Lines of Code
[root]/NALIGNER
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 400 (100.0%) | 19355 (100.0%) | 48.3 |
| oldcode | 34 (8.5%) | 9792 (50.6%) | 288.0 |
| westram | 360 (90.0%) | 9255 (47.8%) | 25.7 |
| meierh | 1 (0.3%) | 295 (1.5%) | 295.0 |
| boehnel | 1 (0.3%) | 9 (0.0%) | 9.0 |
| epruesse | 1 (0.3%) | 2 (0.0%) | 2.0 |
| baderk | 2 (0.5%) | 2 (0.0%) | 1.0 |
| artemov | 1 (0.3%) | 0 (0.0%) | 0.0 |
* 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:
* reintegrates 'ali' into 'trunk'
* adds: log:branches/ali@19183:19205
10 lines of code changed in 1 file:
* reintegrates 'progress' into 'trunk'
- implements #789
* adds: log:branches/progress@18885:18958
8 lines of code changed in 1 file:
* remove trailing whitespace from c source.
2 lines of code changed in 2 files:
* rename {{{CPP_OBJECTS}}} -> {{{OBJECTS}}}.
5 lines of code changed in 1 file:
* select units using {{{wildcard}}}.
1 lines of code changed in 1 file:
* 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:
* 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:
* reintegrates 'gcc' into 'trunk'
- mostly cosmetics changes
* adds: log:branches/gcc@16655,16741:16743,16752:16765
203 lines of code changed in 18 files:
* 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:
* reintegrates 'fixres' into 'trunk'
- fixes #715
* adds: log:branches/fixres@15127:15175
21 lines of code changed in 5 files:
* 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:
* 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:
* 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:
* 'class { public' -> struct
2 lines of code changed in 2 files:
* use cflags before cxxflags
1 lines of code changed in 1 file:
* directly use cflags
1 lines of code changed in 1 file:
* renamed include variables
1 lines of code changed in 1 file:
* 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:
- renamed
* ACC -> A_CC
* CPP -> A_CXX (misleading atm, since it contains c++flags)
1 lines of code changed in 1 file:
- document mechanism used by ARB to export variables to submakefiles
- document most important variables
1 lines of code changed in 1 file:
- 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:
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:
- effect of [9574] (comments only)
1 lines of code changed in 1 file:
- updated depends for [9520]
10 lines of code changed in 1 file:
- reintegrated branch 'cxx11'
10 lines of code changed in 1 file:
* fixed cppcheck warnings
16 lines of code changed in 3 files:
* 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:
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:
* 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:
* removed dead code
(partly reverted by [8316])
0 lines of code changed in 1 file:
* moved much code into static scope
(partly reverted by [8310])
10 lines of code changed in 3 files:
* removed unused(-but-set) variables/params
2 lines of code changed in 1 file:
* 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:
* 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:
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:
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:
merge from dev [7751] [7752]
* updated many old-style typedefs (typedef struct/enum)
5 lines of code changed in 2 files:
merge from dev [7748] [7749] [7750]
* comments (C->C++ style)
* fixed umlauts in TREEGEN
41 lines of code changed in 5 files:
- merge from dev [7450] [7452] [7456] [7457] [7458] [7459] [7460] [7461] [7464] [7465] [7466] [7467] [7468] [7469] [7482]
* tweaked compiler options
- activated -Weffc++
* postfilter warnings where Scott Meyers' advices are too general.
- base classes should not always have virtual destructors, since that renders tiny classes useless and
- members should not always be initialized via initialization list, since that often violates the DRY principle
* fix gcc's inability to detect that Noncopyable implements a private copy-ctor and op=
* this slows down complete ARB recompilation by ~5%
- added -Wold-style-cast (inactive)
- removed -Wno-non-template-friend added in [7447]
* postcompile.pl
- added option --original to show unmodified compiler output
* declared op= for classes which had a copy-ctor
* moved op= macros to arbtools.h
* derived classes containing pointers from Noncopyable (use Noncopyable virtually) or
* made them copyable if needed (awt_mask_item, KnownDB, Code, AWT_registered_itemtype, GEN_gene, !PosGene, !PartialSequence, !PlugIn, Range, Convaln_exception)
* other related changes
- user mask destruction working now
26 lines of code changed in 13 files:
(82 more)