Directory ARBDB/

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westram 2022-06-29 14:54 Rev.: 19100

* reintegrates 'split' into 'trunk'
- implemented beta version of alignment splitter
* adds: log:branches/split@19077:19099

3 lines of code changed in 2 files:

• ARBDB: ad_t_prot.h (+1 -1), adali.cxx (+2 -2)

westram 2022-06-20 12:40 Rev.: 19069

* fix vectorize-checks for gcc 5.4

2 lines of code changed in 2 files:

• ARBDB: adcompr.cxx (+1 -1), adoptimize.cxx (+1 -1)

westram 2022-06-20 12:18 Rev.: 19067

* fix vectorize-checks for gcc 5.5

2 lines of code changed in 2 files:

• ARBDB: adcompr.cxx (+1 -1), adoptimize.cxx (+1 -1)

westram 2022-06-20 12:17 Rev.: 19066

* fix vectorize-checks for gcc 7.x-series

1 lines of code changed in 1 file:

• ARBDB: adoptimize.cxx (+1 -1)

westram 2022-06-20 12:15 Rev.: 19065

* fix vectorize-checks for gcc 8.x-series

4 lines of code changed in 2 files:

• ARBDB: adoptimize.cxx (+1 -1), adseqcompr.cxx (+3 -3)

westram 2022-06-20 12:14 Rev.: 19064

* fix vectorize-checks for gcc 9.x-series

5 lines of code changed in 3 files:

• ARBDB: adcompr.cxx (+1 -1), adoptimize.cxx (+1 -1), adseqcompr.cxx (+3 -3)

westram 2022-06-20 12:12 Rev.: 19063

* fixed LOOP_VECTORIZED expressions that used '*'-count (for gcc 10.x-series).

6 lines of code changed in 3 files:

• ARBDB: adcompr.cxx (+1 -1), adoptimize.cxx (+2 -2), adseqcompr.cxx (+3 -3)

westram 2022-03-23 11:25 Rev.: 18971

* include {{{rpc/types.h}}} under OSX only (fixes compilation under SuSE Leap 15.3).

Notes:
* originally introduced with [14000]
* merged to trunk with [14007]

7 lines of code changed in 1 file:

• ARBDB: arbdb.cxx (+7 -1)

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

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

35 lines of code changed in 1 file:

• ARBDB: Makefile (+35)

westram 2022-03-01 15:38 Rev.: 18939

* add {{{GB_test_delete_possible}}}:
- tests TA + returns security error.
- use it in {{{GB_delete}}} + {{{GB_set_temporary}}}.
* test user has security to delete tree **before** copying the tree (which may take some time).

43 lines of code changed in 4 files:

• ARBDB: ad_prot.h (+1), ad_save_load.cxx (+1 -1), adtree.cxx (+10 -2), arbdb.cxx (+31 -29)

westram 2022-02-28 14:53 Rev.: 18936

* when called with flag==3 now count marked species in
- GBT_mark_all+GBT_mark_all_that
- mark_species_in_tree+mark_species_in_tree_that
* add count feature to all mark menus + submenus
- generate reports for different set of counted species.
- show top-area hint only once per arb session.

25 lines of code changed in 2 files:

• ARBDB: ad_t_prot.h (+2 -2), aditem.cxx (+23 -4)

westram 2022-01-29 15:33 Rev.: 18907

* partial merge from 'stable' into 'trunk'
* adds: log:branches/stable@18903:18906

2 lines of code changed in 2 files:

• ARBDB: ad_prot.h (+1 -1), arbdb.cxx (+1 -1)

westram 2021-12-15 20:11 Rev.: 18851

* add deadlock warning to callback loop in commit_transaction.

10 lines of code changed in 1 file:

• ARBDB: arbdb.cxx (+10 -1)

westram 2021-10-30 19:03 Rev.: 18821

* ignore SIGPIPE while ArbDBWriter exists
- arb does no longer terminate, but instead prints error, when pipe breaks, e.g.:
{{{
19:01.38 While writing '/home/user/data/test with space.arb~': Broken pipe
(close reports: pipe writing to
file='/home/user/data/test with space.arb~'
using cmd='xz > /home/user/data/test with space.arb~'
failed with exitcode=1 (broken pipe? corrupted archive?)
(res=256, exited=1, signaled=0, status=1))
}}}

11 lines of code changed in 2 files:

• ARBDB: Makefile (+1), ad_save_load.cxx (+10 -1)

westram 2021-10-30 17:19 Rev.: 18820

* avoid crash while saving arb database (see #840)
- mark loc where SIGPIPE occurred.
- report an error when compression is enabled and filename contains unwanted characters.

3 lines of code changed in 1 file:

• ARBDB: ad_save_load.cxx (+3 -3)

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

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

13 lines of code changed in 2 files:

• ARBDB: adsocket.cxx (+12 -12), gb_aci.cxx (+1 -1)

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()

11 lines of code changed in 5 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)

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

* remove trailing whitespace from c source.

96 lines of code changed in 23 files:

• ARBDB: ad_cb.cxx (+1 -1), ad_config.cxx (+1 -1), ad_core.cxx (+3 -3), ad_io_inline.h (+1 -1), ad_load.cxx (+13 -13), ad_save_load.cxx (+5 -5), adcache.cxx (+4 -4), adcomm.cxx (+2 -2), adindex.cxx (+21 -21), adlang1.cxx (+1 -1), admalloc.cxx (+6 -6), admap.cxx (+2 -2), adseqcompr.cxx (+6 -6), adsocket.cxx (+4 -4), adtcp.cxx (+3 -3), adtools.cxx (+2 -2), adtree.cxx (+11 -11), arbdb.cxx (+2 -2), arbdbt.h (+2 -2), gb_aci.cxx (+3 -3), gb_local.h (+1 -1), gb_localdata.h (+1 -1), gb_main.h (+1 -1)

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

* change many WARN_TODO triggered warnings into todo markers.

13 lines of code changed in 9 files:

• ARBDB: adChangeKey.cxx (+2 -3), ad_core.cxx (+1 -4), adali.cxx (+1 -3), adindex.cxx (-1), admalloc.cxx (+2 -3), adname.cxx (+2 -4), arbdb.cxx (+3 -8), arbdbpp.cxx (+1 -3), gb_aci_impl.h (+1 -3)

westram 2021-06-15 10:22 Rev.: 18657

* fix crash when previewing printout on OSX (thx to jan)

14 lines of code changed in 1 file:

• ARBDB: adsocket.cxx (+14 -14)

westram 2021-05-31 12:59 Rev.: 18654

* postscript/pdf viewers:
- use {{{open -W}}} under osx (thanks to Jan Gerken).
- add {{{xreader}}} as primary default viewer under Linux.

34 lines of code changed in 1 file:

• ARBDB: adsocket.cxx (+34 -2)

westram 2021-05-31 12:16 Rev.: 18653

* fail if not all possible objects were added to Makefile.
* remove object section GB_PP. add objects to GB_X.

21 lines of code changed in 1 file:

• ARBDB: Makefile (+21 -13)

westram 2021-05-08 15:17 Rev.: 18646

* split TEST_GB_command_interpreter...() into smaller parts.

27 lines of code changed in 1 file:

• ARBDB: gb_aci.cxx (+27 -3)

westram 2021-05-05 14:46 Rev.: 18644

* fixes 2 failing unittest under ubuntu 20.04
- /bin and /sbin are symbolic links there -> use /usr instead

1 lines of code changed in 1 file:

• ARBDB: adsocket.cxx (+1 -1)

westram 2021-02-18 17:33 Rev.: 18643

* allow to 'edit bootstraps'
- document example.
- when a replacement results in an empty string => remove remark.

28 lines of code changed in 2 files:

• ARBDB: TreeNode.cxx (+27), TreeNode.h (+1)

westram 2021-02-18 17:30 Rev.: 18642

* tweak replacement via regular expressions:
- allow replacement of whole line regexpr which matches empty source string.
- test to replace whole string by nothing.
- always fail BOL/EOL operator starting from second replace-operation. fixes some failing replacements.
* doc: describe other simpler, now working replacements.

10 lines of code changed in 1 file:

• ARBDB: gb_aci.cxx (+10 -1)

westram 2020-10-05 16:27 Rev.: 18601

* clear error exported from {{{gbt_nonexisting_alignment}}}
- made case-only rename fail in DEBUG mode.

6 lines of code changed in 1 file:

• ARBDB: adali.cxx (+6)

westram 2020-10-05 16:24 Rev.: 18599

* fix parameters of {{{GBT_rename_alignment}}} + {{{gbt_rename_alignment_of_item}}}
- rename.
- change to bool.
- callers use bool.

13 lines of code changed in 2 files:

• ARBDB: ad_t_prot.h (+1 -1), adali.cxx (+12 -12)

westram 2020-10-05 16:21 Rev.: 18598

* detect attempt to ''copy'' to alignment which differs from source only in case.

13 lines of code changed in 1 file:

• ARBDB: adali.cxx (+13 -7)

westram 2020-05-14 19:21 Rev.: 18463

* reintegrates 'top' into 'trunk'
* adds: log:branches/top@18453:18462

7 lines of code changed in 2 files:

• ARBDB: ad_config.h (+4 -4), adname.cxx (+3 -3)

westram 2020-04-22 15:46 Rev.: 18440

* warn if any path used in ARB does contain spaces (too error-prone)
- added helper functions into CORE
- warn about unwanted chars
* in result from getenv_executable(), getenv_existing_directory(), getenv_autodirectory(), GB_find_executable().
* in path of sina executable and of pigz used in ARB_zfopen().

21 lines of code changed in 1 file:

• ARBDB: adsocket.cxx (+21)

westram 2020-03-16 14:13 Rev.: 18380

* tested vectorization with misc gcc versions:
- number of reported loops differs with 7.5.0
- one vectorization succeeds for gcc 6.5.0

1 lines of code changed in 1 file:

• ARBDB: adseqcompr.cxx (+1 -1)

westram 2020-03-05 17:38 Rev.: 18361

* use prefix 'take' for descends into UNIT_TESTER.
* fix some whitespace.

7 lines of code changed in 1 file:

• ARBDB: adGene.cxx (+7 -7)

westram 2020-03-03 13:23 Rev.: 18352

* full update from child 'fix' into 'trunk'
* adds: log:branches/fix@18339:18351

1 lines of code changed in 1 file:

• ARBDB: arbdb.cxx (+1 -1)

westram 2020-03-02 19:11 Rev.: 18341

* temporary workaround for broken SINA binary compatibility (has been broken by r18159).

9 lines of code changed in 2 files:

• ARBDB: ad_t_prot.h (+1), aditem.cxx (+8)

westram 2020-02-24 19:23 Rev.: 18319

* fix whitespace.

12 lines of code changed in 1 file:

• ARBDB: adstring.cxx (+12 -12)

westram 2020-02-24 19:21 Rev.: 18318

* rename test (test symbol defined twice).
* move testcode from ARBDB->CORE.

0 lines of code changed in 1 file:

• ARBDB: adstring.cxx (-44)

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

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

37 lines of code changed in 5 files:

• ARBDB: ad_t_prot.h (+2), aditem.cxx (+6 -2), adlang1.cxx (+22), arbdb.cxx (+1 -1), gb_aci.cxx (+6)

(1380 more)