Directory TOOLS/

Lines of Code

Developers

Most Recent Commits

westram 2023-08-05 13:40 Rev.: 19446

* 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:

• TOOLS: Makefile (+1 -1)

westram 2023-08-05 13:24 Rev.: 19442

* reactivate implicit-fallthrough warnings and fix code.

3 lines of code changed in 2 files:

• TOOLS: Makefile (+1 -7), arb_a2ps.c (+2)

westram 2023-07-11 12:38 Rev.: 19432

* {{{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:

• TOOLS: arb_dnarates.cxx (+1 -1), arb_export_seq_filtered.cxx (+2 -2), arb_export_sequences.cxx (+13 -7)

westram 2023-05-31 09:21 Rev.: 19365

* 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:

• TOOLS: arb_probe.cxx (+1 -1)

westram 2022-11-13 16:47 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

16 lines of code changed in 2 files:

• TOOLS: arb_probe.cxx (+6 -6), arb_replace.cxx (+10 -11)

westram 2022-11-06 17:09 Rev.: 19297

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

6 lines of code changed in 1 file:

• TOOLS: arb_probe.cxx (+6 -15)

westram 2022-08-03 15:52 Rev.: 19206

* reintegrates 'ali' into 'trunk'
* adds: log:branches/ali@19183:19205

233 lines of code changed in 5 files:

• TOOLS: arb_2_bin.cxx (+10 -6), arb_dnarates.cxx (+67 -62), arb_export_rates.cxx (+118 -110), arb_export_seq_filtered.cxx (+1), arb_export_sequences.cxx (+37 -26)

westram 2022-04-06 14:29 Rev.: 18981

* export/use {{{ARB_CORE_LIBS}}} (instead of using {{{ARB_GLIB_LIBS}}} directly).

1 lines of code changed in 1 file:

• TOOLS: Makefile (+1 -1)

westram 2022-03-04 12:26 Rev.: 18959

* reintegrates 'progress' into 'trunk'
- implements #789
* adds: log:branches/progress@18885:18958

18 lines of code changed in 1 file:

• TOOLS: Makefile (+18)

westram 2021-12-20 18:44 Rev.: 18883

* reintegrates 'nds' into 'trunk'
- fixes #841
* adds: log:branches/nds@18843:18882

28 lines of code changed in 2 files:

• TOOLS: arb_consensus_tree.cxx (+3 -3), arb_export_newick.cxx (+25 -21)

westram 2021-10-10 09:33 Rev.: 18781

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

1 lines of code changed in 1 file:

• TOOLS: arb_consensus_tree.cxx (+1 -1)

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()

1 lines of code changed in 1 file:

• TOOLS: arb_write_tree_comment.cxx (+1 -1)

westram 2021-09-15 13:52 Rev.: 18730

* remove trailing whitespace from c source.

4 lines of code changed in 2 files:

• TOOLS: arb_export_tree.cxx (+2 -2), arb_read_tree.cxx (+2 -2)

westram 2021-09-15 13:48 Rev.: 18729

* eliminate trailing whitespace from Makefiles.

1 lines of code changed in 1 file:

• TOOLS: Makefile (+1 -1)

westram 2021-09-07 10:37 Rev.: 18704

* reintegrates 'tree' into 'trunk'
* adds: log:branches/tree@18666:18703

36 lines of code changed in 3 files:

• TOOLS: Makefile (+3), arb_consensus_tree.cxx (+14 -5), arb_export_newick.cxx (+19 -20)

westram 2021-09-02 09:46 Rev.: 18697

* 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:

• TOOLS: arb_gene_probe.cxx (+1 -1)

westram 2021-08-17 15:15 Rev.: 18665

* change many WARN_TODO triggered warnings into todo markers.

1 lines of code changed in 1 file:

• TOOLS: arb_gene_probe.cxx (+1 -1)

westram 2020-11-10 17:24 Rev.: 18634

* reintegrates 'root' into 'trunk'
- implements #449
* adds: log:branches/root@18451:18633

2 lines of code changed in 2 files:

• TOOLS: Makefile (+1), arb_consensus_tree.cxx (+1 -1)

westram 2020-05-27 12:15 Rev.: 18465

* arb_export_newick
- stuff two leaks
- todo

14 lines of code changed in 1 file:

• TOOLS: arb_export_newick.cxx (+14 -11)

westram 2020-04-06 15:18 Rev.: 18437

* reintegrates 'io' into 'trunk'
* adds: log:branches/io@18428:18436

318 lines of code changed in 3 files:

• TOOLS: Makefile (+33), arb_export_newick.cxx (new 235), arb_test.cxx (+50 -4)

westram 2020-02-21 14:07 Rev.: 18311

* reintegrates 'saicalc' into 'trunk'
- implements #730
* adds: log:branches/saicalc@18141:18310

2 lines of code changed in 1 file:

• TOOLS: arb_export_rates.cxx (+2 -2)

westram 2020-02-10 17:34 Rev.: 18284

* 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:

• TOOLS: arb_2_bin.cxx (+10 -14)

westram 2020-02-10 17:30 Rev.: 18283

* 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:

• TOOLS: Makefile (+5), arb_2_bin.cxx (+45 -5)

westram 2019-11-25 16:19 Rev.: 18222

* typo in documentation
* improve CLI help for arb_probe_match

5 lines of code changed in 1 file:

• TOOLS: arb_probe_match.cxx (+5 -4)

westram 2019-11-25 15:51 Rev.: 18221

* 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:

• TOOLS: arb_probe_match.cxx (+12 -8)

westram 2019-11-21 17:26 Rev.: 18216

* 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:

• TOOLS: arb_probe_match.cxx (-11)

westram 2019-10-08 17:51 Rev.: 18159

* 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:

• TOOLS: arb_gene_probe.cxx (+12 -7)

westram 2019-10-03 10:08 Rev.: 18140

* 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:

• TOOLS: arb_export_sequences.cxx (+1 -1)

westram 2019-09-17 15:46 Rev.: 18092

* 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:

• TOOLS: Makefile (+1 -1), arb_export_sequences.cxx (+6 -4)

westram 2019-07-24 17:34 Rev.: 17991

* 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:

• TOOLS: arb_probe.cxx (+6 -6), arb_probe_match.cxx (+7 -4)

westram 2019-07-24 17:32 Rev.: 17990

* 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:

• TOOLS: arb_probe.cxx (+8 -8), arb_probe_match.cxx (+13 -13)

westram 2019-07-24 17:24 Rev.: 17988

* rename ptserver flags
- MATCH_COMPLEMENT -> COMPLEMENT_FIRST
- MATCH_REVERSED -> MATCH_ALSO_REVCOMP
* comments and TODOs.

8 lines of code changed in 2 files:

• TOOLS: arb_probe.cxx (+3 -3), arb_probe_match.cxx (+5 -5)

westram 2019-07-17 16:22 Rev.: 17980

* 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:

• TOOLS: arb_gene_probe.cxx (+1 -2)

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.

1 lines of code changed in 1 file:

• TOOLS: arb_test.cxx (+1 -1)

westram 2019-05-10 13:57 Rev.: 17877

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

28 lines of code changed in 2 files:

• TOOLS: arb_dnarates.cxx (+25 -25), arb_primer.cxx (+3 -3)

westram 2019-04-29 14:44 Rev.: 17836

* reintegrates 'clone' into 'trunk'
* adds: log:branches/clone@17813:17835

2 lines of code changed in 2 files:

• TOOLS: arb_export_sequences.cxx (+1 -1), arb_sub2ascii.cxx (+1 -1)

westram 2019-04-02 18:15 Rev.: 17729

* 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:

• TOOLS: arb_consensus_tree.cxx (+6 -6)

westram 2018-10-17 11:00 Rev.: 17478

* 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:

• TOOLS: arb_consensus_tree.cxx (+1 -1), arb_read_tree.cxx (+1)

westram 2018-10-02 16:08 Rev.: 17428

* 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:

• TOOLS: arb_read_tree.cxx (+10 -7)

westram 2018-09-20 18:43 Rev.: 17396

* 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:

• TOOLS: arb_primer.cxx (+12 -13), arb_probe_match.cxx (+1 -1)

(379 more)