Directory ARBDB/

Directory Created:
2000-11-23 10:41
Total Files:
85
Deleted Files:
57
Lines of Code:
45917

[root]/ARBDB
        Folder removed from repo EXAMPLES (0 files, 0 lines)

Lines of Code

ARBDB/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 4143 (100.0%) 145765 (100.0%) 35.1
westram 3986 (96.2%) 120709 (82.8%) 30.2
oldcode 44 (1.1%) 23880 (16.4%) 542.7
epruesse 25 (0.6%) 540 (0.4%) 21.6
meierh 7 (0.2%) 230 (0.2%) 32.8
boehnel 43 (1.0%) 181 (0.1%) 4.2
spanfeln 9 (0.2%) 94 (0.1%) 10.4
baderk 15 (0.4%) 59 (0.0%) 3.9
lai 2 (0.0%) 42 (0.0%) 21.0
richter 6 (0.1%) 12 (0.0%) 2.0
yadhu 2 (0.0%) 7 (0.0%) 3.5
artemov 2 (0.0%) 6 (0.0%) 3.0
jobb 2 (0.0%) 5 (0.0%) 2.5

Most Recent Commits

westram 2022-11-13 18:29 Rev.: 19346


* reintegrates 'refactor' into 'trunk'
- polish {{{GBS_strstruct}}}
* adds: log:branches/refactor@19339:19345

11 lines of code changed in 6 files:

  • ARBDB: aditem.cxx (+1 -1), adlang1.cxx (+1 -1), adname.cxx (+1 -1), adsocket.cxx (+1 -1), adstring.cxx (+6 -6), gb_aci.cxx (+1 -1)
westram 2022-11-13 15:47 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

220 lines of code changed in 12 files:

  • ARBDB: adGene.cxx (+17 -27), ad_config.cxx (+7 -10), ad_config.h (+5 -2), adali.cxx (+5), adhash.cxx (+9 -12), adindex.cxx (+27 -24), aditem.cxx (+6 -7), adlang1.cxx (+80 -80), adname.cxx (+5 -7), adsocket.cxx (+10 -10), adstring.cxx (+46 -58), gb_aci.cxx (+3 -3)
westram 2022-10-22 18:24 Rev.: 19282


* reject groupnames which would be misinterpreted as bootstrap values
- misinterpretation would happen during re-import after export

22 lines of code changed in 1 file:

  • ARBDB: adtree.cxx (+22)
westram 2022-10-22 18:19 Rev.: 19281


* pull-out {{{parse_treelabel()}}} from {{{setBranchName_acceptingBootstrap()}}}.

38 lines of code changed in 1 file:

  • ARBDB: TreeNode.h (+38)
westram 2022-10-22 18:14 Rev.: 19279


* use + add wrapped concatenators to {{{GBS_strstruct}}}

1 lines of code changed in 1 file:

  • ARBDB: adstring.cxx (+1 -3)
westram 2022-10-21 15:08 Rev.: 19278


* warn about..
- {{{;}}} in group names (conflicts with taxonomy).
- group names containing underscores (reserved for group overlaps).
- group names ending with {{{~NUM}}} (reserved for splitted groups).

24 lines of code changed in 1 file:

  • ARBDB: adtree.cxx (+24 -4)
westram 2022-10-21 15:04 Rev.: 19277

* use {{{MessageSpamFilter}}} when generating groups:
- from callers which may spam arbs message box.
* part of #832

5 lines of code changed in 2 files:

  • ARBDB: Makefile (+1), adtree.cxx (+4)
westram 2022-10-19 16:24 Rev.: 19272


* define + use KEELED_INDICATOR instead of hardcoding '!'\\=> related code is now easy to find.

8 lines of code changed in 3 files:

  • ARBDB: TreeNode.h (+2), adlang1.cxx (+3 -2), adtree.cxx (+3 -3)
westram 2022-09-02 13:38 Rev.: 19249


* revive old version of {{{GBT_add_new_changekey}}} (=interface before [19140]).
- mark as deprecated
- implement via {{{GBT_add_new_species_changekey}}}
- fixes binary compatibility for sina 1.3 binary (still used on ubuntu 10.04)

11 lines of code changed in 2 files:

  • ARBDB: adChangeKey.cxx (+10), ad_t_prot.h (+1)
westram 2022-09-02 13:35 Rev.: 19248


* rename {{{GBT_add_new_changekey}}} -> {{{GBT_add_new_species_changekey}}}.

3 lines of code changed in 2 files:

  • ARBDB: adChangeKey.cxx (+2 -2), ad_t_prot.h (+1 -1)
westram 2022-09-01 15:19 Rev.: 19245


* reintegrates 'sina' into 'trunk'
- build/deliver sina together with arb
* adds: log:branches/sina@18984:19043,19046:19069,19072:19244

8 lines of code changed in 4 files:

  • ARBDB: adali.cxx (+1 -1), adoptimize.cxx (+1 -1), adseqcompr.cxx (+3 -3), adtcp.cxx (+3 -1)
westram 2022-08-06 18:25 Rev.: 19222


* reintegrates 'split' into 'trunk'
- completes #846
* adds: log:branches/split@19169:19221

24 lines of code changed in 1 file:

  • ARBDB: adali.cxx (+24 -19)
westram 2022-08-03 14:52 Rev.: 19206


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

138 lines of code changed in 5 files:

  • ARBDB: Makefile (+1), ad_t_prot.h (+2), adali.cxx (+128 -25), adlang1.cxx (+6 -4), adseqcompr.cxx (+1 -2)
westram 2022-07-21 13:01 Rev.: 19167


* reintegrates 'split' into 'trunk'
* adds: log:branches/split@19102:19166

178 lines of code changed in 10 files:

  • ARBDB: adChangeKey.cxx (+9), ad_config.cxx (+1 -4), ad_t_prot.h (+5 -2), adali.cxx (+119 -34), adfile.cxx (+1 -3), adtcp.cxx (+8 -14), adtools.cxx (+5 -7), adtree.cxx (+1 -6), arbdb.h (+8 -1), arbdbpp.cxx (+21 -4)
westram 2022-07-09 09:15 Rev.: 19142


* correct recursive call used to create hierarchical key-prefixes:
- did use wrong keypath for ALL BUT species.

1 lines of code changed in 1 file:

  • ARBDB: adChangeKey.cxx (+1 -1)
westram 2022-07-09 09:14 Rev.: 19141


* javadoc {{{GBT_add_new_changekey_to_keypath}}}.

7 lines of code changed in 1 file:

  • ARBDB: adChangeKey.cxx (+7)
westram 2022-07-09 09:12 Rev.: 19140


* in "add new changekey"-functions:
- change type of param 'type' (int -> GB_TYPES)
- fix callers where needed.

10 lines of code changed in 2 files:

  • ARBDB: adChangeKey.cxx (+6 -6), ad_t_prot.h (+4 -4)
westram 2022-07-01 13:26 Rev.: 19105


* allow 1 or 3 vectorizations
* fixes linux RELEASE build

2 lines of code changed in 1 file:

  • ARBDB: adoptimize.cxx (+2 -2)
westram 2022-06-29 13:54 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 11:40 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 11:18 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 11:17 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 11:15 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 11:14 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 11:12 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 10:25 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 11:26 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 14:38 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 13:53 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 14:33 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 19:11 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 18:03 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 16:19 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 08:33 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 09:43 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 17:23 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 16:58 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 12:52 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 14:15 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 09:22 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)

(1398 more)

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