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westram 2021-12-20 17:44 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 08:33 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 16:58 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 12:52 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 12:48 Rev.: 18729

* eliminate trailing whitespace from Makefiles.

1 lines of code changed in 1 file:

• TOOLS: Makefile (+1 -1)

westram 2021-09-07 09:37 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 08:46 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 14:15 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 16:24 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 11:15 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 14:18 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 13:07 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 16:34 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 16:30 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 15:19 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 14:51 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 16:26 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 16:51 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 09:08 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 14:46 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 16:34 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 16:32 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 16:24 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 15:22 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 09:19 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 12:57 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 13:44 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 17:15 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 10:00 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 15:08 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 17:43 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)

westram 2018-07-10 15:48 Rev.: 17178

* reintegrates 'gcc' into 'trunk'
- complete arb port to gcc 8.1
- fixes NDEBUG-related issues (not handled by [16986])
* adds: log:branches/gcc@17164:17177

10 lines of code changed in 1 file:

• TOOLS: arb_primer.cxx (+10 -3)

westram 2018-06-25 16:04 Rev.: 17121

* reintegrates 'saiexport' into 'trunk'
- no longer expand dangerous ranges (e.g. {{{--pass allbut .-=012345}}})
* adds: log:branches/saiexport@17112:17120

36 lines of code changed in 2 files:

• TOOLS: arb_export_seq_filtered.cxx (+3 -1), arb_test.cxx (+33 -18)

westram 2018-06-15 12:08 Rev.: 17110

* reintegrates 'tree' into 'trunk'
- implements #735
* adds:
- log:branches/addtest@17040:17044
- log:branches/tree@16921:17109

4 lines of code changed in 2 files:

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

westram 2018-05-19 09:30 Rev.: 17050

* fix builds w/o unit tests (e.g. RELEASE)
- was broken by [16919]
- complained about dependency file for "unknown" binary {{{arb_sub2ascii}}} (only build for UNIT_TESTS)
* dependencies in TOOLS change with variable UNIT_TESTS (force to 1 for 'depends')

1 lines of code changed in 1 file:

• TOOLS: Makefile (+1 -1)

westram 2018-05-04 17:06 Rev.: 16986

* reintegrates 'gcc' into 'trunk'
- ports arb to gcc 8.1 (fixing warnings)
* adds: log:branches/gcc@16965:16985

Update: continued by [17178]

1 lines of code changed in 1 file:

• TOOLS: arb_probe.cxx (+1 -1)

westram 2018-04-25 10:08 Rev.: 16919

* reintegrates 'pvp' into 'trunk'
- adds {{{arb_calc_pvp}}} (CLI tool to calculate posvar)
* adds: log:branches/pvp@16906:16918

369 lines of code changed in 4 files:

• TOOLS: Makefile (+55), arb_calc_pvp.cxx (new 188), arb_sub2ascii.cxx (new 79), arb_test.cxx (+47 -1)

westram 2017-12-04 11:18 Rev.: 16782

* typo

1 lines of code changed in 1 file:

• TOOLS: arb_2_ascii.cxx (+1 -1)

westram 2017-11-28 18:22 Rev.: 16766

* reintegrates 'gcc' into 'trunk'
- mostly cosmetics changes
* adds: log:branches/gcc@16655,16741:16743,16752:16765

32 lines of code changed in 9 files:

• TOOLS: arb_a2ps.c (+6 -8), arb_dnarates.cxx (+14 -14), arb_export_sequences.cxx (+1 -2), arb_gene_probe.cxx (+3 -6), arb_perf_test.cxx (+1 -2), arb_primer.cxx (+4 -8), arb_probe.cxx (+1 -2), arb_read_tree.cxx (+1 -2), arb_write_tree_comment.cxx (+1 -2)

westram 2017-11-28 17:09 Rev.: 16763

* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751

254 lines of code changed in 18 files:

• TOOLS: arb_2_ascii.cxx (+3 -3), arb_2_bin.cxx (+4 -4), arb_a2ps.c (+25 -25), arb_consensus_tree.cxx (+19 -19), arb_dnarates.cxx (+28 -28), arb_export_rates.cxx (+6 -6), arb_export_seq_filtered.cxx (+7 -7), arb_export_sequences.cxx (+16 -15), arb_export_tree.cxx (+3 -3), arb_gene_probe.cxx (+11 -11), arb_message.cxx (+2 -2), arb_perf_test.cxx (+7 -7), arb_primer.cxx (+12 -12), arb_probe.cxx (+61 -61), arb_probe_match.cxx (+21 -17), arb_read_tree.cxx (+12 -12), arb_test.cxx (+11 -11), arb_write_tree_comment.cxx (+6 -6)

(370 more)