/trunk Developers: westram

Login name:
westram
Total Commits:
40,480 (86.5%)
Lines of Code:
1,163,973 (47.0%)
Most Recent Commit:
2019-07-12 15:38
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Activity in Directories

Directory Changes Lines of Code Lines per Change
Totals 40480 (100.0%) 1163973 (100.0%) 28.7
ARBDB/ 3770 (9.3%) 118975 (10.2%) 31.5
lib/nas/ 29 (0.1%) 66560 (5.7%) 2295.1
GDE/PHYLIP/ 146 (0.4%) 56082 (4.8%) 384.1
WINDOW/ 2563 (6.3%) 55191 (4.7%) 21.5
AWT/ 2171 (5.4%) 48671 (4.2%) 22.4
UNIT_TESTER/run/display/ 184 (0.5%) 46525 (4.0%) 252.8
NTREE/ 2417 (6.0%) 45823 (3.9%) 18.9
EDIT4/ 2299 (5.7%) 42567 (3.7%) 18.5
HELP_SOURCE/oldhelp/ 1815 (4.5%) 35850 (3.1%) 19.7
CONVERTALN/ 456 (1.1%) 29080 (2.5%) 63.7
TOOLS/ 682 (1.7%) 22715 (2.0%) 33.3
GDE/PHYLIP/doc/ 42 (0.1%) 21478 (1.8%) 511.3
GENOM_IMPORT/ 377 (0.9%) 19944 (1.7%) 52.9
PARSIMONY/ 731 (1.8%) 18974 (1.6%) 25.9
PROBE/ 673 (1.7%) 18827 (1.6%) 27.9
UNIT_TESTER/run/ 115 (0.3%) 17835 (1.5%) 155.0
DIST/ 721 (1.8%) 17207 (1.5%) 23.8
GDE/PHYML/ 31 (0.1%) 15188 (1.3%) 489.9
SOURCE_TOOLS/ 743 (1.8%) 15028 (1.3%) 20.2
GENOM/ 865 (2.1%) 14159 (1.2%) 16.3
/ 983 (2.4%) 14098 (1.2%) 14.3
SECEDIT/ 575 (1.4%) 13412 (1.2%) 23.3
GDE/PHYML20130708/phyml/ 9 (0.0%) 13410 (1.2%) 1490.0
MERGE/ 687 (1.7%) 13166 (1.1%) 19.1
SL/FAST_ALIGNER/ 291 (0.7%) 12346 (1.1%) 42.4
lib/ 59 (0.1%) 12300 (1.1%) 208.4
ARB_GDE/ 571 (1.4%) 11644 (1.0%) 20.3
PROBE_DESIGN/ 481 (1.2%) 10540 (0.9%) 21.9
CORE/ 498 (1.2%) 10127 (0.9%) 20.3
SL/TREEDISP/ 473 (1.2%) 10047 (0.9%) 21.2
NALIGNER/ 352 (0.9%) 9219 (0.8%) 26.1
TEMPLATES/ 297 (0.7%) 9184 (0.8%) 30.9
MULTI_PROBE/ 517 (1.3%) 9044 (0.8%) 17.4
UNIT_TESTER/ 496 (1.2%) 8729 (0.7%) 17.5
ptpan/ 124 (0.3%) 8692 (0.7%) 70.0
PROBE_WEB/CLIENT/ 267 (0.7%) 8512 (0.7%) 31.8
AWTI/ 361 (0.9%) 7454 (0.6%) 20.6
GDE/FASTDNAML/ 37 (0.1%) 7391 (0.6%) 199.7
AWTC/ 349 (0.9%) 6988 (0.6%) 20.0
PRIMER_DESIGN/ 281 (0.7%) 6874 (0.6%) 24.4
AISC/ 199 (0.5%) 6857 (0.6%) 34.4
EISPACK/ 16 (0.0%) 6736 (0.6%) 421.0
GDE/RAxML/ 61 (0.2%) 6650 (0.6%) 109.0
lib/pictures/ 302 (0.7%) 6339 (0.5%) 20.9
GDE/AxML/ 17 (0.0%) 6003 (0.5%) 353.1
lib/import/ 211 (0.5%) 5908 (0.5%) 28.0
HELP_SOURCE/ 218 (0.5%) 5664 (0.5%) 25.9
PHYLO/ 397 (1.0%) 4754 (0.4%) 11.9
ALIV3/ 174 (0.4%) 4669 (0.4%) 26.8
CONSENSUS_TREE/ 311 (0.8%) 4411 (0.4%) 14.1
UNIT_TESTER/run/impexp/ 49 (0.1%) 4402 (0.4%) 89.8
PROBE_SERVER/PROBE_GROUP/ 91 (0.2%) 4351 (0.4%) 47.8
PROBE_SET/ 306 (0.8%) 4319 (0.4%) 14.1
AISC_COM/C/ 280 (0.7%) 4058 (0.3%) 14.4
STAT/ 266 (0.7%) 3842 (0.3%) 14.4
ISLAND_HOPPING/ 132 (0.3%) 3810 (0.3%) 28.8
lib/pixmaps/ 302 (0.7%) 3582 (0.3%) 11.8
AISC_MKPTPS/ 108 (0.3%) 3567 (0.3%) 33.0
AISC_COM/AISC/ 108 (0.3%) 3467 (0.3%) 32.1
GDE/CLUSTALW/ 41 (0.1%) 3373 (0.3%) 82.2
RNA3D/ 296 (0.7%) 3354 (0.3%) 11.3
ARBDBPP/ 72 (0.2%) 2998 (0.3%) 41.6
SL/DB_QUERY/ 160 (0.4%) 2935 (0.3%) 18.3
SH/ 158 (0.4%) 2893 (0.2%) 18.3
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 (0.3%) 2531 (0.2%) 24.1
SEQ_QUALITY/ 232 (0.6%) 2516 (0.2%) 10.8
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
SL/AP_TREE/ 147 (0.4%) 2285 (0.2%) 15.5
ALEIO/ 53 (0.1%) 2265 (0.2%) 42.7
PROBE_SERVER/PROBE_GROUP_DESIGN/ 46 (0.1%) 2253 (0.2%) 48.9
SL/PRONUC/ 122 (0.3%) 2217 (0.2%) 18.1
SL/DB_SCANNER/ 126 (0.3%) 2178 (0.2%) 17.2
util/ 205 (0.5%) 2167 (0.2%) 10.5
GL/glAW/ 72 (0.2%) 2108 (0.2%) 29.2
NAMES/ 120 (0.3%) 2062 (0.2%) 17.1
SL/ALILINK/ 30 (0.1%) 2057 (0.2%) 68.5
READSEQ/ 34 (0.1%) 2002 (0.2%) 58.8
lib/pixmaps/unused/ 147 (0.4%) 1993 (0.2%) 13.5
SL/TREE_READ/ 91 (0.2%) 1991 (0.2%) 21.8
lib/pictures/edit4/ 29 (0.1%) 1988 (0.2%) 68.5
SL/AW_NAME/ 167 (0.4%) 1813 (0.2%) 10.8
RNACMA/ 64 (0.2%) 1813 (0.2%) 28.3
PROBE_SERVER/ 85 (0.2%) 1809 (0.2%) 21.2
ORS_CGI/ 55 (0.1%) 1633 (0.1%) 29.6
lib/pictures/consensus/ 11 (0.0%) 1586 (0.1%) 144.1
SL/DB_UI/ 116 (0.3%) 1562 (0.1%) 13.4
GL/glpng/ 35 (0.1%) 1550 (0.1%) 44.2
SL/HELIX/ 90 (0.2%) 1500 (0.1%) 16.6
SL/SEQIO/ 69 (0.2%) 1495 (0.1%) 21.6
UNIT_TESTER/run/consense/2/ 13 (0.0%) 1468 (0.1%) 112.9
PERL2ARB/ 148 (0.4%) 1467 (0.1%) 9.9
PROBE_SERVER/WORKER/ 33 (0.1%) 1432 (0.1%) 43.3
SL/ITEMS/ 109 (0.3%) 1408 (0.1%) 12.9
SL/GUI_ALIVIEW/ 155 (0.4%) 1400 (0.1%) 9.0
SERVERCNTRL/ 125 (0.3%) 1392 (0.1%) 11.1
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/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/ 129 (0.3%) 1098 (0.1%) 8.5
XML/ 70 (0.2%) 1063 (0.1%) 15.1
SL/SEQUENCE/ 135 (0.3%) 990 (0.1%) 7.3
SL/NDS/ 79 (0.2%) 954 (0.1%) 12.0
lib/pictures/awt/ 54 (0.1%) 945 (0.1%) 17.5
TREE_COMPRESS/ 9 (0.0%) 909 (0.1%) 101.0
PROBE_COM/ 96 (0.2%) 901 (0.1%) 9.3
lib/pictures/merge/ 35 (0.1%) 898 (0.1%) 25.6
SL/TREE_WRITE/ 81 (0.2%) 879 (0.1%) 10.8
ARBDBS/ 29 (0.1%) 850 (0.1%) 29.3
UNIT_TESTER/run/consense/1/ 17 (0.0%) 813 (0.1%) 47.8
SL/GROUP_SEARCH/ 19 (0.0%) 782 (0.1%) 41.1
GDE/MOLPHY/doc/ 4 (0.0%) 758 (0.1%) 189.5
SL/LOCATION/ 27 (0.1%) 751 (0.1%) 27.8
PERL_SCRIPTS/ARBTOOLS/ 14 (0.0%) 731 (0.1%) 52.2
TREEGEN/ 123 (0.3%) 701 (0.1%) 5.6
DBSERVER/ 67 (0.2%) 695 (0.1%) 10.3
SL/FILTER/ 68 (0.2%) 692 (0.1%) 10.1
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/ 72 (0.2%) 657 (0.1%) 9.1
lib/pixmaps/edit/ 72 (0.2%) 632 (0.1%) 8.7
UNIT_TESTER/run/pars/ 52 (0.1%) 597 (0.1%) 11.4
PERL_SCRIPTS/SPECIES/ 24 (0.1%) 591 (0.1%) 24.6
UNIT_TESTER/run/help/ 7 (0.0%) 584 (0.1%) 83.4
ORS_SERVER/ 33 (0.1%) 580 (0.0%) 17.5
PROBE_SERVER/TREE_MERGE/ 14 (0.0%) 572 (0.0%) 40.8
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
SOURCE_TOOLS/release/ 15 (0.0%) 507 (0.0%) 33.8
UNIT_TESTER/run/tools/ 43 (0.1%) 499 (0.0%) 11.6
SL/FILE_BUFFER/ 43 (0.1%) 495 (0.0%) 11.5
GDE/SUPPORT/ 26 (0.1%) 494 (0.0%) 19.0
PERL_SCRIPTS/GENOME/ 15 (0.0%) 478 (0.0%) 31.8
SL/REGEXPR/ 47 (0.1%) 473 (0.0%) 10.0
lib/pixmaps/edit/unused/ 48 (0.1%) 469 (0.0%) 9.7
lib/pictures/unused/ 11 (0.0%) 462 (0.0%) 42.0
GDE/RAxML8/ 8 (0.0%) 461 (0.0%) 57.6
NAMES_COM/ 70 (0.2%) 457 (0.0%) 6.5
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/ 70 (0.2%) 400 (0.0%) 5.7
SL/TREE_ADMIN/ 34 (0.1%) 396 (0.0%) 11.6
SL/ARB_TREE/ 81 (0.2%) 396 (0.0%) 4.8
GDEHELP/HELP_PLAIN/ 11 (0.0%) 371 (0.0%) 33.7
bin/ 26 (0.1%) 352 (0.0%) 13.5
SL/ROOTED_TREE/ 17 (0.0%) 350 (0.0%) 20.5
SL/NEIGHBOURJOIN/ 57 (0.1%) 349 (0.0%) 6.1
SL/MATRIX/ 50 (0.1%) 326 (0.0%) 6.5
SL/PTCLEAN/ 37 (0.1%) 319 (0.0%) 8.6
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/pictures/faligner/ 13 (0.0%) 292 (0.0%) 22.4
lib/pictures/query/ 12 (0.0%) 283 (0.0%) 23.5
lib/pixmaps/print/ 20 (0.0%) 281 (0.0%) 14.0
lib/pictures/pars/ 4 (0.0%) 271 (0.0%) 67.7
lib/pictures/awtc/ 14 (0.0%) 270 (0.0%) 19.2
HELP_SOURCE/genhelp/ 23 (0.1%) 267 (0.0%) 11.6
GDE/ 44 (0.1%) 253 (0.0%) 5.7
BUGEX/ 11 (0.0%) 250 (0.0%) 22.7
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/ 39 (0.1%) 210 (0.0%) 5.3
HEADERLIBS/ 11 (0.0%) 210 (0.0%) 19.0
SL/REFENTRIES/ 42 (0.1%) 204 (0.0%) 4.8
GDE/MrBAYES/mrbayes_3.2.1/ 7 (0.0%) 194 (0.0%) 27.7
lib/macros/ 26 (0.1%) 188 (0.0%) 7.2
GDE/CLUSTAL/ 24 (0.1%) 184 (0.0%) 7.6
BINDEP/ 44 (0.1%) 183 (0.0%) 4.1
UNIT_TESTER/valgrind/ 5 (0.0%) 182 (0.0%) 36.4
AISC_COM/ 9 (0.0%) 182 (0.0%) 20.2
SL/TRANSLATE/ 38 (0.1%) 176 (0.0%) 4.6
SL/INSDEL/ 37 (0.1%) 176 (0.0%) 4.7
PERLTOOLS/ 43 (0.1%) 176 (0.0%) 4.0
SL/ITEM_SHADER/ 38 (0.1%) 173 (0.0%) 4.5
PERL_SCRIPTS/SAI/ 5 (0.0%) 163 (0.0%) 32.6
CHIP/ 29 (0.1%) 160 (0.0%) 5.5
WETC/ 53 (0.1%) 157 (0.0%) 2.9
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/sellists/ 28 (0.1%) 139 (0.0%) 4.9
lib/pixmaps/print/unused/ 8 (0.0%) 138 (0.0%) 17.2
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
GDE/TREEPUZZLE/src/ 14 (0.0%) 113 (0.0%) 8.0
lib/dtd/ 8 (0.0%) 111 (0.0%) 13.8
GL/ 14 (0.0%) 110 (0.0%) 7.8
lib/pictures/cpro/ 4 (0.0%) 107 (0.0%) 26.7
AWDEMO/ 18 (0.0%) 107 (0.0%) 5.9
PERL_SCRIPTS/GENERAL/ 1 (0.0%) 99 (0.0%) 99.0
SL/FILTSEQEXP/ 14 (0.0%) 89 (0.0%) 6.3
ARBDB/EXAMPLES/ 19 (0.0%) 89 (0.0%) 4.6
PERL_SCRIPTS/lib/ 2 (0.0%) 80 (0.0%) 40.0
SOURCE_TOOLS/docs/ 1 (0.0%) 79 (0.0%) 79.0
lib/pictures/phylo/ 6 (0.0%) 78 (0.0%) 13.0
GDE/PHYML20130708/ 11 (0.0%) 74 (0.0%) 6.7
lib/BUGS/ 5 (0.0%) 71 (0.0%) 14.2
SL/QUERY/ 14 (0.0%) 71 (0.0%) 5.0
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
SL/ALIVIEW/ 29 (0.1%) 54 (0.0%) 1.8
XML_IMPORT/IMP_TREE/ 27 (0.1%) 53 (0.0%) 1.9
XML_IMPORT/ 10 (0.0%) 47 (0.0%) 4.7
PROBE_WEB/ 4 (0.0%) 46 (0.0%) 11.5
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
GDE/MAFFT/mafft-7.055-with-extensions/core/ 2 (0.0%) 35 (0.0%) 17.5
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/ 2 (0.0%) 32 (0.0%) 16.0
lib/pictures/window/ 2 (0.0%) 30 (0.0%) 15.0
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
SL/PVP/ 5 (0.0%) 14 (0.0%) 2.8
doc/ 2 (0.0%) 11 (0.0%) 5.5
GDE/SATIVA/ 6 (0.0%) 11 (0.0%) 1.8
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
UNIT_TESTER/sockets/ 3 (0.0%) 7 (0.0%) 2.3
GDE/PROBCONS/probcons/ 3 (0.0%) 7 (0.0%) 2.3
lib/pictures/unused/findcorr/ 27 (0.1%) 5 (0.0%) 0.1
BINDINGS/ 5 (0.0%) 5 (0.0%) 1.0
fig2dev/dev/ 62 (0.2%) 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
PERL_SCRIPTS/ARBTOOLS/TESTS/ 1 (0.0%) 3 (0.0%) 3.0
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
PERL_SCRIPTS/MACROS/ 3 (0.0%) 1 (0.0%) 0.3
lib/rna3d/images/ 22 (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/MUSCLE/src/ 3 (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 2019-07-12 15:38 Rev.: 17957


* add GB_countEntries.

17 lines of code changed in 2 files:

  • ARBDB: ad_prot.h (+1), adquery.cxx (+16 -6)
westram 2019-07-12 14:08 Rev.: 17956


* implement GB_copy_overlay
- works like GB_copy_std if destination is empty container.
- completely overwrites existing entries including protection + marks.
- added unittests (overlay onto empty container + onto filled container). both reproduce original database ("TEST_copy.arb").
- adds an assertion vs accidently overwriting temp entries (doing so currently is "undefined behavior").

109 lines of code changed in 3 files:

  • ARBDB: ad_prot.h (+1), arbdb.cxx (+106 -14)
  • UNIT_TESTER/run: TEST_copy_noProtect.arb (+2 -2)
westram 2019-07-08 10:26 Rev.: 17953


* fix number of tabs between key and data (ASCII DB format)
- auto-updated all databases.

3274 lines of code changed in 21 files:

  • ARBDB: ad_save_load.cxx (+3 -2)
  • DBSERVER: db_server.cxx (+1 -1)
  • UNIT_TESTER/run: AB735678_expected.arb (+346 -346), TEST_arbdbserver_save_expected.arb (+78 -78), TEST_copy.arb (+79 -79), TEST_copy_noProtect.arb (+79 -79), TEST_loadsave_ascii.arb (+78 -78), TEST_opti_ascii_in.arb (+1162 -1162), TEST_opti_ascii_renamed_expected.arb (+1162 -1162), TEST_pt_cleaned_expected.arb (+149 -149)
  • UNIT_TESTER/run/pvp: custom.dump.expected (+13 -13), flippedTreeImported.dump.expected (new), gottree.dump.expected (+2 -2), standard.dump.expected (new)
  • UNIT_TESTER/run/tools: dnarates_expected.arb (+15 -15), exseq_ascii.arb.expected (+40 -40), read_tree_out_expected.arb (+41 -41)
westram 2019-07-08 10:21 Rev.: 17952


* add missing auto-update.

12 lines of code changed in 1 file:

  • ARBDB: ad_save_load.cxx (+12 -5)
westram 2019-07-08 10:19 Rev.: 17951


* change priority of tests depending on database {{{"TEST_loadsave_ascii.arb"}}} to get executed after {{{TEST_SLOW_loadsave}}}
- needed if that database should get auto-updated.

4 lines of code changed in 3 files:

  • ARBDB: adoptimize.cxx (+2 -4), arbdb.cxx (+1 -1)
  • TOOLS: arb_test.cxx (+1 -1)
westram 2019-07-08 10:16 Rev.: 17950


* increase {{{BUFSIZE}}} in {{{ARB_textfiles_have_difflines}}}. did overflow with databases used in unittests.

2 lines of code changed in 1 file:

  • CORE: arb_diff.cxx (+2 -2)
westram 2019-07-02 14:45 Rev.: 17944


* FIXES crash in RELEASE version (when invalid color group occurs in database).
* add assertions against
- invalid color_groups and
- invalid unshaded GCs.
* ARBDB color-group interface:
- define number of allowed color groups in ARBDB
- fix interface types (long->int)
- report error when color_group passed to {{{GBT_set_color_group}}} is out-of-range.
- {{{GBT_get_color_group}}} does range check. returns 0 if out-of-range.

119 lines of code changed in 19 files:

  • ARBDB: ad_colorset.cxx (+19 -5), ad_colorset.h (+3 -2)
  • EDIT4: ED4_text_terminals.cxx (-1), Makefile (+56)
  • GENOM: GEN_graphic.cxx (-1), Makefile (+2)
  • MULTI_PROBE: Makefile (+4)
  • NTREE: Makefile (+1), NT_extern.cxx (-1)
  • PARSIMONY: Makefile (+2)
  • RNA3D: Makefile (+2)
  • SECEDIT: Makefile (+6)
  • SL/AP_TREE: AP_TreeShader.hxx (+6 -2)
  • SL/DB_QUERY: db_query.cxx (+3 -4)
  • SL/ITEM_SHADER: Makefile (+6)
  • SL/TREEDISP: Makefile (+4)
  • WINDOW: AW_preset.cxx (-1), Makefile (+1), aw_color_groups.hxx (+4 -1)
westram 2019-07-02 14:36 Rev.: 17943


* fix {{{ColumnStat}}}-ctor (still used memset to init whole object)\\=> fixes sanitizer abort when running arb_parsimony

20 lines of code changed in 3 files:

  • SL/GUI_ALIVIEW: ColumnStat.cxx (+17 -5), ColumnStat.hxx (+2 -2), Makefile (+1)
westram 2019-06-25 13:51 Rev.: 17942


* progress overflow bug (#807):
- improved progress overflow message.
- in case of progress overflow:
* dump progress/counter-cascade (to stderr, i.e. to session log).
* may slow down progress in general a bit (see DUMP_PROGRESS which is now defined in RELEASE version).
- {{{dump()}}} shall not modify object -> become const.

60 lines of code changed in 2 files:

  • CORE: arb_progress.cxx (+55 -18), arb_progress.h (+5 -6)
westram 2019-06-25 13:08 Rev.: 17941


* fix warnings:
- two maybe-uninitialized-warning (one def. bogus).
- conditionally compile code which is only used from unittests.

13 lines of code changed in 4 files:

  • ARBDB: ad_cb.cxx (+4 -2)
  • SL/DB_SCANNER: db_scanner.cxx (+1 -1)
  • SL/FAST_ALIGNER: fast_aligner.cxx (+2 -2)
  • SL/ITEM_SHADER: item_shader.cxx (+6 -1)
westram 2019-06-11 12:08 Rev.: 17909


* refactored {{{KeyOccur}}} into new class {{{StrUniquifier}}} (in CORE).
- really compare strings (not only pointers to keys; did only work by luck).
- document restrictions.
- {{{make_unique_key}}} return pointer to static buffer (valid until next call).
- allow to define string to separate key and counter.
- only change key when duplicated.

80 lines of code changed in 4 files:

  • CORE: StrUniquifier.h (new 67)
  • SL/DB_SCANNER: Makefile (+1), db_scanner.cxx (+10 -27)
  • SOURCE_TOOLS: generate_all_links.sh (+2 -1)
westram 2019-05-27 09:49 Rev.: 17904


* workaround SuSE build problem
- for whatever reasons SuSE delivers a gcc which identifies as 7.4.1 (no such version has been released yet)
* IIRC the same did happen with gcc 5.3.1
- generally ignore subversions (in top level compiler check) for gcc-major>=5

23 lines of code changed in 2 files:

  • Makefile (+6 -1)
  • SOURCE_TOOLS: arb_compiler_version.pl (+17 -1)
westram 2019-05-23 15:49 Rev.: 17901


* replace SEGFAULTs in class {{{containing}}} by assertion failures.

2 lines of code changed in 1 file:

  • UNIT_TESTER: test_unit.h (+2 -1)
westram 2019-05-21 16:01 Rev.: 17899


* refactored GB_check_hkey
- avoids strdup using check_key()
- avoid multiple calls to strlen in former calls to GB_check_key

19 lines of code changed in 1 file:

  • ARBDB: adstring.cxx (+19 -29)
westram 2019-05-21 15:53 Rev.: 17898


* forbid '->' in hierarchical keys.
* use strchr in GB_check_hkey.
* refactor GB_check_key.
* pull-out check_key() from GB_check_key()
- allows to test only a part of char-sequence -> will allow to avoid strdup in GB_check_hkey
- simplify using isalnum.

39 lines of code changed in 2 files:

  • ARBDB: adquery.cxx (+6 -9), adstring.cxx (+33 -37)
westram 2019-05-21 15:36 Rev.: 17897


* annotate
- TEST_IN_HKEYS_USING_EXPECT_NO_ERROR and
- TEST_IN_HKEYS_USING_EXPECT_ERROR_CONTAINS.

11 lines of code changed in 1 file:

  • ARBDB: adstring.cxx (+11 -5)
westram 2019-05-21 15:34 Rev.: 17896


* document behavior of GB_check_key + GB_check_hkey including
- behavior that is accepted (but obsolete) by GB_check_hkey,
- behavior of NULp keys.
- behavior in some edge cases of GB_check_hkey.

44 lines of code changed in 2 files:

  • ARBDB: adquery.cxx (+8), adstring.cxx (+36 -7)
westram 2019-05-14 13:59 Rev.: 17890


* reintegrates 'dbui' into 'trunk'
* adds: log:branches/dbui@17881:17889

134 lines of code changed in 7 files:

  • ARBDB: arbdb.cxx (+4 -2)
  • GENOM: EXP_interface.cxx (+1 -1), GEN_interface.cxx (+1 -1)
  • SL/DB_SCANNER: db_scanner.cxx (+108 -90), db_scanner.hxx (+15 -4)
  • SL/DB_UI: ui_species.cxx (+1 -1)
  • WINDOW: aw_select.hxx (+4 -4)
westram 2019-05-10 13:57 Rev.: 17877


* reintegrates 'gcc' into 'trunk'
* adds: log:branches/gcc@17850:17876

409 lines of code changed in 56 files:

  • Makefile (+40 -9)
  • AISC: aisc_parser.h (+32 -20)
  • ARBDB: TreeNode.h (+6 -4), adcompr.cxx (+1 -1), adlang1.cxx (+1 -1), adseqcompr.cxx (+1 -1), adstring.cxx (+1 -1), arbdb.cxx (+1 -1)
  • AWT: AWT_input_mask.cxx (+15 -1)
  • CONVERTALN: genbank.cxx (+1 -1), reader.h (+12 -1), seq.h (+1 -1)
  • CORE: BufferedFileReader.h (+3 -1), arb_progress.h (+6 -6), arb_strarray.cxx (+2 -2), arb_strarray.h (+1), pos_range.h (+5)
  • DIST: DI_protdist.cxx (+1 -1)
  • EDIT4: ED4_flags.cxx (+1 -1), ED4_protein_2nd_structure.cxx (+8 -5), ED4_seq_colors.cxx (+1 -1), ed4_class.hxx (+40 -39)
  • GENOM: GEN_interface.cxx (+1 -1), GEN_nds.cxx (+1 -1)
  • GENOM_IMPORT: SequenceBuffer.cxx (+2 -2)
  • MERGE: MG_checkfield.cxx (+1 -1)
  • MULTI_PROBE: MP_noclass.cxx (+1 -1), MP_probe.cxx (+3 -2), MP_sonde.cxx (+1 -1)
  • NTREE: ad_spec.cxx (+2 -2)
  • PARSIMONY: PARS_main.cxx (+1 -1)
  • PROBE: PT_family.cxx (+7 -8), PT_match.cxx (+1 -1)
  • RNACMA: Makefile (+2 -2)
  • SECEDIT: SEC_paint.cxx (+3 -3)
  • SL/AP_TREE: AP_Tree.cxx (+1 -1), AP_Tree.hxx (+9 -7)
  • SL/ARB_TREE: ARB_Tree.hxx (+13 -3)
  • SL/FAST_ALIGNER: ClustalV.cxx (+2 -2)
  • SL/FILTER: AP_filter.cxx (+1 -1)
  • SL/HELIX: BI_basepos.hxx (+1 -1)
  • SL/NEIGHBOURJOIN: NJ.cxx (+1 -1)
  • SL/TREEDISP: GroupIterator.hxx (+17 -15), TreeDisplay.hxx (+2 -1)
  • SOURCE_TOOLS: postcompile.pl (+38 -12), remake_after_change.pl (+1 -1), vectorize.README (+3 -4), vectorized.source (+14)
  • TEMPLATES: cxxforward.h (+56 -8)
  • TOOLS: arb_dnarates.cxx (+25 -25), arb_primer.cxx (+3 -3)
  • UNIT_TESTER: test_unit.h (+3 -3)
  • WINDOW: aw_device.hxx (+4 -4), aw_font_group.hxx (+1 -1), aw_position.hxx (+1), aw_window.hxx (+7 -6)
westram 2019-05-02 15:58 Rev.: 17841


* expect no error has been exported in {{{GB_create}}} + {{{GB_create_container}}}.

5 lines of code changed in 2 files:

  • ARBDB: arbdb.cxx (+4)
  • WINDOW: AW_option_toggle.cxx (+1 -1)

(8496 more)

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