/trunk Developers: westram

Login name:
westram
Total Commits:
42,342 (87.0%)
Lines of Code:
1,185,660 (47.6%)
Most Recent Commit:
2021-10-12 15:20
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Activity in Directories

Directory Changes Lines of Code Lines per Change
Totals 42342 (100.0%) 1185660 (100.0%) 28.0
ARBDB/ 3901 (9.2%) 119839 (10.1%) 30.7
lib/nas/ 30 (0.1%) 66561 (5.6%) 2218.7
GDE/PHYLIP/ 146 (0.3%) 56082 (4.7%) 384.1
WINDOW/ 2609 (6.2%) 55461 (4.7%) 21.2
AWT/ 2203 (5.2%) 48911 (4.1%) 22.2
NTREE/ 2473 (5.8%) 47105 (4.0%) 19.0
UNIT_TESTER/run/display/ 203 (0.5%) 46525 (3.9%) 229.1
EDIT4/ 2387 (5.6%) 43374 (3.7%) 18.1
HELP_SOURCE/oldhelp/ 2246 (5.3%) 30060 (2.5%) 13.3
CONVERTALN/ 461 (1.1%) 29087 (2.5%) 63.0
UNIT_TESTER/run/ 128 (0.3%) 27930 (2.4%) 218.2
TOOLS/ 716 (1.7%) 23236 (2.0%) 32.4
GDE/PHYLIP/doc/ 42 (0.1%) 21478 (1.8%) 511.3
GENOM_IMPORT/ 388 (0.9%) 19993 (1.7%) 51.5
PARSIMONY/ 744 (1.8%) 19001 (1.6%) 25.5
PROBE/ 693 (1.6%) 18866 (1.6%) 27.2
DIST/ 740 (1.7%) 17338 (1.5%) 23.4
SOURCE_TOOLS/ 782 (1.8%) 15431 (1.3%) 19.7
GDE/PHYML/ 32 (0.1%) 15189 (1.3%) 474.6
/ 1034 (2.4%) 14673 (1.2%) 14.1
GENOM/ 882 (2.1%) 14198 (1.2%) 16.0
MERGE/ 708 (1.7%) 13889 (1.2%) 19.6
SECEDIT/ 586 (1.4%) 13478 (1.1%) 23.0
GDE/PHYML20130708/phyml/ 9 (0.0%) 13410 (1.1%) 1490.0
SL/FAST_ALIGNER/ 305 (0.7%) 12456 (1.1%) 40.8
lib/ 60 (0.1%) 12302 (1.0%) 205.0
ARB_GDE/ 580 (1.4%) 11662 (1.0%) 20.1
PROBE_DESIGN/ 491 (1.2%) 10592 (0.9%) 21.5
CORE/ 537 (1.3%) 10552 (0.9%) 19.6
SL/TREEDISP/ 491 (1.2%) 10154 (0.9%) 20.6
TEMPLATES/ 320 (0.8%) 9433 (0.8%) 29.4
NALIGNER/ 357 (0.8%) 9234 (0.8%) 25.8
UNIT_TESTER/ 525 (1.2%) 9155 (0.8%) 17.4
MULTI_PROBE/ 538 (1.3%) 9085 (0.8%) 16.8
ptpan/ 128 (0.3%) 8692 (0.7%) 67.9
lib/pictures/ 410 (1.0%) 8600 (0.7%) 20.9
PROBE_WEB/CLIENT/ 267 (0.6%) 8512 (0.7%) 31.8
AWTI/ 374 (0.9%) 7963 (0.7%) 21.2
GDE/FASTDNAML/ 37 (0.1%) 7391 (0.6%) 199.7
EISPACK/ 20 (0.0%) 7294 (0.6%) 364.7
AWTC/ 353 (0.8%) 7003 (0.6%) 19.8
AISC/ 208 (0.5%) 6893 (0.6%) 33.1
PRIMER_DESIGN/ 288 (0.7%) 6889 (0.6%) 23.9
GDE/RAxML/ 61 (0.1%) 6650 (0.6%) 109.0
GDE/AxML/ 17 (0.0%) 6003 (0.5%) 353.1
CONSENSUS_TREE/ 325 (0.8%) 5918 (0.5%) 18.2
lib/import/ 211 (0.5%) 5908 (0.5%) 28.0
HELP_SOURCE/ 233 (0.6%) 5719 (0.5%) 24.5
PHYLO/ 399 (0.9%) 4756 (0.4%) 11.9
ALIV3/ 174 (0.4%) 4669 (0.4%) 26.8
UNIT_TESTER/run/impexp/ 50 (0.1%) 4434 (0.4%) 88.6
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/ 275 (0.6%) 3873 (0.3%) 14.0
ISLAND_HOPPING/ 136 (0.3%) 3818 (0.3%) 28.0
lib/pixmaps/ 302 (0.7%) 3582 (0.3%) 11.8
AISC_MKPTPS/ 110 (0.3%) 3573 (0.3%) 32.4
AISC_COM/AISC/ 112 (0.3%) 3501 (0.3%) 31.2
GDE/CLUSTALW/ 41 (0.1%) 3373 (0.3%) 82.2
RNA3D/ 302 (0.7%) 3366 (0.3%) 11.1
ARBDBPP/ 72 (0.2%) 2998 (0.3%) 41.6
SH/ 167 (0.4%) 2986 (0.3%) 17.8
SL/DB_QUERY/ 169 (0.4%) 2976 (0.3%) 17.6
lib/addlibs/ 13 (0.0%) 2859 (0.2%) 219.9
EDIT/ 91 (0.2%) 2810 (0.2%) 30.8
GDEHELP/MENUS/ 240 (0.6%) 2635 (0.2%) 10.9
GDE/MOLPHY/ 105 (0.2%) 2531 (0.2%) 24.1
SEQ_QUALITY/ 238 (0.6%) 2529 (0.2%) 10.6
PGT/ 178 (0.4%) 2495 (0.2%) 14.0
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/ 152 (0.4%) 2296 (0.2%) 15.1
PERL2ARB/ 158 (0.4%) 2296 (0.2%) 14.5
util/ 214 (0.5%) 2282 (0.2%) 10.6
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/ 133 (0.3%) 2247 (0.2%) 16.8
SL/PRONUC/ 128 (0.3%) 2224 (0.2%) 17.3
RNACMA/ 80 (0.2%) 2193 (0.2%) 27.4
GL/glAW/ 73 (0.2%) 2109 (0.2%) 28.8
SL/ALILINK/ 34 (0.1%) 2070 (0.2%) 60.8
NAMES/ 123 (0.3%) 2068 (0.2%) 16.8
READSEQ/ 36 (0.1%) 2004 (0.2%) 55.6
SL/TREE_READ/ 95 (0.2%) 1995 (0.2%) 21.0
lib/pixmaps/unused/ 147 (0.3%) 1993 (0.2%) 13.5
SL/AW_NAME/ 178 (0.4%) 1880 (0.2%) 10.5
PROBE_SERVER/ 85 (0.2%) 1809 (0.2%) 21.2
lib/pictures/consensus/ 13 (0.0%) 1667 (0.1%) 128.2
ORS_CGI/ 55 (0.1%) 1633 (0.1%) 29.6
SL/SEQIO/ 78 (0.2%) 1624 (0.1%) 20.8
SL/ITEMS/ 118 (0.3%) 1584 (0.1%) 13.4
SL/DB_UI/ 123 (0.3%) 1582 (0.1%) 12.8
GL/glpng/ 37 (0.1%) 1553 (0.1%) 41.9
SL/HELIX/ 99 (0.2%) 1514 (0.1%) 15.2
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/GUI_ALIVIEW/ 164 (0.4%) 1411 (0.1%) 8.6
SERVERCNTRL/ 128 (0.3%) 1399 (0.1%) 10.9
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/ 46 (0.1%) 1288 (0.1%) 28.0
TRS/ 37 (0.1%) 1279 (0.1%) 34.5
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
SEER/ 41 (0.1%) 1115 (0.1%) 27.1
GDEHELP/ 130 (0.3%) 1100 (0.1%) 8.4
SL/NDS/ 86 (0.2%) 1076 (0.1%) 12.5
XML/ 72 (0.2%) 1069 (0.1%) 14.8
PERL_SCRIPTS/SPECIES/ 28 (0.1%) 1020 (0.1%) 36.4
SL/SEQUENCE/ 140 (0.3%) 999 (0.1%) 7.1
SL/TREE_WRITE/ 90 (0.2%) 945 (0.1%) 10.5
PROBE_COM/ 98 (0.2%) 912 (0.1%) 9.3
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/ 21 (0.0%) 784 (0.1%) 37.3
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/ 70 (0.2%) 700 (0.1%) 10.0
SL/FILTER/ 70 (0.2%) 696 (0.1%) 9.9
lib/macros/.checks/ 3 (0.0%) 675 (0.1%) 225.0
lib/pixmaps/icons/unused/ 32 (0.1%) 662 (0.1%) 20.6
SL/AW_HELIX/ 77 (0.2%) 662 (0.1%) 8.5
lib/pixmaps/edit/ 72 (0.2%) 632 (0.1%) 8.7
UNIT_TESTER/run/help/ 11 (0.0%) 600 (0.1%) 54.5
UNIT_TESTER/run/pars/ 52 (0.1%) 597 (0.1%) 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/ 17 (0.0%) 555 (0.0%) 32.6
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
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
GDE/RAxML8/ 10 (0.0%) 469 (0.0%) 46.9
lib/pictures/unused/ 11 (0.0%) 462 (0.0%) 42.0
NAMES_COM/ 71 (0.2%) 459 (0.0%) 6.4
lib/submit/ 2 (0.0%) 446 (0.0%) 223.0
lib/inputMasks/ 25 (0.1%) 436 (0.0%) 17.4
GDEHELP/HELP_WRITTEN/ 15 (0.0%) 431 (0.0%) 28.7
GDE/HGL_SRC/ 27 (0.1%) 418 (0.0%) 15.4
SL/MACROS/ 72 (0.2%) 404 (0.0%) 5.6
SL/TREE_ADMIN/ 35 (0.1%) 400 (0.0%) 11.4
SL/ARB_TREE/ 85 (0.2%) 400 (0.0%) 4.7
GDEHELP/HELP_PLAIN/ 11 (0.0%) 371 (0.0%) 33.7
lib/pictures/faligner/ 16 (0.0%) 369 (0.0%) 23.0
lib/pictures/query/ 18 (0.0%) 368 (0.0%) 20.4
SL/MATRIX/ 57 (0.1%) 367 (0.0%) 6.4
bin/ 28 (0.1%) 357 (0.0%) 12.7
SL/NEIGHBOURJOIN/ 63 (0.1%) 355 (0.0%) 5.6
SL/ROOTED_TREE/ 17 (0.0%) 350 (0.0%) 20.5
lib/pictures/pars/ 7 (0.0%) 335 (0.0%) 47.8
lib/pictures/awtc/ 19 (0.0%) 327 (0.0%) 17.2
SL/PTCLEAN/ 39 (0.1%) 323 (0.0%) 8.2
TESTAWT/ 17 (0.0%) 317 (0.0%) 18.6
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/ 46 (0.1%) 261 (0.0%) 5.6
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
HEADERLIBS/ 12 (0.0%) 213 (0.0%) 17.7
SL/ 40 (0.1%) 212 (0.0%) 5.3
SL/REFENTRIES/ 43 (0.1%) 205 (0.0%) 4.7
GDE/MrBAYES/mrbayes_3.2.1/ 8 (0.0%) 195 (0.0%) 24.3
lib/macros/ 26 (0.1%) 188 (0.0%) 7.2
BINDEP/ 45 (0.1%) 187 (0.0%) 4.1
GDE/CLUSTAL/ 24 (0.1%) 184 (0.0%) 7.6
PERLTOOLS/ 46 (0.1%) 183 (0.0%) 3.9
AISC_COM/ 10 (0.0%) 183 (0.0%) 18.3
UNIT_TESTER/valgrind/ 5 (0.0%) 182 (0.0%) 36.4
SL/TRANSLATE/ 43 (0.1%) 181 (0.0%) 4.2
SL/INSDEL/ 38 (0.1%) 180 (0.0%) 4.7
SL/ITEM_SHADER/ 40 (0.1%) 175 (0.0%) 4.3
WETC/ 56 (0.1%) 164 (0.0%) 2.9
PERL_SCRIPTS/SAI/ 5 (0.0%) 163 (0.0%) 32.6
CHIP/ 29 (0.1%) 160 (0.0%) 5.5
SOURCE_TOOLS/COMPILE_COMPAT/ 14 (0.0%) 154 (0.0%) 11.0
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/ 28 (0.1%) 139 (0.0%) 4.9
lib/pixmaps/print/unused/ 8 (0.0%) 138 (0.0%) 17.2
SL/XFERGUI/ 5 (0.0%) 136 (0.0%) 27.2
UNIT_TESTER/run/general/ 12 (0.0%) 134 (0.0%) 11.1
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/ 16 (0.0%) 94 (0.0%) 5.8
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/ 15 (0.0%) 75 (0.0%) 5.0
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
UNIT_TESTER/run/consense/4/ 6 (0.0%) 61 (0.0%) 10.1
SL/ALIVIEW/ 33 (0.1%) 58 (0.0%) 1.7
GDE/MAFFT/mafft-7.055-with-extensions/core/ 3 (0.0%) 58 (0.0%) 19.3
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
etc/ 11 (0.0%) 38 (0.0%) 3.4
GDE/MrBAYES/ 5 (0.0%) 37 (0.0%) 7.4
BINDINGS/PERL/ 1 (0.0%) 37 (0.0%) 37.0
SL/XFERSET/ 10 (0.0%) 36 (0.0%) 3.6
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
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
GDE/MUSCLE/ 5 (0.0%) 30 (0.0%) 6.0
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
lib/gde/ 3 (0.0%) 23 (0.0%) 7.6
UNIT_TESTER/run/distance/ 6 (0.0%) 19 (0.0%) 3.1
PERL_SCRIPTS/IFTHELP/ 10 (0.0%) 18 (0.0%) 1.8
GDE/FASTTREE/ 5 (0.0%) 18 (0.0%) 3.6
GDE/SATIVA/ 7 (0.0%) 16 (0.0%) 2.2
SL/PVP/ 6 (0.0%) 15 (0.0%) 2.5
doc/ 2 (0.0%) 11 (0.0%) 5.5
GDE/PROBCONS/probcons/ 4 (0.0%) 10 (0.0%) 2.5
GDE/PROBCONS/ 3 (0.0%) 10 (0.0%) 3.3
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/MUSCLE/src/ 5 (0.0%) 3 (0.0%) 0.6
SOURCE_TOOLS/refactor/ 4 (0.0%) 2 (0.0%) 0.5
SL/SAICALC/ 7 (0.0%) 2 (0.0%) 0.2
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/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 2021-10-12 15:20 Rev.: 18789


* DEBUG and NDEBUG version of helpfiles:
- have to differ '''only''' in ''content'', not in ''line count''.
- now two lines differ
- fixes unittest for NDEBUG version
* fix whitespace.

6 lines of code changed in 3 files:

  • HELP_SOURCE: arb_help2xml.cxx (+1 -1), to_help.xsl (+4 -2)
  • UNIT_TESTER/run/help: unittest.hlp (+1 -1)
westram 2021-10-10 09:33 Rev.: 18781


* reintegrates 'help' into 'trunk'
- relocate help sources
* adds: log:branches/help@18763:18780

142 lines of code changed in 467 files:

  • arb_OS_X.txt (-1)
  • ARBDB: adsocket.cxx (+12 -12), gb_aci.cxx (+1 -1)
  • ARB_GDE: GDE_ParseMenu.cxx (+1 -1)
  • EDIT4: ED4_text_terminals.cxx (+1 -1)
  • GENOM_IMPORT: Importer.cxx (+1 -1)
  • HELP_SOURCE: Makefile (+1 -1), arb_help.dtd (+1 -1), arb_help2xml.cxx (+5 -5), arb_xslt.sh (+1 -1), generate_index.pl (+1 -1), help.readme (+24 -7), to_help.xsl (+3 -2)
  • HELP_SOURCE/oldhelp: FAQS.hlp (del), FORM.hlp (del), Makefile (del), Protection.hlp (del), aaali.hlp (del), accessibility_sai.hlp (del), aci.hlp (del), acisrt.hlp (del), ad_align.hlp (del), ad_extended.hlp (del), advice.hlp (del), ae2_ift.hlp (del), agde_MAUS.hlp (del), agde_sativa.hlp (del), ale.hlp (del), align.hlp (del), alignment.hlp (del), ap_stack.hlp (del), arb.hlp (del), arb.pdf.gz (del), arb.ps.gz (del), arb_comm (del), arb_commands.hlp (del), arb_db.hlp (del), arb_edit.hlp (del), arb_edit4.hlp (del), arb_envar.hlp (del), arb_export.hlp (del), arb_export_nds.hlp (del), arb_gde.hlp (del), arb_import.hlp (del), arb_intro.hlp (del), arb_merge.hlp (del), arb_merge_into.hlp (del), arb_merge_outof.hlp (del), arb_merge_workflow.hlp (del), arb_ntree.hlp (del), arb_pars.hlp (del), arb_pars_init.hlp (del), arb_secedit.hlp (del), asciiprint.hlp (del), awt_csp.hlp (del), bonds.hlp (del), bootstrap.hlp (del), branch_analysis.hlp (del), change_security.hlp (del), check_quality.hlp (del), checkfield.hlp (del), checkgcg.hlp (del), chimera_check.hlp (del), cluster_group.hlp (del), color.hlp (del), color_loadsave.hlp (del), color_props.hlp (del), color_props_groups.hlp (del), color_ranges.hlp (del), colorize.hlp (del), commands.hlp (del), compare_taxonomy.hlp (del), compare_topo.hlp (del), concatenate.hlp (del), config_saveload.hlp (del), configuration.hlp (del), configurations.hlp (del), cons_params.hlp (del), consense_algo.hlp (del), consense_tree.hlp (del), consensus.hlp (del), consensus.ps.gz (del), consensus_def.hlp (del), console.hlp (del), copyNpaste.hlp (del), copyright.hlp (del), count_chars.hlp (del), csp_2_gnuplot.hlp (del), del_list.hlp (del), dewachter_ift.hlp (del), di_clusters.hlp (del), displayField.hlp (del), dist.hlp (del), dssp_ift.hlp (del), e4.hlp (del), e4_background_priority.hlp (del), e4_block.hlp (del), e4_consensus.hlp (del), e4_defaults.hlp (del), e4_get_species.hlp (del), e4_mode.hlp (del), e4_modsai.hlp (del), e4_options.hlp (del), e4_replace.hlp (del), e4_search.hlp (del), ebi_ift.hlp (del), ecoliref.hlp (del), ed4_flags.hlp (del), ed4_nds.hlp (del), edit_config.hlp (del), exec_bug.hlp (del), experiment_info.hlp (del), experiment_search.hlp (del), export_format.hlp (del), export_test.hlp (del), exportcursor.hlp (del), extended.hlp (del), faligner.hlp (del), fasta_ift.hlp (del), fastdnaml.hlp (del), field_sel_new.hlp (del), field_shader.hlp (del), galign_main.hlp (del), gde.hlp (del), gde_flat_ift.hlp (del), gde_ift.hlp (del), gde_menus.hlp (del), gen_create.hlp (del), gen_disp_style.hlp (del), gen_jump.hlp (del), gen_mode.hlp (del), gen_new_view.hlp (del), gen_options.hlp (del), gene_extract.hlp (del), gene_hide.hlp (del), gene_info.hlp (del), gene_map.hlp (del), gene_mark.hlp (del), gene_mode.hlp (del), gene_options.hlp (del), gene_pseudo.hlp (del), gene_search.hlp (del), gene_species.hlp (del), gene_species_field_transfer.hlp (del), gene_species_mark.hlp (del), genes.hlp (del), glossary.hlp (del), group_by_field.hlp (del), group_rename.hlp (del), group_search.hlp (del), group_trees.hlp (del), helix.hlp (del), helixsym.hlp (del), help.hlp (del), help.tar (del), import_test.hlp (del), importift.hlp (del), index (del), input_mask.hlp (del), input_mask_format.hlp (del), input_mask_new.hlp (del), insdel.hlp (del), insdel_sai.hlp (del), insdelchar.hlp (del), islandhopping.hlp (del), iupac-codes.hlp (del), join_species.hlp (del), keeled_groups.hlp (del), kernlin.hlp (del), macro.hlp (del), man_arb_edit4.hlp (del), manage_test.hlp (del), manual.hlp (del), mark.hlp (del), mark_configs.hlp (del), mark_duplicates.hlp (del), mark_genes.hlp (del), mark_list.hlp (del), mark_long_branches.hlp (del), markbyref.hlp (del), markcolor.hlp (del), matrix_settings.hlp (del), max_freq.hlp (del), merge_species.hlp (del), mergetaggedfield.hlp (del), mg_alignment.hlp (del), mg_configs.hlp (del), mg_extendeds.hlp (del), mg_names.hlp (del), mg_preserve.hlp (del), mg_spec_sel_field.hlp (del), mg_species.hlp (del), mg_species_configs.hlp (del), mg_trees.hlp (del), mg_xfer_field_of_listed.hlp (del), mg_xfer_field_of_sel.hlp (del), missbase.hlp (del), mod_field_list.hlp (del), mode.hlp (del), mode_angle.hlp (del), mode_group.hlp (del), mode_info.hlp (del), mode_kernlin.hlp (del), mode_length.hlp (del), mode_lzoom.hlp (del), mode_mark.hlp (del), mode_move.hlp (del), mode_nni.hlp (del), mode_optimize.hlp (del), mode_pzoom.hlp (del), mode_reset.hlp (del), mode_rotate.hlp (del), mode_select.hlp (del), mode_set_root.hlp (del), mode_setroot.hlp (del), mode_spread.hlp (del), mode_swap.hlp (del), mode_width.hlp (del), mode_www.hlp (del), move_groups.hlp (del), mp_params.hlp (del), multifurcate.hlp (del), multiprobe.hlp (del), multiproberesults.hlp (del), namesadmin.hlp (del), ne_align_seq.hlp (del), ne_compl.hlp (del), ne_copy_sequence.hlp (del), ne_new_sequence.hlp (del), ne_pretty.hlp (del), ne_replace.hlp (del), ne_search.hlp (del), nekey_map.hlp (del), neprops.hlp (del), neprops_data.hlp (del), newwindow.hlp (del), next_neighbours.hlp (del), next_neighbours_common.hlp (del), next_neighbours_listed.hlp (del), nni.hlp (del), no_tree.hlp (del), nt_align_select.hlp (del), nt_keys.hlp (del), nt_props_data.hlp (del), nt_tree_marker_settings.hlp (del), nt_tree_select.hlp (del), nt_tree_settings.hlp (del), nt_tree_settings_bootstrap.hlp (del), nt_tree_settings_expert.hlp (del), optimize.hlp (del), organism_mark.hlp (del), organisms.hlp (del), pa_add.hlp (del), pa_add_sel.hlp (del), pa_bootstrap.hlp (del), pa_branchlengths.hlp (del), pa_globopti.hlp (del), pa_kernlin.hlp (del), pa_locopti.hlp (del), pa_mixtree.hlp (del), pa_optimizer.hlp (del), pa_partial.hlp (del), pa_quick.hlp (del), pa_quick_sel.hlp (del), pa_ranchlengths.hlp (del), pa_reset.hlp (del), pa_value.hlp (del), pars.hlp (del), parser.hlp (del), partial_sequences.hlp (del), pd_match_iupac.hlp (del), pd_spec_param.hlp (del), pfold.hlp (del), pfold_props.hlp (del), pfold_sai.hlp (del), ph_export_markerline.hlp (del), phyl.hlp (del), phylo.hlp (del), pm_spec_param.hlp (del), pos_var_pars.hlp (del), pos_variability.ps.gz (del), primer.hlp (del), primer_new.hlp (del), primer_parameters.hlp (del), primer_result.hlp (del), probe_param.hlp (del), probeadmin.hlp (del), probedesign.hlp (del), probedesignresult.hlp (del), probematch.hlp (del), probespec.hlp (del), prop_configs.hlp (del), prop_configs_edit.hlp (del), props_frame.hlp (del), props_nds.hlp (del), props_www.hlp (del), proteinViewer.hlp (del), pt_server.hlp (del), questions.hlp (del), quit.hlp (del), rdp_ift.hlp (del), realign_dna.hlp (del), reg.hlp (del), regexpr.hlp (del), registration.hlp (del), rename.hlp (del), rerepair.hlp (del), reset_win_layout.hlp (del), resortbyother.hlp (del), resorttree.hlp (del), result.hlp (del), rl_dna_prot.hlp (del), rna3d_changeMolecule.hlp (del), rna3d_dispBases.hlp (del), rna3d_dispHelices.hlp (del), rna3d_dispMolecule.hlp (del), rna3d_general.hlp (del), rna3d_manual.pdf (del), rna3d_manual.pdf.gz (del), rna3d_manual.ps.gz (del), rna3d_mapSeqData.hlp (del), rst_log_zoom.hlp (del), rst_phys_zoom.hlp (del), saiProbe.hlp (del), saiProbeHelp.hlp (del), saicalc.hlp (del), save.hlp (del), save_def.hlp (del), save_matrix.hlp (del), saveas.hlp (del), savedef.hlp (del), scandb.hlp (del), search_duplicates.hlp (del), search_equal_fields.hlp (del), searching.hlp (del), sec_bonddef.hlp (del), sec_display.hlp (del), sec_imexport.hlp (del), sec_keys.hlp (del), sec_main.hlp (del), sec_mode.hlp (del), sec_props.hlp (del), secedit_imexport.hlp (del), security.hlp (del), sel_box.hlp (del), sel_fil.hlp (del), sel_spec.hlp (del), selected.hlp (del), selected_gene.hlp (del), seq_quality.hlp (del), sequence_colors.hlp (del), set_color_of_listed.hlp (del), set_meny_fields.hlp (del), set_protection.hlp (del), set_reference.hlp (del), sina_main.hlp (del), sp_IDs.hlp (del), sp_count_mrk.hlp (del), sp_del_mrkd.hlp (del), sp_info.hlp (del), sp_info_locked.hlp (del), sp_invert_mrk.hlp (del), sp_mark.hlp (del), sp_mrk_all.hlp (del), sp_mrk_tree.hlp (del), sp_rename.hlp (del), sp_search.hlp (del), sp_sort_fld.hlp (del), sp_sort_phyl.hlp (del), sp_sp_2_ext.hlp (del), sp_umrk_all.hlp (del), sp_umrk_tree.hlp (del), spa_copy.hlp (del), spa_create.hlp (del), spa_delete.hlp (del), spa_rename.hlp (del), spaf_convert.hlp (del), spaf_create.hlp (del), spaf_delete.hlp (del), spaf_reorder.hlp (del), spaf_scandb.hlp (del), species.hlp (del), species_configs.hlp (del), species_configs_highlight.hlp (del), species_configs_saveload.hlp (del), species_info.hlp (del), species_join.hlp (del), srt.hlp (del), st_ml.hlp (del), submission.hlp (del), sv_def.hlp (del), sync_colors.hlp (del), syncroots.hlp (del), syncscroll.hlp (del), tags.hlp (del), tbl_boot2len.hlp (del), tbl_justify.hlp (del), tbl_reset.hlp (del), tbl_scale.hlp (del), ted_boot.hlp (del), tgroupall.hlp (del), tgroupcolor.hlp (del), tgroupnmrkd.hlp (del), tkeep_mrkd.hlp (del), toggle_secinfo.hlp (del), topology_shader.hlp (del), tr_export.hlp (del), tr_import.hlp (del), tr_jump.hlp (del), tr_type_irs.hlp (del), tr_type_list.hlp (del), tr_type_nds.hlp (del), tr_type_radial.hlp (del), track_ali_changes.hlp (del), trans_anal.hlp (del), transl_table.hlp (del), translate_dna_2_pro.hlp (del), tree2file.hlp (del), tree2prt.hlp (del), tree_cmp.hlp (del), tree_diff.hlp (del), tree_group.hlp (del), tree_pseudo.hlp (del), tree_shading.hlp (del), treeadm.hlp (del), trees.hlp (del), trm_boot.hlp (del), trm_del.hlp (del), trm_mrkd.hlp (del), tungroupall.hlp (del), undo.hlp (del), unittest.hlp (del), universal_ift.hlp (del), unmark_list.hlp (del), user_matrix.hlp (del), version.hlp (del), viewdiff.hlp (del), visualizeSAI.hlp (del), vn_delete.hlp (del), vn_delete.hlp~ (del), vn_import.hlp (del), vn_import.hlp~ (del), vn_search.hlp (del), vn_search.hlp~ (del), vn_suggest.hlp (del), vn_suggest.hlp~ (del), write_field_list.hlp (del), xferset.hlp (del), xterm.hlp (del)
  • HELP_SOURCE/oldhelp/prompt: format_alignments.hlp (del)
  • HELP_SOURCE/oldhelp/seer: login.hlp (del), main_help.hlp (del), select_attributes.hlp (del), select_upload.hlp (del)
  • NTREE: AP_consensus.cxx (+2 -2)
  • PARSIMONY: PARS_main.cxx (+2 -2)
  • PERL_SCRIPTS/lib: ali_dnapro.pm (+1 -1)
  • PROBE: PT_new_design.cxx (+1 -1)
  • SL/PRONUC: AP_codon_table.cxx (+1 -1)
  • SL/PVP: AP_pos_var.cxx (+1 -1)
  • SOURCE_TOOLS: check_resources.pl (+22 -6), diff2grep.pl (+19 -7)
  • TOOLS: arb_consensus_tree.cxx (+1 -1)
  • UNIT_TESTER/run/help: unittest.hlp (+2 -2), unittest.xml (+2 -2)
  • WINDOW: AW_help.cxx (+34 -28)
  • util: arb_srclst.pl (+2 -2)
westram 2021-10-08 16:16 Rev.: 18762


* update documentation:
- reference most important SAI information from main SAI doc.
- add backlinks.

38 lines of code changed in 7 files:

  • HELP_SOURCE/oldhelp: accessibility_sai.hlp (+1), e4_modsai.hlp (+1), extended.hlp (+32 -13), helix.hlp (+1), saiProbe.hlp (+1 -1), saicalc.hlp (+1), visualizeSAI.hlp (+1)
westram 2021-10-08 16:14 Rev.: 18761


* update documentation:
- link between accessibilty SAIs and SAI visualizers.
- shorten help titles (did not differ in first 38 characters (=part which is visible in help SUBTOPICS).
- uncapitalize + correct menu names etc.
- link from SAI visualizers to Probetools and editors.

46 lines of code changed in 5 files:

  • HELP_SOURCE/oldhelp: accessibility_sai.hlp (+1), displayField.hlp (+1 -2), e4.hlp (+1), saiProbe.hlp (+12 -12), visualizeSAI.hlp (+31 -23)
westram 2021-10-08 16:07 Rev.: 18760


* change layout of 'Color Translation Table' properties window (make space for HELP button).
* add help button (fixes #326)
* change documentation of 'Define Color Translations'.

32 lines of code changed in 4 files:

  • AWT: AWT_asciiprint.cxx (-1)
  • HELP_SOURCE/oldhelp: saiProbe.hlp (+6 -5)
  • PROBE_DESIGN: SaiProbeVisualization.cxx (+19 -12)
  • lib/pictures: probeSaiColors.fig (+7 -6)
westram 2021-10-07 19:41 Rev.: 18756


* add {{{DbScanner::remap_item}}}
- callback to remap scanner item.
- remaps selected item using {{{ItemSelector}}} (Note: may fail if non-standard AWAR used for item; e.g used in merge-tool)
- use it as {{{set_popup_callback}}} for window displaying {{{DbScanner}}}
* {{{DbScanner::Map}}} now accepts missing key-path (if scanner is no DB_KEYVIEWER).
* fixes bug in SAI manager:
* fields of selected SAI were not shown when SAI selection changed while SAI manager was closed.
* user needed to change selected SAI to work-around problem

11 lines of code changed in 2 files:

  • SL/DB_SCANNER: db_scanner.cxx (+9 -2), db_scanner.hxx (+2)
westram 2021-10-07 19:28 Rev.: 18755


* add run_popup_callbacks().
- call from {{{AW_window::show()}}}, if window was hidden before.
* repairs {{{set_popup_callback()}}}, which had no effect since [2]

13 lines of code changed in 2 files:

  • WINDOW: AW_window.cxx (+12), aw_window.hxx (+1)
westram 2021-10-07 19:18 Rev.: 18754


* define {{{ItemSelector}}} for SAIs (lacks changekey functionality, i.e. does not fit into a search&query).
* mark places where species-selector is misused for SAIs.

134 lines of code changed in 5 files:

  • MERGE: MG_extendeds.cxx (+2 -2)
  • NTREE: ad_ext.cxx (+1 -1)
  • SL/ITEMS: Makefile (+36), SAIs.cxx (new 93), items.h (+2)
westram 2021-10-06 10:46 Rev.: 18753


* list some useful character classes.
* show usage in double-brackets.
* {{{[:word:]}}} is not known in arb -> removed.

12 lines of code changed in 1 file:

  • HELP_SOURCE/oldhelp: reg.hlp (+12 -2)
westram 2021-10-06 10:43 Rev.: 18752


* eliminate obsolete {{{GBT_read_name}}} from perl interface
- To fix your skript you have to replace {{{BIO::read_name}}} by
* {{{BIO::get_name}}} or
* {{{BIO::get_name_or_description}}} (=1:1 replacement).

2 lines of code changed in 2 files:

  • ARBDB: ad_t_prot.h (+1 -1), aditem.cxx (+1 -1)
westram 2021-10-04 18:23 Rev.: 18751


* also rename overloaded {{{GB_path_in_ARBHOME()}}} -> {{{GB_concat_path_in_ARBHOME()}}}.
- Note: before, simply removing the static modifier did break the perl interface.

11 lines of code changed in 2 files:

  • ARBDB: ad_prot.h (+1 -1), adsocket.cxx (+10 -11)
westram 2021-10-04 17:58 Rev.: 18750


* fix unwanted export of overloaded functions to perl interface:
- GBT_log_to_tree_remark()
- GB_path_in_ARBLIB()

16 lines of code changed in 10 files:

  • ARBDB: ad_prot.h (+1 -1), ad_t_prot.h (+1 -1), adfile.cxx (+1 -1), adsocket.cxx (+7 -4), adtree.cxx (+1 -1)
  • SL/AW_NAME: AW_names_admin.cxx (+1 -1)
  • SL/DB_QUERY: db_query.cxx (+1 -1)
  • TOOLS: arb_write_tree_comment.cxx (+1 -1)
  • WINDOW: AW_button.cxx (+1 -1), AW_xfig.cxx (+1 -1)
westram 2021-10-04 17:54 Rev.: 18749


* bail out when overloaded functions are exported into perl interface.
- fails build with
{{{
Error: ambiguous function definition for 'GBT_log_to_tree_remark' (overloaded method exported to perl?)
Makefile.main:153: recipe for target 'perl-interface-function-list.txt' failed
}}}
- fixed by [18750]

1 lines of code changed in 1 file:

  • PERL2ARB: extract_perl_interface.pl (+1 -1)
westram 2021-10-04 17:51 Rev.: 18748


* explicitely define function prefixes.
* link to interface generator code (and vv).
* bail out on ambiguous function suffix.

19 lines of code changed in 2 files:

  • PERL2ARB: extract_perl_interface.pl (+18 -12)
  • PERLTOOLS: arb_proto_2_xsub.cxx (+1)
westram 2021-10-02 13:13 Rev.: 18747


* gitignore file generated since [18746]

1 lines of code changed in 1 file:

  • PERL2ARB: .gitignore (+1)
westram 2021-10-01 18:07 Rev.: 18746


* adds a script which generates a list of perl interface functions
- call during arb build
* update DOC.txt
- mention that list
- very basic description of interface
- describe the ancient information which already has been in this document.

784 lines of code changed in 5 files:

  • PERL2ARB: DOC.html (del), DOC.txt (new 587), Makefile.main (+7 -2), extract_perl_interface.pl (new 189)
  • util: arb_srclst.pl (+1)
westram 2021-09-22 15:08 Rev.: 18742


* use terminal background color (=default, marked or colorized) also if SAI-translation isnt defined for a position.

10 lines of code changed in 3 files:

  • EDIT4: ED4_text_terminals.cxx (+7 -8)
  • HELP_SOURCE/oldhelp: e4_background_priority.hlp (+1 -1), visualizeSAI.hlp (+2 -2)
westram 2021-09-20 17:30 Rev.: 18741


* warn if all columns mapped in editor.

17 lines of code changed in 1 file:

  • EDIT4: ED4_manager.cxx (+17 -1)
westram 2021-09-20 12:21 Rev.: 18740


* refactored edit4 column remapper:
- result of {{{compile()}}} now indicates whether mapping has changed (previously returned error which never was set).
* {{{mapping_changed}}} now handled in local variable (previously was stored in class member).
- changed several method/variable types (int->bool)

31 lines of code changed in 2 files:

  • EDIT4: ED4_manager.cxx (+22 -28), ed4_class.hxx (+9 -11)
westram 2021-09-17 13:44 Rev.: 18735


* fix another obsolete URL

1 lines of code changed in 1 file:

  • arb_README.txt (+1 -1)

(8716 more)

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