[root]/TOOLS
Author | Changes | Lines of Code | Lines per Change |
---|---|---|---|
Totals | 792 (100.0%) | 30678 (100.0%) | 38.7 |
westram | 735 (92.8%) | 23559 (76.8%) | 32.0 |
oldcode | 20 (2.5%) | 5941 (19.4%) | 297.0 |
richter | 3 (0.4%) | 425 (1.4%) | 141.6 |
jobb | 3 (0.4%) | 397 (1.3%) | 132.3 |
meierh | 3 (0.4%) | 296 (1.0%) | 98.6 |
epruesse | 19 (2.4%) | 37 (0.1%) | 1.9 |
boehnel | 2 (0.3%) | 14 (0.0%) | 7.0 |
baderk | 6 (0.8%) | 9 (0.0%) | 1.5 |
artemov | 1 (0.1%) | 0 (0.0%) | 0.0 |
* introduce {{{onlyC_flags}}}
- flags used for C compilation only.
- similar to {{{cxxflags}}} (references added).
- pass down onlyC_flags into AxML, CLUSTAL, CLUSTALW, FASTDNAML, FASTTREE, GL, MrBAYES, PHYLIP, PHYML*, RAxML, SINA(unused), SOURCE_TOOLS, SUPPORT, TOOLS, TREEGEN + TREEPUZZLE.
- set flags to {{{-Werror-implicit-function-declaration}}}
* error is only effective in a small part of these modules.
* TODO: need to activate warnings -> will activate the error as well.
1 lines of code changed in 1 file:
* reactivate implicit-fallthrough warnings and fix code.
3 lines of code changed in 2 files:
* {{{GBT_get_alignment_len}}}
- now also reports error if alignment length is zero
* this case often was unhandled and did easily lead to allocation problems.
- catch error in case of zero alignment length => fixes alloc-size-larger-than-warning (in {{{NT_count_different_chars}}}).
- check + fix callers.
16 lines of code changed in 3 files:
* string splitters:
- unittests for {{{GBT_split_string}}}:
* add tests for dropEmptyTokens.
* document special behavior for empty string.
- define enum {{{SplitMode}}}. use enum instead of bool param for GBT_splitNdestroy_string + GBT_split_string.
1 lines of code changed in 1 file:
* 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
16 lines of code changed in 2 files:
* reintegrates 'refactor' into 'trunk'
- refactored MULTI_PROBE to support unittest.
* adds: log:branches/refactor@19286:19296
6 lines of code changed in 1 file:
* reintegrates 'ali' into 'trunk'
* adds: log:branches/ali@19183:19205
233 lines of code changed in 5 files:
* export/use {{{ARB_CORE_LIBS}}} (instead of using {{{ARB_GLIB_LIBS}}} directly).
1 lines of code changed in 1 file:
* reintegrates 'progress' into 'trunk'
- implements #789
* adds: log:branches/progress@18885:18958
18 lines of code changed in 1 file:
* reintegrates 'nds' into 'trunk'
- fixes #841
* adds: log:branches/nds@18843:18882
28 lines of code changed in 2 files:
* reintegrates 'help' into 'trunk'
- relocate help sources
* adds: log:branches/help@18763:18780
1 lines of code changed in 1 file:
* fix unwanted export of overloaded functions to perl interface:
- GBT_log_to_tree_remark()
- GB_path_in_ARBLIB()
1 lines of code changed in 1 file:
* remove trailing whitespace from c source.
4 lines of code changed in 2 files:
* eliminate trailing whitespace from Makefiles.
1 lines of code changed in 1 file:
* reintegrates 'tree' into 'trunk'
* adds: log:branches/tree@18666:18703
36 lines of code changed in 3 files:
* full update from child 'stable' into 'trunk'
- merge changes done to arb-7.0 release candidate
* adds: log:branches/stable@18690:18695
1 lines of code changed in 1 file:
* change many WARN_TODO triggered warnings into todo markers.
1 lines of code changed in 1 file:
* reintegrates 'root' into 'trunk'
- implements #449
* adds: log:branches/root@18451:18633
2 lines of code changed in 2 files:
* arb_export_newick
- stuff two leaks
- todo
14 lines of code changed in 1 file:
* reintegrates 'io' into 'trunk'
* adds: log:branches/io@18428:18436
318 lines of code changed in 3 files:
* reintegrates 'saicalc' into 'trunk'
- implements #730
* adds: log:branches/saicalc@18141:18310
2 lines of code changed in 1 file:
* fix compiler warnings.
* do not use 'error' in error messages (to avoid duplicate 'error' term).
* fix use of GB_end_transaction (has to be called unconditionally for each started TA).
* remove TA around GB_save (refused since [18282])
10 lines of code changed in 1 file:
* arb_2_bin may now optimize database using an external tree. thx to Jan for the patch :)
50 lines of code changed in 2 files:
* typo in documentation
* improve CLI help for arb_probe_match
5 lines of code changed in 1 file:
* fixes to error handling:
- {{{aisc_open}}} may return neighter link nor error (was not handled)
- always showed {{{locs_error}}} - even if empty (=no error)
- prefix main connection error with toolname
12 lines of code changed in 1 file:
* cleanup arb_probe_match:
- remove help for parameter {{{--db}}} (was removed with r13186)
- remove some coders editor preferences from code.
0 lines of code changed in 1 file:
* full update from child 'fix' into 'trunk'
- fix item name accessors ({{{GBT_get_name}}} + {{{GBT_get_name_or_description}}})
- add {{{null2empty}}}
* adds: log:branches/fix@18140:18158
12 lines of code changed in 1 file:
* full update from child 'fix' into 'trunk'
- improve target 'cleanRelinkable'
- fix crash in inotify file tracker (occurred when moving a tracked file)
- minor tweaks for fts
* adds: log:branches/fix@18131:18139
1 lines of code changed in 1 file:
* full update from child 'fts' into 'trunk'
- implements #562
* adds:
- [18091/branches/fts]
- log:branches/gui@17754:17924,17926:18090
7 lines of code changed in 2 files:
* rename CLI params:
- complement -> complementFirst
- reversed -> alsoRevCompl
- matchcomplement -> matchAlsoRevcomp
* improve CLI help: mention precedence and interaction between complementFirst + alsoRevCompl.
13 lines of code changed in 2 files:
* rename client variables:
- match_kompl -> match_also_revcompl
- COMPLEMENT -> ALSO_REVCOMPL
- reversed -> alsoRevCompl
- complement -> alsoRevcompl (probe_design)
- complement -> complementFirst (arb_probe_match)
* rename AWAR: AWAR_PD_MATCH_COMPLEMENT -> AWAR_PD_MATCH_ALSO_REVCOMP
* fix doc.
21 lines of code changed in 2 files:
* rename ptserver flags
- MATCH_COMPLEMENT -> COMPLEMENT_FIRST
- MATCH_REVERSED -> MATCH_ALSO_REVCOMP
* comments and TODOs.
8 lines of code changed in 2 files:
* use security objects instead of manually calling GB_push/pop_my_security.
* eliminate GB_push/pop_my_security.
* fix scoping using a TA object.
1 lines of code changed in 1 file:
* 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.
1 lines of code changed in 1 file:
* reintegrates 'gcc' into 'trunk'
* adds: log:branches/gcc@17850:17876
28 lines of code changed in 2 files:
* reintegrates 'clone' into 'trunk'
* adds: log:branches/clone@17813:17835
2 lines of code changed in 2 files:
* fix test condition "contains":
- checking for empty part
* always returned 'true'
* now fails assertion and returns 'false' (it is unwanted to test that)
- fix callers
6 lines of code changed in 1 file:
* reintegrates 'svalues' into 'trunk'
- implements #614
* adds: log:branches/svalues@17357:17419,17428:17464,17469,17471:17477
2 lines of code changed in 2 files:
* partial merge from 'svalues' into 'trunk'
- root branches always need to have identical remarks (associated with the root-edge)
* condition previously implicit, now hardened by tests/assertions/...
* fixed several bugs that violated this condition
* adds: log:branches/svalues@17420:17427
10 lines of code changed in 1 file:
* reintegrates 'fix' into 'trunk'
- elim dead code
- use const hash loop
* adds: log:branches/fix@17380,17388:17395
13 lines of code changed in 2 files:
(379 more)