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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.

2 lines of code changed in 2 files:

• SL/HELIX: BI_basepos.cxx (+1 -1), BI_helix.cxx (+1 -1)

westram 2023-07-04 12:14 Rev.: 19425

* reintegrates 'ali' into 'trunk'
- refactorings + fixes related to SEQ_QUALITY + HELIX
* adds: log:branches/ali@19407:19424

12 lines of code changed in 1 file:

• SL/HELIX: BI_helix.hxx (+12 -15)

westram 2023-06-25 16:30 Rev.: 19407

* reintegrates 'ali' into 'trunk'
- use bond settings from EDIT4 in SECEDIT
- fix refresh logic
- refactor underlying code
* adds: log:branches/ali@19393:19406

138 lines of code changed in 2 files:

• SL/HELIX: BI_helix.cxx (+98 -95), BI_helix.hxx (+40 -17)

westram 2023-06-15 15:31 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

67 lines of code changed in 2 files:

• SL/HELIX: BI_helix.cxx (+46 -65), BI_helix.hxx (+21 -26)

westram 2023-06-03 13:36 Rev.: 19376

* reintegrates 'ali' into 'trunk'
- completes #854
* adds: log:branches/ali@19363:19375

3 lines of code changed in 1 file:

• SL/HELIX: BI_helix.hxx (+3)

westram 2023-05-25 14:50 Rev.: 19363

* reintegrates 'ali' into 'trunk'
* basically implements #854
* adds: log:branches/ali@19357:19362

2 lines of code changed in 2 files:

• SL/HELIX: BI_helix.cxx (+1 -1), BI_helix.hxx (+1 -1)

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

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

46 lines of code changed in 3 files:

• SL/HELIX: BI_basepos.cxx (+6 -3), BI_helix.cxx (+30 -20), BI_helix.hxx (+10 -9)

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

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

2 lines of code changed in 1 file:

• SL/HELIX: Makefile (+2)

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

* remove trailing whitespace from c source.

1 lines of code changed in 1 file:

• SL/HELIX: BI_helix.cxx (+1 -1)

westram 2021-09-15 13:37 Rev.: 18724

* directly use {{{OBJECTS}}}.

1 lines of code changed in 1 file:

• SL/HELIX: Makefile (+1 -2)

westram 2021-09-15 13:31 Rev.: 18723

* remove .c rules.
* add .c suffix (in SOURCE_TOOLS).

1 lines of code changed in 1 file:

• SL/HELIX: Makefile (+1 -4)

westram 2021-09-15 13:00 Rev.: 18720

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

1 lines of code changed in 1 file:

• SL/HELIX: Makefile (+1 -1)

westram 2021-09-15 12:53 Rev.: 18718

* eliminate unused {{{C_OBJECTS}}}.

1 lines of code changed in 1 file:

• SL/HELIX: Makefile (+1 -2)

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

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

6 lines of code changed in 2 files:

• SL/HELIX: BI_basepos.cxx (+3 -1), BI_helix.cxx (+3 -1)

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

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

3 lines of code changed in 2 files:

• SL/HELIX: BI_basepos.cxx (+1 -1), BI_helix.cxx (+2 -2)

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

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

1 lines of code changed in 1 file:

• SL/HELIX: BI_basepos.hxx (+1 -1)

westram 2018-10-24 15:58 Rev.: 17534

* partial merge from 'fix' into 'trunk'
- globally define what are "gaps"
- kept behavioral changes to a minimum:
* defaults for (user-defined) gap-definition in EDIT4 changed
* EDIT sequence search also uses user-defined gaps
* adds: log:branches/fix@17529:17533

3 lines of code changed in 2 files:

• SL/HELIX: BI_basepos.cxx (+2 -1), Makefile (+1)

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

2 lines of code changed in 1 file:

• SL/HELIX: BI_helix.cxx (+2 -3)

westram 2017-11-28 19:22 Rev.: 16766

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

10 lines of code changed in 1 file:

• SL/HELIX: BI_helix.cxx (+10 -13)

westram 2017-11-28 18:09 Rev.: 16763

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

19 lines of code changed in 4 files:

• SL/HELIX: BI_basepos.cxx (+1 -1), BI_basepos.hxx (+3 -3), BI_helix.cxx (+14 -14), BI_helix.hxx (+1 -1)

westram 2017-11-06 14:54 Rev.: 16628

* reintegrates 'vectorize' into 'trunk'
- fixes #700
* documented vectorization-checks
* fine-grained check based on gcc-version
- drops old gcc-versions (<4.4.3)
- new attribute {{{__ATTR__DONT_VECTORIZE}}}
* disabled vectorization of {{{POS_TREE2::init_static()}}} for newer gcc-versions (generated code fails tests)
- added a bunch of new vectorization-checks (probably irrelevant to overall performance)
* adds: log:branches/vectorize@15531:16585,16595:16627

2 lines of code changed in 2 files:

• SL/HELIX: BI_basepos.cxx (+1 -1), BI_basepos.hxx (+1 -1)

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

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

6 lines of code changed in 2 files:

• SL/HELIX: BI_helix.cxx (+4 -4), Makefile (+2)

westram 2015-01-23 15:19 Rev.: 13443

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

2 lines of code changed in 1 file:

• SL/HELIX: Makefile (+2 -2)

westram 2014-10-13 17:34 Rev.: 13044

* revert [13041:13043]
- instead forbid gcc 4.8.0

1 lines of code changed in 1 file:

• SL/HELIX: BI_basepos.hxx (+1 -1)

westram 2014-10-12 17:18 Rev.: 13043

* ~~harden patches [13041:13042]~~
- ~~add safebool (=bool for non 4.8.0)~~
- ~~use in all bool-arrays~~

(reverted by [13044])

1 lines of code changed in 1 file:

• SL/HELIX: BI_basepos.hxx (+1 -1)

westram 2014-09-01 14:10 Rev.: 12803

* merge from 'alilink' into 'trunk'
* adds:
- log:branches/alilink@12801:12802

3 lines of code changed in 2 files:

• SL/HELIX: BI_basepos.cxx (+1 -1), BI_helix.cxx (+2 -2)

westram 2013-10-31 16:40 Rev.: 11002

* 'class { public' -> struct

1 lines of code changed in 1 file:

• SL/HELIX: BI_basepos.hxx (+1 -2)

westram 2013-10-31 15:10 Rev.: 10996

* use cflags before cxxflags

1 lines of code changed in 1 file:

• SL/HELIX: Makefile (+1 -1)

westram 2013-10-30 16:58 Rev.: 10974

* renamed include variables

2 lines of code changed in 1 file:

• SL/HELIX: Makefile (+2 -2)

westram 2013-10-29 13:55 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:

• SL/HELIX: Makefile (+1 -1)

westram 2013-10-29 13:23 Rev.: 10955

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

2 lines of code changed in 1 file:

• SL/HELIX: Makefile (+2 -2)

westram 2013-10-29 12:43 Rev.: 10954

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

1 lines of code changed in 1 file:

• SL/HELIX: Makefile (+1 -1)

westram 2013-09-09 16:36 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)

4 lines of code changed in 1 file:

• SL/HELIX: Makefile (+4)

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

- effect of [9574] (comments only)

1 lines of code changed in 1 file:

• SL/HELIX: Makefile (+1 -1)

westram 2013-02-09 13:52 Rev.: 9521

- updated depends for [9520]

2 lines of code changed in 1 file:

• SL/HELIX: Makefile (+2)

westram 2013-02-09 12:16 Rev.: 9516

- reintegrated branch 'cxx11'

2 lines of code changed in 1 file:

• SL/HELIX: Makefile (+2)

westram 2012-09-24 15:27 Rev.: 8936

* fixed cppcheck warnings

1 lines of code changed in 1 file:

• SL/HELIX: BI_basepos.cxx (+1 -1)

westram 2012-04-20 08:14 Rev.: 8623

merge from e4fix [8376] [8377] [8378] [8379] [8380] [8386] [8387] [8388] [8389]

* do not save AWARs which have default values
- motivation: edit4-props saved after [8362] did not load with older versions
- pros:
* if the user did not change the default, changing the default in code will propagate to the user
- cons:
* AWARs used by multiple applications will trigger in non-saving application, when the database containing the awar is saved
- only happens once if AWAR was previously stored with default-value
- the most obvious ones were those edit4-search-strings linked to ntree (primer, probe, gene). disarmed them by setting the default to NULL
* always generate definitions of SAI color translation tables (since default no longer saved)
- drawback: when user deletes a default color translation table, it will re-appear after restart
* allow experts to save fast-aligner protection to properties
* deliver errors exported by awar callbacks (when triggered by widget change)
* sequence color mapping
- translate stored old default ('=0') to new default (!'') on awar creation
- removed code talking to AWARs via ARBDB interface - just use AWARs straightforward
* ignore request_refresh_for_sequence_terminals when there is no hierarchy yet (now triggered by seq colors)
* lib/arb_default/edit4.arb
- removed default values (where code defaulted to same value)
- changed some defaults
* aligner (explicit, but empty ref)
* helix setting (stolen from WL)
* lib/arb_default/ntree.arb
- removed all values
* equal to default value
* obsolete entries (former awar names)
* entries that are now stored in main DB
* removed unused AWARS (AWTC_create_rename_awars)
* default for AWAR_TREE now "" everywhere
* removed unused AISC variable
* renamed edit direction related variables/awars

12 lines of code changed in 1 file:

• SL/HELIX: BI_helix.cxx (+12 -12)

westram 2012-04-11 13:19 Rev.: 8574

* [8567] failed on WCs where shared libs were up-to-date, but not yet present in $ARBHOME/lib
- link libs directly in $ARBHOME/lib
* no longer create 'SHARED.a' in shared-library-dirs
* unit tests caused build of 'SHARED.so' (instead of 'libSHARED.so'). Every library existed twice.
- changed test-target-names for shared libaries (e.g. ARBDB/ARBDB.test -> ARBDB/libARBDB.test)
- added failing stopper targets to main-Makefile and shared-lib-Makefiles
* changed all dependencies to shared libs
* fixed dependency scripts to perform correct translations from lib/libUNIT.so <-> UNIT/UNIT.(dummy|a). omg :/
* updated predefined RESTRICT_LIB entries in UNIT_TESTER/Makefile.setup.template
- check whether RESTRICT_LIB uses obsolete test-names (e.g. ARBDB instead of libARBDB) and fail if.

1 lines of code changed in 1 file:

• SL/HELIX: needs_libs (+1 -1)

westram 2011-12-20 13:29 Rev.: 8309

* moved much code into static scope

(partly reverted by [8310])

2 lines of code changed in 1 file:

• SL/HELIX: BI_helix.cxx (+2 -2)

(42 more)