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westram 2025-12-16 17:09 Rev.: 19613

* reintegrates 'lib' into 'trunk'
- replace dynamic library {{{AWT}}} by several static libraries: APP, ARB_SPEC, MASKS, CANVAS, MAPKEY, GUI_TK
- now also check wrong library dependencies for untested units (only4me)
* adds: log:branches/lib@19578:19612

1 lines of code changed in 1 file:

• NALIGNER: Makefile (+1 -1)

westram 2023-06-15 14:31 Rev.: 19393

* reintegrates 'ali' into 'trunk'
- refactored misused enum
- support for helix pairs:
* drop non-standard defs
* add more user defs
- change defaults
- add several predefined configs (esp. for IUPAC ambiguity codes)
* adds: log:branches/ali@19376:19392

3 lines of code changed in 1 file:

• NALIGNER: ali_profile.cxx (+3 -5)

westram 2022-08-03 14:52 Rev.: 19206

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

10 lines of code changed in 1 file:

• NALIGNER: ali_arbdb.cxx (+10 -5)

westram 2022-03-04 11:26 Rev.: 18959

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

8 lines of code changed in 1 file:

• NALIGNER: Makefile (+8)

westram 2021-09-15 12:52 Rev.: 18730

* remove trailing whitespace from c source.

2 lines of code changed in 2 files:

• NALIGNER: ali_pathmap.cxx (+1 -1), ali_pt.cxx (+1 -1)

westram 2021-09-15 12:39 Rev.: 18725

* rename {{{CPP_OBJECTS}}} -> {{{OBJECTS}}}.

5 lines of code changed in 1 file:

• NALIGNER: Makefile (+5 -5)

westram 2021-09-15 12:00 Rev.: 18720

* select units using {{{wildcard}}}.

1 lines of code changed in 1 file:

• NALIGNER: Makefile (+1 -11)

westram 2019-07-17 15:27 Rev.: 17982

* reduced use of GB_change_my_security:
- use GB_securityLevel instead of manually fiddling around with GB_change_my_security.
- inspected and accepted leftover uses (see comments).

7 lines of code changed in 1 file:

• NALIGNER: ali_arbdb.cxx (+7 -7)

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:

• NALIGNER: ali_main.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

203 lines of code changed in 18 files:

• NALIGNER: ali_aligner.cxx (+22 -31), ali_aligner.hxx (+8 -9), ali_arbdb.cxx (+6 -14), ali_global.cxx (+1 -2), ali_main.cxx (+1 -2), ali_misc.hxx (+54 -82), ali_pathmap.cxx (+11 -22), ali_pathmap.hxx (+2 -4), ali_prealigner.cxx (+7 -10), ali_prealigner.hxx (+4 -5), ali_profile.cxx (+10 -18), ali_profile.hxx (+2 -3), ali_pt.cxx (+19 -35), ali_sequence.cxx (+8 -18), ali_sequence.hxx (+2 -2), ali_solution.cxx (+29 -50), ali_tarray.hxx (+4 -6), ali_tlist.hxx (+13 -21)

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

120 lines of code changed in 18 files:

• NALIGNER: ali_aligner.cxx (+6 -6), ali_aligner.hxx (+3 -3), ali_arbdb.cxx (+7 -7), ali_arbdb.hxx (+3 -3), ali_global.cxx (+3 -3), ali_main.cxx (+4 -4), ali_pathmap.cxx (+11 -11), ali_pathmap.hxx (+1 -1), ali_prealigner.cxx (+6 -6), ali_prealigner.hxx (+6 -6), ali_profile.cxx (+7 -7), ali_profile.hxx (+1 -1), ali_pt.cxx (+27 -27), ali_sequence.cxx (+3 -3), ali_sequence.hxx (+2 -2), ali_solution.cxx (+7 -7), ali_tarray.hxx (+1 -1), ali_tlist.hxx (+22 -22)

westram 2016-08-11 10:05 Rev.: 15176

* reintegrates 'fixres' into 'trunk'
- fixes #715
* adds: log:branches/fixres@15127:15175

21 lines of code changed in 5 files:

• NALIGNER: Makefile (+14), ali_arbdb.cxx (+1 -1), ali_global.cxx (+1 -1), ali_pt.cxx (+1 -1), ali_sequence.cxx (+4 -2)

westram 2015-11-17 13:54 Rev.: 14498

* globally add explicit casts (either long or double) for all numeric ellipse arguments of aisc_put, aisc_nput and aisc_create
- errors caused by just changing the type of a passed variable are far too subtle

1 lines of code changed in 1 file:

• NALIGNER: ali_pt.cxx (+1 -1)

westram 2015-01-23 14:19 Rev.: 13443

* reintegrates 'vectorize' into 'trunk'
- adds vectorization check for gcc 4.9.x / NDEBUG compile
* adds:
- log:branches/vectorize@13428:13442

1 lines of code changed in 1 file:

• NALIGNER: Makefile (+1 -1)

westram 2013-11-03 14:42 Rev.: 11060

* reintegrates 'ptsfix' into 'trunk':
* adds:
- log:branches/ptsdump@8966:9000
- log:branches/ptsfix@8965:9012,9014:9017,9019:9023,9025:9046,9048:9089,9091:9114,9116:9132,9134:9139,9141:9145,9147:9151,9153:9158,9160:9379,9381:11059
- log:branches/ptsstartup@9160:9235,9237:9278,9280:9336,9339:9361,9363:9446
- log:branches/ptsundef@9061:9358

7 lines of code changed in 1 file:

• NALIGNER: ali_pt.cxx (+7 -1)

westram 2013-10-31 15:40 Rev.: 11002

* 'class { public' -> struct

2 lines of code changed in 2 files:

• NALIGNER: ali_profile.hxx (+1 -2), ali_pt.hxx (+1 -2)

westram 2013-10-31 14:10 Rev.: 10996

* use cflags before cxxflags

1 lines of code changed in 1 file:

• NALIGNER: Makefile (+1 -1)

westram 2013-10-31 13:48 Rev.: 10994

* directly use cflags

1 lines of code changed in 1 file:

• NALIGNER: Makefile (+1 -5)

westram 2013-10-30 15:58 Rev.: 10974

* renamed include variables

1 lines of code changed in 1 file:

• NALIGNER: Makefile (+1 -1)

westram 2013-10-29 12:55 Rev.: 10956

* made A_CC and A_CXX consistent
- A_CXX previously contained cxxflags
- cxxflags are now passed down and used separately

1 lines of code changed in 1 file:

• NALIGNER: Makefile (+1 -1)

westram 2013-10-29 12:23 Rev.: 10955

- renamed
* ACC -> A_CC
* CPP -> A_CXX (misleading atm, since it contains c++flags)

1 lines of code changed in 1 file:

• NALIGNER: Makefile (+1 -1)

westram 2013-10-29 11:43 Rev.: 10954

- document mechanism used by ARB to export variables to submakefiles
- document most important variables

1 lines of code changed in 1 file:

• NALIGNER: Makefile (+1 -1)

westram 2013-09-09 15:36 Rev.: 10563

- include downcast.h from arbdbt.h
(this break C++11 compilation, i.e. gcc4.8 or newer)[[BR]]
amendment:
* also broke compilation on ubuntu 13.04 and with gcc 4.7.3 (due to nameclash with boost)

16 lines of code changed in 1 file:

• NALIGNER: Makefile (+16)

epruesse 2013-04-13 18:23 Rev.: 9899

pass down argc/argv to AW_root::AW_root (for GTK)
GTK will pick its parameters (e.g. --g-fatal-warnings) from argv and
remove them, hence argv must not be const and AW_root() should
be called before command line parsing (if possible).

2 lines of code changed in 1 file:

• NALIGNER: ali_main.cxx (+2 -2)

westram 2013-02-13 12:24 Rev.: 9575

- effect of [9574] (comments only)

1 lines of code changed in 1 file:

• NALIGNER: Makefile (+1 -1)

westram 2013-02-09 12:52 Rev.: 9521

- updated depends for [9520]

10 lines of code changed in 1 file:

• NALIGNER: Makefile (+10)

westram 2013-02-09 11:16 Rev.: 9516

- reintegrated branch 'cxx11'

10 lines of code changed in 1 file:

• NALIGNER: Makefile (+10)

westram 2012-09-15 17:20 Rev.: 8894

* fixed cppcheck warnings

16 lines of code changed in 3 files:

• NALIGNER: ali_pathmap.cxx (+4 -5), ali_tarray.hxx (+1 -1), ali_tlist.hxx (+11 -18)

westram 2012-05-22 17:11 Rev.: 8744

* AISC clients
- client-handles for server-side objects are distinguishable types now (esp. can no longer be confounded w/o compiler messages)
- main server object has to be passed to aisc_close

25 lines of code changed in 2 files:

• NALIGNER: Makefile (+2), ali_pt.cxx (+23 -17)

westram 2012-04-19 17:39 Rev.: 8616

merge from e4fix [8190] [8196] [8198] [8197] [8199] [8221] [8226]

* callallcallbacks
- allow repeated calls for all orders
- avoid infinite descent into recursive filters
- avoid config managers
* fixes via callallcallbacks
- some un-/over-handled errors
- missing transaction
* make
- optionally keep preprocesser output
* tests
- only explain broken/wanted expectations if warning was shown
- added TEST_EXPECT!__BROKENIF
* spelling
- intervall -> interval

16 lines of code changed in 4 files:

• NALIGNER: ali_global.cxx (+6 -6), ali_main.cxx (+5 -5), ali_prealigner.cxx (+3 -3), ali_prealigner.hxx (+2 -2)

westram 2012-03-21 15:28 Rev.: 8511

* use GBT_get_species_data instead of inlined code
- replaced all occurrances where
* either code was identical
* or search mode was GB_FIND instead of GB_CREATE_CONTAINER, but following code assumed that the container was found

4 lines of code changed in 1 file:

• NALIGNER: ali_arbdb.cxx (+4 -4)

westram 2011-12-20 15:11 Rev.: 8313

* removed dead code

(partly reverted by [8316])

0 lines of code changed in 1 file:

• NALIGNER: ali_prealigner.cxx (-2)

westram 2011-12-20 12:29 Rev.: 8309

* moved much code into static scope

(partly reverted by [8310])

10 lines of code changed in 3 files:

• NALIGNER: ali_global.cxx (+2 -2), ali_main.cxx (+7 -7), ali_prealigner.cxx (+1 -1)

westram 2011-11-29 17:42 Rev.: 8257

* removed unused(-but-set) variables/params

2 lines of code changed in 1 file:

• NALIGNER: ali_prealigner.cxx (+2 -4)

westram 2011-11-29 09:33 Rev.: 8249

* wrap main for untested (but testable) units
- still untestable
* ptpan (wont change in this branch)
* GENOM (cyclic dependency with GENOM_IMPORT due to Location)
* fix missing lib dependencies
- DIST -> SL/NDS
- STAT -> SL/ITEMS
- AW_NAME -> libAWT (instead of libWINDOW)

1 lines of code changed in 1 file:

• NALIGNER: ali_main.cxx (+1 -2)

westram 2011-11-28 21:26 Rev.: 8246

* eliminated several main()'s from lib/obj-code
- replaced by ARB_main
- link executable with wrapper-object (main->ARB_main)
* unit-tests now use their own main()
- this ensures that all static data is initialized when the unit-test starts (previous behavior was working, but undefined)
- all tests pass (versus [8243])

9 lines of code changed in 3 files:

• NALIGNER: ali_global.cxx (+2 -2), ali_global.hxx (+6 -6), ali_main.cxx (+1 -1)

westram 2011-10-17 13:34 Rev.: 8104

merge from ptpan_back [8085] [8088] [8091]
* avoid shadow warnings from some TEST_ASSERTions
* patch name shows whether tests were valgrinded
* added template IGNORE_RESULT(), to ignore results tagged with !__ATTR!__USERESULT

11 lines of code changed in 1 file:

• NALIGNER: ali_other_stuff.hxx (+11 -2)

westram 2011-10-17 13:17 Rev.: 8100

merge from ptpan_back [8016] [8017] [8021] [8051] [8067]
* added method to get status of GB_shell object
* removed possibility to execute command via DB-server - always use GB_system instead
* valgrinded external tools called by arb_test

4 lines of code changed in 2 files:

• NALIGNER: ali_pt.cxx (+3 -3), ali_pt.hxx (+1 -1)

westram 2011-08-08 00:06 Rev.: 7812

merge from dev [7751] [7752]
* updated many old-style typedefs (typedef struct/enum)

5 lines of code changed in 2 files:

• NALIGNER: ali_profile.hxx (+2 -3), ali_pt.hxx (+3 -3)

westram 2011-08-08 00:01 Rev.: 7811

merge from dev [7748] [7749] [7750]
* comments (C->C++ style)
* fixed umlauts in TREEGEN

41 lines of code changed in 5 files:

• NALIGNER: ali_global.cxx (+13 -13), ali_global.hxx (+6 -6), ali_profile.hxx (+8 -8), ali_pt.cxx (+3 -3), ali_tlist.hxx (+11 -11)

(83 more)