100 (2.5%) 15564 (1.3%) 14.1
GDE/PHYML/ 48 (0.1%) 15276 (1.3%) 318.2
GENOM/ 898 (2.0%) 14301 (1.2%) 15.9
MERGE/ 744 (1.7%) 14100 (1.2%) 18.9
SECEDIT/ 607 (1.4%) 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/ 600 (1.3%) 11808 (1.0%) 19.6
CORE/ 577 (1.3%) 11168 (0.9%) 19.3
PROBE_DESIGN/ 510 (1.1%) 11060 (0.9%) 21.6
SL/TREEDISP/ 519 (1.2%) 10485 (0.9%) 20.2
TEMPLATES/ 335 (0.7%) 9647 (0.8%) 28.7
MULTI_PROBE/ 563 (1.3%) 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/ 421 (0.9%) 8729 (0.7%) 20.7
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/ 387 (0.9%) 8012 (0.7%) 20.7
EISPACK/ 21 (0.0%) 7295 (0.6%) 347.3
AWTC/ 360 (0.8%) 7026 (0.6%) 19.5
PRIMER_DESIGN/ 294 (0.7%) 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 (0.6%) 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/ 410 (0.9%) 4812 (0.4%) 11.7
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
HELP_SOURCE/source/ 748 (1.7%) 4150 (0.3%) 5.5
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/ 192 (0.4%) 3404 (0.3%) 17.7
GDEHELP/MENUS/ 262 (0.6%) 3324 (0.3%) 12.6
SL/DB_QUERY/ 181 (0.4%) 3030 (0.2%) 16.7
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/ 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/ 157 (0.4%) 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/ 138 (0.3%) 2253 (0.2%) 16.3
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/ 75 (0.2%) 2111 (0.2%) 28.1
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/ 98 (0.2%) 2005 (0.2%) 20.4
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
lib/pictures/consensus/ 13 (0.0%) 1667 (0.1%) 128.2
SL/SEQIO/ 82 (0.2%) 1641 (0.1%) 20.0
SL/DB_UI/ 134 (0.3%) 1639 (0.1%) 12.2
ORS_CGI/ 55 (0.1%) 1633 (0.1%) 29.6
SL/ITEMS/ 129 (0.3%) 1621 (0.1%) 12.5
GL/glpng/ 39 (0.1%) 1555 (0.1%) 39.8
SERVERCNTRL/ 133 (0.3%) 1523 (0.1%) 11.4
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/ 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/ 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
SL/MACROS/ 95 (0.2%) 931 (0.1%) 9.8
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/pixmaps/edit/ 72 (0.2%) 632 (0.1%) 8.7
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
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
lib/inputMasks/ 25 (0.1%) 436 (0.0%) 17.4
SL/TREE_ADMIN/ 41 (0.1%) 422 (0.0%) 10.2
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
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/ 13 (0.0%) 147 (0.0%) 11.3
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
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
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/ 13 (0.0%) 40 (0.0%) 3.0
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/ 19 (0.0%) 33 (0.0%) 1.7
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
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 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)
westram 2025-10-29 10:27 Rev.: 19549


* reintegrates 'sync' into 'trunk'
- fixes #869
* introduces synchronisation of external commands via DB
* macros now wait for these external commands to finish => macro can continue with results
* adds: log:branches/sync@19535:19548

821 lines of code changed in 44 files:

  • ARBDB: Makefile (+3), ad_prot.h (+4 -1), adcomm.cxx (+3), adsocket.cxx (+103 -59), arbdb.h (-12), arbdbt.h (+1)
  • ARB_GDE: GDE_event.cxx (+38 -1), Makefile (+2), needs_libs (+1)
  • AWT: AWT_misc.cxx (+3 -5), Makefile (+1), awt_misc.hxx (+7 -4)
  • BINDEP: needs_libs.arb_sync (new 4)
  • EDIT4: ED4_naligner.cxx (-1), Makefile (+1), graph_aligner_gui.cxx (+2 -1), needs_libs (-4)
  • GDE: README (+1 -1)
  • HELP_SOURCE/source: gde_menus.hlp (+7 -2)
  • NTREE: ColumnStat_2_gnuplot.cxx (+2 -1), Makefile (+3), NT_extern.cxx (+9 -7), NT_main.cxx (+3 -1), ad_trees.cxx (+3 -2)
  • PROBE_DESIGN: Makefile (+1), probe_design.cxx (+7 -6)
  • SH: arb_wait (+18 -3)
  • SL/MACROS: Makefile (+23), dbserver.cxx (+32 -2), dbserver.hxx (+1), macro_gui.cxx (+29 -1), macros.hxx (+3 -1), trackers.cxx (+40 -5), xcmd.cxx (new 187), xcmd.hxx (new 84)
  • SOURCE_TOOLS: dep.4dummy (+2 -2), dep.alltargets (+1), dependency_graphs.pl (+3 -1), generate_all_links.sh (+1)
  • TEMPLATES: arb_sleep.h (+8)
  • TOOLS: Makefile (+24), arb_sync.cxx (new 154)
  • WINDOW: aw_root.hxx (+1 -1)
  • bin: .gitignore (+1)
westram 2025-10-27 11:38 Rev.: 19536


* mark test as "slow" (to avoid warnings).
* fix warning introduced with 'track-ali-changes'.

2 lines of code changed in 2 files:

  • NTREE: NT_syncroot.cxx (+1 -1), NT_trackAliChanges.cxx (+1 -1)
westram 2025-09-11 12:43 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 09:25 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 (+5 -5), Protection.hlp (new), aaali.hlp (new), accessibility_sai.hlp (+5 -5), aci.hlp (new), acisrt.hlp (+7 -8), ad_align.hlp (new), ad_extended.hlp (+8 -8), advice.hlp (new), alignment.hlp (+9 -9), ap_stack.hlp (+8 -8), arb.hlp (+18 -18), arb_commands.hlp (new), 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 (+13 -13), arb_intro.hlp (new), arb_merge.hlp (+10 -10), arb_merge_into.hlp (+7 -7), arb_merge_outof.hlp (+9 -9), arb_merge_workflow.hlp (new), arb_ntree.hlp (+73 -44), arb_pars.hlp (new), arb_pars_init.hlp (+8 -8), arb_secedit.hlp (+10 -10), asciiprint.hlp (new), awt_csp.hlp (new), bonds.hlp (new), bootstrap.hlp (new), branch_analysis.hlp (new), bugtracker.hlp (new 30), checkfield.hlp (new), chimera_check.hlp (+7 -7), cluster_group.hlp (+8 -8), color.hlp (new), color_loadsave.hlp (new), color_props.hlp (+7 -7), color_props_groups.hlp (new), color_ranges.hlp (+7 -7), colorize.hlp (+10 -10), compare_taxonomy.hlp (+7 -7), compare_topo.hlp (new), concatenate.hlp (+6 -7), consense_algo.hlp (+4 -4), consense_tree.hlp (new), consensus.hlp (+10 -10), consensus_def.hlp (+4 -4), console.hlp (+5 -5), copyNpaste.hlp (+8 -8), count_chars.hlp (new), csp_2_gnuplot.hlp (new), del_list.hlp (+11 -11), di_clusters.hlp (new), displayField.hlp (+6 -6), dist.hlp (+18 -18), dssp_ift.hlp (new), 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 (+7 -7), e4_mode.hlp (+5 -5), e4_modsai.hlp (+9 -9), e4_options.hlp (+9 -9), e4_replace.hlp (new), e4_search.hlp (new), ecoliref.hlp (+5 -5), ed4_flags.hlp (+6 -6), ed4_nds.hlp (+6 -6), exec_bug.hlp (new), experiment_info.hlp (+7 -7), experiment_search.hlp (+7 -7), export_format.hlp (new), export_test.hlp (+5 -5), extended.hlp (new), faligner.hlp (+12 -12), field_sel_new.hlp (+8 -8), field_shader.hlp (+4 -4), gde_flat_ift.hlp (new), gde_menus.hlp (+1 -1), gen_create.hlp (+9 -9), gen_disp_style.hlp (+7 -7), gen_jump.hlp (+8 -8), gen_mode.hlp (new), gen_new_view.hlp (+5 -5), gen_options.hlp (+7 -7), 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 (+8 -8), gene_search.hlp (+16 -16), gene_species.hlp (new), gene_species_field_transfer.hlp (new), gene_species_mark.hlp (+8 -8), genes.hlp (new), glossary.hlp (+13 -13), group_by_field.hlp (new), group_rename.hlp (+7 -7), group_search.hlp (new), group_trees.hlp (new), helix.hlp (+11 -11), helixsym.hlp (+10 -10), help.hlp (new), import_test.hlp (new), importift.hlp (+8 -8), input_mask.hlp (new), input_mask_format.hlp (new), input_mask_new.hlp (new), insdel.hlp (new), insdel_sai.hlp (+7 -7), islandhopping.hlp (new), iupac-codes.hlp (+7 -7), keeled_groups.hlp (+4 -4), kernlin.hlp (new), macro.hlp (+7 -7), man_arb_edit4.hlp (new), manage_test.hlp (new), manual.hlp (new), 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 (+10 -8), merge_species.hlp (+7 -7), mergetaggedfield.hlp (new), mg_alignment.hlp (new), mg_extendeds.hlp (new), mg_names.hlp (+4 -4), mg_preserve.hlp (new), 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 (+7 -7), missbase.hlp (new), mod_field_list.hlp (+10 -10), mode.hlp (+21 -21), mode_group.hlp (new), mode_info.hlp (new), mode_kernlin.hlp (new), mode_length.hlp (new), mode_lzoom.hlp (new), mode_mark.hlp (new), mode_move.hlp (new), mode_nni.hlp (new), mode_optimize.hlp (new), mode_pzoom.hlp (+8 -8), mode_rotate.hlp (new), mode_select.hlp (+9 -9), mode_setroot.hlp (new), mode_spread.hlp (+8 -8), mode_swap.hlp (new), mode_width.hlp (new), mode_www.hlp (new), move_groups.hlp (new), mp_params.hlp (new), multifurcate.hlp (+5 -5), multiprobe.hlp (new), multiproberesults.hlp (new), namesadmin.hlp (new), ne_align_seq.hlp (+9 -9), nekey_map.hlp (new), newwindow.hlp (new), next_neighbours.hlp (+9 -9), next_neighbours_common.hlp (+13 -13), next_neighbours_listed.hlp (new), nni.hlp (+14 -14), no_tree.hlp (new), nt_align_select.hlp (new), nt_keys.hlp (+7 -7), nt_tree_marker_settings.hlp (+5 -5), nt_tree_select.hlp (+14 -20), nt_tree_settings.hlp (+7 -7), nt_tree_settings_bootstrap.hlp (new), nt_tree_settings_expert.hlp (new), optimize.hlp (+5 -5), organism_mark.hlp (+8 -8), organisms.hlp (+10 -10), pa_add.hlp (+7 -7), pa_bootstrap.hlp (+3 -3), pa_branchlengths.hlp (new), pa_globopti.hlp (new), pa_kernlin.hlp (new), pa_locopti.hlp (new), pa_mixtree.hlp (+7 -7), pa_optimizer.hlp (new), pa_partial.hlp (+9 -9), pa_quick.hlp (+9 -9), pa_reset.hlp (+8 -8), pa_value.hlp (new), pars.hlp (new), partial_sequences.hlp (+7 -7), pd_match_iupac.hlp (+8 -8), pd_spec_param.hlp (new), pfold.hlp (new), pfold_props.hlp (+8 -8), pfold_sai.hlp (new), ph_export_markerline.hlp (new), phylo.hlp (new), pm_spec_param.hlp (+7 -7), pos_var_pars.hlp (new), primer.hlp (new), primer_new.hlp (+6 -6), primer_result.hlp (+7 -7), probe_param.hlp (+9 -9), probeadmin.hlp (new), probedesign.hlp (+9 -9), probedesignresult.hlp (new), probematch.hlp (+5 -5), probespec.hlp (new), prop_configs.hlp (+8 -8), prop_configs_edit.hlp (new), props_frame.hlp (new), props_nds.hlp (+11 -11), props_www.hlp (new), proteinViewer.hlp (new), pt_server.hlp (+4 -4), questions.hlp (new), quit.hlp (+7 -7), realign_dna.hlp (new), reg.hlp (+11 -11), rename.hlp (new), rerepair.hlp (+7 -7), reset_win_layout.hlp (new), resortbyother.hlp (new), resorttree.hlp (new), rna3d_changeMolecule.hlp (new), rna3d_dispBases.hlp (new), rna3d_dispHelices.hlp (+10 -10), rna3d_dispMolecule.hlp (new), rna3d_general.hlp (+12 -10), rna3d_mapSeqData.hlp (+13 -13), rst_log_zoom.hlp (+8 -8), rst_phys_zoom.hlp (+8 -8), saiProbe.hlp (new), saicalc.hlp (new), save.hlp (+4 -4), save_matrix.hlp (+5 -5), savedef.hlp (+7 -7), scandb.hlp (new), search_duplicates.hlp (+7 -7), search_equal_fields.hlp (new), searching.hlp (+8 -8), sec_bonddef.hlp (+5 -5), sec_display.hlp (new), sec_imexport.hlp (new), sec_keys.hlp (new), sec_main.hlp (+10 -10), sec_mode.hlp (new), sec_props.hlp (new), secedit_imexport.hlp (new), security.hlp (new), 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 (+8 -8), sina_main.hlp (+6 -7), sp_IDs.hlp (new), sp_del_mrkd.hlp (new), sp_info.hlp (+4 -4), sp_info_locked.hlp (new), sp_mark.hlp (+8 -8), sp_search.hlp (+15 -15), sp_sort_fld.hlp (new), sp_sort_phyl.hlp (+8 -8), sp_sp_2_ext.hlp (+8 -8), spa_copy.hlp (+4 -4), spa_create.hlp (new), spa_delete.hlp (+9 -9), spa_rename.hlp (+4 -4), spaf_convert.hlp (+7 -7), spaf_create.hlp (new), spaf_delete.hlp (+8 -8), spaf_reorder.hlp (new), species.hlp (new), species_configs.hlp (+8 -8), species_configs_highlight.hlp (+7 -7), species_configs_saveload.hlp (+7 -7), species_join.hlp (new), srt.hlp (+5 -5), st_ml.hlp (new), submission.hlp (+5 -5), sync_colors.hlp (+7 -7), syncroots.hlp (+5 -5), syncscroll.hlp (+5 -5), tags.hlp (new), tbl_boot2len.hlp (+7 -7), 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 (new), tr_type_dendro.hlp (new 34), tr_type_irs.hlp (+16 -16), tr_type_list.hlp (del), tr_type_nds.hlp (+16 -16), tr_type_radial.hlp (+16 -21), track_ali_changes.hlp (+7 -7), trans_anal.hlp (new), transl_table.hlp (+4 -4), translate_dna_2_pro.hlp (new), tree2file.hlp (+7 -7), tree2prt.hlp (+6 -6), tree_group.hlp (+5 -5), tree_pseudo.hlp (+7 -7), tree_shading.hlp (new), treeadm.hlp (+7 -7), trees.hlp (new), trm_boot.hlp (new), trm_del.hlp (+6 -6), trm_mrkd.hlp (+7 -7), undo.hlp (new), unittest.hlp (new), universal_ift.hlp (+5 -5), unmark_list.hlp (new), user_matrix.hlp (new), version.hlp (+5 -5), viewdiff.hlp (+8 -8), visualizeSAI.hlp (+7 -7), vn_delete.hlp (new), vn_import.hlp (new), vn_search.hlp (new), vn_suggest.hlp (new), write_field_list.hlp (+5 -5), xferset.hlp (+5 -5), xterm.hlp (new)
  • 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 17:50 Rev.: 19517


* fix typo.

1 lines of code changed in 1 file:

  • HELP_SOURCE/source: macro.hlp (+1 -1)
westram 2025-08-07 17:30 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 17:27 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 (new)
  • SH: arb_launcher (+9 -4)
westram 2025-08-07 17:24 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 14:00 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 15:29 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 15:02 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)

(8991 more)

Generated by StatSVN 0.7.0