/trunk Developers: westram

Login name:
westram
Total Commits:
43,293 (87.2%)
Lines of Code:
1,201,010 (48.0%)
Most Recent Commit:
2022-12-13 11:06
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Activity in Directories

Directory Changes Lines of Code Lines per Change
Totals 43293 (100.0%) 1201010 (100.0%) 27.7
ARBDB/ 3986 (9.2%) 120709 (10.1%) 30.2
lib/nas/ 30 (0.1%) 66561 (5.5%) 2218.7
GDE/PHYLIP/ 146 (0.3%) 56082 (4.7%) 384.1
WINDOW/ 2653 (6.1%) 55923 (4.7%) 21.0
AWT/ 2224 (5.1%) 49055 (4.1%) 22.0
NTREE/ 2541 (5.9%) 48536 (4.0%) 19.1
UNIT_TESTER/run/display/ 204 (0.5%) 46531 (3.9%) 228.0
EDIT4/ 2456 (5.7%) 44336 (3.7%) 18.0
UNIT_TESTER/run/ 133 (0.3%) 30642 (2.6%) 230.3
HELP_SOURCE/oldhelp/ 2246 (5.2%) 30060 (2.5%) 13.3
CONVERTALN/ 463 (1.1%) 29090 (2.4%) 62.8
TOOLS/ 728 (1.7%) 23538 (2.0%) 32.3
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/ 704 (1.6%) 18994 (1.6%) 26.9
DIST/ 756 (1.7%) 17560 (1.5%) 23.2
SOURCE_TOOLS/ 819 (1.9%) 15965 (1.3%) 19.4
/ 1086 (2.5%) 15428 (1.3%) 14.2
GDE/PHYML/ 32 (0.1%) 15189 (1.3%) 474.6
GENOM/ 886 (2.0%) 14227 (1.2%) 16.0
MERGE/ 734 (1.7%) 14077 (1.2%) 19.1
SECEDIT/ 591 (1.4%) 13510 (1.1%) 22.8
GDE/PHYML20130708/phyml/ 9 (0.0%) 13410 (1.1%) 1490.0
SL/FAST_ALIGNER/ 318 (0.7%) 12517 (1.0%) 39.3
lib/ 60 (0.1%) 12302 (1.0%) 205.0
ARB_GDE/ 593 (1.4%) 11757 (1.0%) 19.8
PROBE_DESIGN/ 501 (1.2%) 11033 (0.9%) 22.0
CORE/ 566 (1.3%) 11028 (0.9%) 19.4
SL/TREEDISP/ 513 (1.2%) 10459 (0.9%) 20.3
TEMPLATES/ 329 (0.8%) 9557 (0.8%) 29.0
MULTI_PROBE/ 559 (1.3%) 9438 (0.8%) 16.8
NALIGNER/ 359 (0.8%) 9252 (0.8%) 25.7
UNIT_TESTER/ 536 (1.2%) 9241 (0.8%) 17.2
ptpan/ 128 (0.3%) 8692 (0.7%) 67.9
lib/pictures/ 414 (1.0%) 8630 (0.7%) 20.8
PROBE_WEB/CLIENT/ 267 (0.6%) 8512 (0.7%) 31.8
AWTI/ 380 (0.9%) 7999 (0.7%) 21.0
GDE/FASTDNAML/ 37 (0.1%) 7391 (0.6%) 199.7
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/ 61 (0.1%) 6650 (0.6%) 109.0
GDE/AxML/ 17 (0.0%) 6003 (0.5%) 353.1
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 (0.7%) 4069 (0.3%) 14.3
STAT/ 279 (0.6%) 3886 (0.3%) 13.9
ISLAND_HOPPING/ 136 (0.3%) 3818 (0.3%) 28.0
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
GDE/CLUSTALW/ 41 (0.1%) 3373 (0.3%) 82.2
SH/ 186 (0.4%) 3360 (0.3%) 18.0
GDEHELP/MENUS/ 260 (0.6%) 3303 (0.3%) 12.7
SL/DB_QUERY/ 177 (0.4%) 3004 (0.3%) 16.9
ARBDBPP/ 72 (0.2%) 2998 (0.2%) 41.6
lib/addlibs/ 13 (0.0%) 2859 (0.2%) 219.9
EDIT/ 91 (0.2%) 2810 (0.2%) 30.8
util/ 231 (0.5%) 2548 (0.2%) 11.0
SEQ_QUALITY/ 241 (0.6%) 2539 (0.2%) 10.5
GDE/MOLPHY/ 105 (0.2%) 2531 (0.2%) 24.1
PGT/ 178 (0.4%) 2495 (0.2%) 14.0
PERL2ARB/ 163 (0.4%) 2391 (0.2%) 14.6
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/ 45 (0.1%) 2300 (0.2%) 51.1
SL/AP_TREE/ 153 (0.4%) 2298 (0.2%) 15.0
RNACMA/ 83 (0.2%) 2284 (0.2%) 27.5
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/ 73 (0.2%) 2109 (0.2%) 28.8
SL/ALILINK/ 40 (0.1%) 2099 (0.2%) 52.4
NAMES/ 123 (0.3%) 2068 (0.2%) 16.8
SL/TREE_READ/ 97 (0.2%) 2004 (0.2%) 20.6
READSEQ/ 36 (0.1%) 2004 (0.2%) 55.6
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 (0.2%) 21.2
lib/pictures/consensus/ 13 (0.0%) 1667 (0.1%) 128.2
SL/SEQIO/ 80 (0.2%) 1638 (0.1%) 20.4
ORS_CGI/ 55 (0.1%) 1633 (0.1%) 29.6
SL/ITEMS/ 126 (0.3%) 1617 (0.1%) 12.8
SL/DB_UI/ 130 (0.3%) 1598 (0.1%) 12.2
SL/HELIX/ 103 (0.2%) 1562 (0.1%) 15.1
GL/glpng/ 37 (0.1%) 1553 (0.1%) 41.9
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/ 172 (0.4%) 1443 (0.1%) 8.3
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/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
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
ARBDBS/ 29 (0.1%) 850 (0.1%) 29.3
UNIT_TESTER/run/consense/1/ 17 (0.0%) 813 (0.1%) 47.8
PERL_SCRIPTS/ARBTOOLS/ 18 (0.0%) 801 (0.1%) 44.5
SL/GROUP_SEARCH/ 25 (0.1%) 790 (0.1%) 31.6
GDE/MOLPHY/doc/ 4 (0.0%) 758 (0.1%) 189.5
SL/LOCATION/ 29 (0.1%) 754 (0.1%) 26.0
TREEGEN/ 126 (0.3%) 706 (0.1%) 5.6
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
SL/AW_HELIX/ 78 (0.2%) 663 (0.1%) 8.5
lib/pixmaps/icons/unused/ 32 (0.1%) 662 (0.1%) 20.6
lib/pixmaps/edit/ 72 (0.2%) 632 (0.1%) 8.7
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
GDEHELP/HELP_WRITTEN/ 27 (0.1%) 579 (0.0%) 21.4
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
SL/FILE_BUFFER/ 43 (0.1%) 495 (0.0%) 11.5
GDE/SUPPORT/ 26 (0.1%) 494 (0.0%) 19.0
GDE/RAxML8/ 15 (0.0%) 491 (0.0%) 32.7
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
HELP_SOURCE/source/ 39 (0.1%) 437 (0.0%) 11.2
lib/inputMasks/ 25 (0.1%) 436 (0.0%) 17.4
GDE/HGL_SRC/ 27 (0.1%) 418 (0.0%) 15.4
SL/MACROS/ 74 (0.2%) 409 (0.0%) 5.5
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
lib/pictures/awtc/ 19 (0.0%) 327 (0.0%) 17.2
TESTAWT/ 17 (0.0%) 317 (0.0%) 18.6
GDE/FASTTREE/ 10 (0.0%) 312 (0.0%) 31.2
lib/pixmaps/icons/ 17 (0.0%) 310 (0.0%) 18.2
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
lib/pixmaps/print/ 20 (0.0%) 281 (0.0%) 14.0
HELP_SOURCE/genhelp/ 24 (0.1%) 272 (0.0%) 11.3
GDE/ 47 (0.1%) 271 (0.0%) 5.7
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/CONSENSUS/ 17 (0.0%) 225 (0.0%) 13.2
SL/ 41 (0.1%) 225 (0.0%) 5.4
HEADERLIBS/ 12 (0.0%) 213 (0.0%) 17.7
SL/INSDEL/ 44 (0.1%) 212 (0.0%) 4.8
SL/REFENTRIES/ 45 (0.1%) 207 (0.0%) 4.6
GDE/MrBAYES/mrbayes_3.2.1/ 10 (0.0%) 203 (0.0%) 20.3
PERLTOOLS/ 48 (0.1%) 191 (0.0%) 3.9
BINDEP/ 45 (0.1%) 187 (0.0%) 4.1
GDE/CLUSTAL/ 24 (0.1%) 184 (0.0%) 7.6
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
WETC/ 57 (0.1%) 165 (0.0%) 2.8
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/ 28 (0.1%) 154 (0.0%) 5.5
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
lib/sellists/ 29 (0.1%) 142 (0.0%) 4.8
SL/XFERGUI/ 8 (0.0%) 142 (0.0%) 17.7
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
GDE/TREEPUZZLE/src/ 14 (0.0%) 113 (0.0%) 8.0
lib/dtd/ 8 (0.0%) 111 (0.0%) 13.8
GL/ 15 (0.0%) 111 (0.0%) 7.4
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/ 11 (0.0%) 74 (0.0%) 6.7
lib/BUGS/ 5 (0.0%) 71 (0.0%) 14.2
ORS_COM/ 23 (0.1%) 66 (0.0%) 2.8
GDE/MAFFT/mafft-7.055-with-extensions/core/ 4 (0.0%) 65 (0.0%) 16.2
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/ 6 (0.0%) 43 (0.0%) 7.1
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/ 5 (0.0%) 37 (0.0%) 7.4
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
UNIT_TESTER/run/consense/6/ 2 (0.0%) 26 (0.0%) 13.0
SL/SAICALC/ 13 (0.0%) 24 (0.0%) 1.8
GDE/SATIVA/ 12 (0.0%) 20 (0.0%) 1.6
PERL_SCRIPTS/IFTHELP/ 10 (0.0%) 18 (0.0%) 1.8
GDE/PROBCONS/ 4 (0.0%) 18 (0.0%) 4.5
doc/ 2 (0.0%) 11 (0.0%) 5.5
GDE/PROBCONS/probcons/ 4 (0.0%) 10 (0.0%) 2.5
GDE/TREEPUZZLE/doc/ 5 (0.0%) 9 (0.0%) 1.8
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
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/PHYML20130708/phyml/src/ 2 (0.0%) 4 (0.0%) 2.0
GDE/MAFFT/mafft-7.055-with-extensions/extensions/mxscarna_src/ 2 (0.0%) 4 (0.0%) 2.0
GDE/SINA/builddir/src/ 2 (0.0%) 3 (0.0%) 1.5
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/extensions/ 2 (0.0%) 2 (0.0%) 1.0
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/SINA/ 2 (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 2022-12-13 11:06 Rev.: 19355


* adds script to detect new field content in marked subset of species (compared with unmarked subset).
* fix whitespace only in {{{listMarkedSpecies.pl}}}.

129 lines of code changed in 2 files:

  • PERL_SCRIPTS/SPECIES: findNewContent.pl (new 121), listMarkedSpecies.pl (+8 -8)
westram 2022-11-30 19:27 Rev.: 19354


* deny execution.

1 lines of code changed in 1 file:

  • lib/macros: keep_listed_trees.amc (+1 -1)
westram 2022-11-30 19:16 Rev.: 19353


* added script to delete unlisted trees.

88 lines of code changed in 3 files:

  • HELP_SOURCE/source: treeadm.hlp (new)
  • lib/macros: keep_listed_trees.amc (new 88)
westram 2022-11-30 19:12 Rev.: 19352


* added script to delete unlisted species selections.

85 lines of code changed in 3 files:

  • HELP_SOURCE/source: mg_species_configs.hlp (changed)
  • lib/macros: keep_listed_speciesSelections.amc (new 85)
westram 2022-11-30 19:00 Rev.: 19351


* added script to delete unlisted SAIs.

106 lines of code changed in 3 files:

  • HELP_SOURCE/source: ad_extended.hlp (new)
  • lib/macros: keep_listed_SAIs.amc (new 106)
westram 2022-11-30 18:41 Rev.: 19350


* fix info message: protected are only kept when they exist.
* show warning after deletion.

4 lines of code changed in 1 file:

  • lib/macros: keep_listed_fields.amc (+4 -1)
westram 2022-11-26 10:49 Rev.: 19349


* fix mnemonics:
- in 'Tree' menu:
* p: was used for 'Print tree' + 'Compare topology...'
* o: 'Sync tree scrolling..' -> 'Compare topology...'
* e: 'Beautify tree' -> 'Sync tree scrolling..'
* u: 'Mark duplicates' -> 'Beautify tree'
* k: now used for 'Mark duplicates'
* removed 'Select tree' (also bound to tree button).
* T: used for 'Tree admin' now (was 'Select tree')
* i: used for (genome-only) 'Relink tree to organisms' (was 'Tree admin')
- in 'Sequence' menu:
* S: was used for 'Split sequences' + 'Align Sequences'.
* l: now used for 'Align sequences'.
- in species transfer of merge tool.
- in properties menu of 'ARB gene map'.
- in properties menu of 'PROBE and SAI' (most changed).

18 lines of code changed in 4 files:

  • GENOM: GEN_map.cxx (+1 -1)
  • MERGE: MG_species.cxx (+1 -1)
  • NTREE: NT_extern.cxx (+11 -15)
  • PROBE_DESIGN: SaiProbeVisualization.cxx (+5 -5)
westram 2022-11-17 11:29 Rev.: 19348


* emphasize reference- and ptserver-database have to be the same database!

18 lines of code changed in 1 file:

  • HELP_SOURCE/source: sina_main.hlp (+18 -6)
westram 2022-11-13 18:29 Rev.: 19346


* reintegrates 'refactor' into 'trunk'
- polish {{{GBS_strstruct}}}
* adds: log:branches/refactor@19339:19345

101 lines of code changed in 9 files:

  • ARBDB: aditem.cxx (+1 -1), adlang1.cxx (+1 -1), adname.cxx (+1 -1), adsocket.cxx (+1 -1), adstring.cxx (+6 -6), gb_aci.cxx (+1 -1)
  • CORE: arb_strbuf.h (+87 -55)
  • PROBE: PT_findEx.cxx (+1 -1)
  • SL/DB_SCANNER: db_scanner.cxx (+2 -2)
westram 2022-11-13 15:47 Rev.: 19339


* reintegrates 'refactor' into 'trunk'
- eliminates old interface of {{{GBS_strstruct}}}
- add a few new unittests (editor-config string + some PT-SERVER-functions)
* adds: log:branches/refactor@19300:19338

987 lines of code changed in 58 files:

  • Makefile (+1 -1)
  • ARBDB: adGene.cxx (+17 -27), ad_config.cxx (+7 -10), ad_config.h (+5 -2), adali.cxx (+5), adhash.cxx (+9 -12), adindex.cxx (+27 -24), aditem.cxx (+6 -7), adlang1.cxx (+80 -80), adname.cxx (+5 -7), adsocket.cxx (+10 -10), adstring.cxx (+46 -58), gb_aci.cxx (+3 -3)
  • AWT: AWT_sel_boxes.cxx (+4 -2)
  • AWTC: AWTC_next_neighbours.cxx (+4 -4), AWTC_submission.cxx (+9 -9)
  • AWTI: AWTI_import.cxx (+25 -26)
  • CORE: arb_match.cxx (+9 -12), arb_pattern.cxx (+5 -5), arb_strarray.cxx (+5 -5), arb_strbuf.cxx (+23 -146), arb_strbuf.h (+14 -16), arb_string.cxx (+1 -1)
  • EDIT4: ED4_cursor.cxx (+4 -5), ED4_naligner.cxx (+41 -50), EDB_root_bact.cxx (+2 -2), Makefile (+2)
  • MERGE: MG_adapt_ali.cxx (+32 -25), MG_checkfield.cxx (+11 -8), Makefile (+1)
  • MULTI_PROBE: MP_sonde.cxx (+33 -26)
  • NTREE: Makefile (+1), NT_edconf.cxx (+223 -60), NT_extern.cxx (-50)
  • PERLTOOLS: arb_proto_2_xsub.cxx (+7 -14)
  • PROBE: PT_etc.cxx (+8 -5), PT_findEx.cxx (+7 -7), PT_match.cxx (+58 -74)
  • PROBE_DESIGN: Makefile (+1), probe_design.cxx (+98 -30)
  • SECEDIT: SEC_helix.cxx (+8 -8)
  • SL/DB_QUERY: db_query.cxx (+5 -5)
  • SL/DB_UI: ui_species.cxx (+7 -5)
  • SL/GUI_ALIVIEW: AWT_filter.cxx (+17 -18), ColumnStat.cxx (+6 -6)
  • SL/PVP: AP_pos_var.cxx (+4 -5)
  • SL/TREE_ADMIN: TreeAdmin.cxx (+5 -7)
  • SL/TREE_WRITE: TreeWrite.cxx (+8 -8)
  • STAT: ST_quality.cxx (+7 -8)
  • TOOLS: arb_probe.cxx (+6 -6), arb_replace.cxx (+10 -11)
  • UNIT_TESTER: test_helpers.h (+6 -6), test_unit.h (+33 -18)
  • UNIT_TESTER/run: TEST_gpt.arb.expected (changed), TEST_gpt_src.arb (+3), TEST_trees.arb (changed)
  • WINDOW: AW_file.cxx (+9 -9), AW_select.cxx (+4 -4)
westram 2022-11-06 16:26 Rev.: 19300


* reintegrates 'refactor' into 'trunk'
- new unittest for MULTI_PROBE functionality
* adds: log:branches/refactor@19297:19299

97 lines of code changed in 2 files:

  • MULTI_PROBE: MP_sonde.cxx (+95 -1), Makefile (+2)
westram 2022-11-06 16:09 Rev.: 19297


* reintegrates 'refactor' into 'trunk'
- refactored MULTI_PROBE to support unittest.
* adds: log:branches/refactor@19286:19296

221 lines of code changed in 14 files:

  • MULTI_PROBE: MP_Window.cxx (-2), MP_externs.hxx (+1 -3), MP_mo_liste.cxx (+79 -81), MP_noclass.cxx (+1 -17), MP_permute.cxx (+1 -1), MP_sonde.cxx (+73 -59), MP_sondentopf.cxx (+9 -5), Makefile (+2 -1), MultiProbe.hxx (+21 -25), mpdefs.h (+2 -3)
  • PROBE_DESIGN: probe_design.cxx (+2 -21)
  • SERVERCNTRL: servercntrl.cxx (+23), servercntrl.h (+1)
  • TOOLS: arb_probe.cxx (+6 -15)
westram 2022-10-27 13:59 Rev.: 19285


* again update prerequisites: use libxerces-c-dev
* also use changed prerequisites in {{{arb_INSTALL.txt}}}

4 lines of code changed in 2 files:

  • arb_INSTALL.txt (+3 -2)
  • SH: arb_installubuntu4arb.sh (+1 -2)
westram 2022-10-27 13:18 Rev.: 19284


* fix prerequisites for motif library.

7 lines of code changed in 1 file:

  • SH: arb_installubuntu4arb.sh (+7 -2)
westram 2022-10-22 18:30 Rev.: 19283


* allow to define a separator used to generate clusternames
- old hardcoded default was '_' (which interferes with groupname conventions)
- new customisable default is '-'
- use custom separator
* in get_upgroup_info().
* for matchrate.
- correctly handle empty separator.
* change other hardcoded characters
- avoid '_' in {{{WHOLE_TREE}}} (now uses {{{<WHOLE TREE>}}}).
- neighter use '/' nor '-' when inserting relative notation (old: {{{3-4/7}}} new {{{3.4[7]}}}).
* part of #832

22 lines of code changed in 4 files:

  • DIST: DI_clusters.cxx (+16 -8), DI_foundclusters.cxx (+3 -3), di_foundclusters.hxx (+1 -1)
  • HELP_SOURCE/source: cluster_group.hlp (+2)
westram 2022-10-22 18:24 Rev.: 19282


* reject groupnames which would be misinterpreted as bootstrap values
- misinterpretation would happen during re-import after export

22 lines of code changed in 1 file:

  • ARBDB: adtree.cxx (+22)
westram 2022-10-22 18:19 Rev.: 19281


* pull-out {{{parse_treelabel()}}} from {{{setBranchName_acceptingBootstrap()}}}.

45 lines of code changed in 2 files:

  • ARBDB: TreeNode.h (+38)
  • SL/TREE_READ: TreeRead.cxx (+7 -18)
westram 2022-10-22 18:17 Rev.: 19280


* document collaboration between 'create groups' with 'append original' and 'delete groups'.

0 lines of code changed in 2 files:

  • HELP_SOURCE/source: cluster_group.hlp (new)
westram 2022-10-22 18:14 Rev.: 19279


* use + add wrapped concatenators to {{{GBS_strstruct}}}

13 lines of code changed in 4 files:

  • ARBDB: adstring.cxx (+1 -3)
  • CORE: arb_msg.cxx (+1 -5), arb_strbuf.h (+10)
  • EDIT4: graph_aligner_gui.cxx (+1 -1)
westram 2022-10-21 15:08 Rev.: 19278


* warn about..
- {{{;}}} in group names (conflicts with taxonomy).
- group names containing underscores (reserved for group overlaps).
- group names ending with {{{~NUM}}} (reserved for splitted groups).

24 lines of code changed in 1 file:

  • ARBDB: adtree.cxx (+24 -4)

(8909 more)

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