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| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 265 (100.0%) | 13608 (100.0%) | 51.3 |
| baderk | 86 (32.5%) | 11111 (81.7%) | 129.1 |
| westram | 178 (67.2%) | 2495 (18.3%) | 14.0 |
| epruesse | 1 (0.4%) | 2 (0.0%) | 2.0 |
- removes PGT (sacrificed to gtk port)
0 lines of code changed in 32 files:
* changed dynamic value-initializations into default-initializations
- i believe/know they were used with ignorance of [http://stackoverflow.com/questions/620137/do-the-parentheses-after-the-type-name-make-a-difference-with-new?answertab=active#tab-top ctor-behavior].
1 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]
20 lines of code changed in 1 file:
- reintegrated branch 'cxx11'
10 lines of code changed in 1 file:
* fixed cppcheck warnings
102 lines of code changed in 6 files:
* cppcheck (1.56 dev)
- fixed several resource-/mem-leaks
- fixed alloc/dealloc mismatches
7 lines of code changed in 2 files:
* fixed some C++11 incompatibilities (-Wnarrowing)
2 lines of code changed in 1 file:
* fixed warnings
- possible uninitialized variables
- DEBUG-mode variables
- ISLAND_HOPPING/Makefile: disabled warnings (i wont touch that module, except for removal)
3 lines of code changed in 2 files:
* [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:
- cppchecked (1.53)
35 lines of code changed in 3 files:
* removed dead code
(partly reverted by [8316])
0 lines of code changed in 2 files:
* moved much code into static scope
(partly reverted by [8310])
1229 lines of code changed in 17 files:
- cppchecked (1.52)
15 lines of code changed in 2 files:
* removed unused(-but-set) variables/params
2 lines of code changed in 2 files:
* 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)
6 lines of code changed in 1 file:
merge from dev [7950] [7951] [7952] [7953] [7954] [7955] [7957]
* replaced weird GBS_find_lib_file (GB_lib_file, GB_property_file, GB_arbtcpdat_path, GB_path_in_ARBLIB, ..)
* changed handling of property-files (removed path prefix '.arb_prop')
* replaced several hardcoded paths
* fixed arb_notify
* fixed crash when showing "lib/message" on startup (outside GB_shell)
* cleaned up error handling in start_macro_recording
17 lines of code changed in 2 files:
merge from dev [7720] [7721] [7722] [7723] [7724] [7725] [7726] [7747]
* !ItemSelector
- is now const by default (org struct is called !MutableItemSelector)
- now passed/stored as reference
- hide !MutableItemSelectors using access functions (so only const !ItemSelectors can be passed around)
* !BoundItemSel
- color_mark_data was in fact a !BoundItemSel
- !BoundItemSel is now const by default (org struct is called !MutableBoundItemSel)
* renames
- !DbScanner -> GB_DbScanner
- db_scanner_data -> !DbScanner
* fixes
- skip query if querying empty set (e.g. db w/o experiments)
- assertion failure on multiple instances of field admin menu entries (genes + experiments)
- gene-info shows selected gene when opened 1st time
- error no longer exported in experiment create
- deleting current item and then selecting a new one failed to remove callback on keydata
* added TODOs for genes/experiment UI/ItemSelectors
1 lines of code changed in 1 file:
- 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:
merges [7164] [7165] [7166] [7167] [7168] [7169] [7170] from refactor
* replaced last call to atexit() in ARBDB by GB_atexit()
* introduce GB_shell() - you need an instance for DB access
- handles ARBDB internal memory
- handles GB_atexit calls
* added tests for GB_shell and GB_remove_on_exit
* use GB_shell where needed
* fixed pending callbacks in PGT
43 lines of code changed in 6 files:
merges [7084] [7086] [7087] [7088] from refactor
* added CORE lib
- added arb_progress (unused yet)
- moved some code from ARBDB to CORE
* added tests to CORE lib
* generate_all_links.sh
- now tests link targets
- able to replace links (if link stays the same, but target changes)
* fixed perl interface
- link with libCORE
- DRYed LINUX.PL and DARWIN.PL
- added wrapper functionality (ARBDB->CORE). Functions starting with GBC_ are wrappers for code that moved into libCORE (which is NOT xsub'd)
20 lines of code changed in 1 file:
- updated prototypes and dependencies
1 lines of code changed in 1 file:
* compiler-messages (merges [6848] [6849] [6850] [6851] [6853] [6855] [6856] [6860] from refactor)
- errors get listed before warnings
- pipe all compilations through postcompile filter
- optionally filter warnings and/or stop at 1st error (controllable by POST_COMPILE in ARB Makefile)
- no warnings for ptpan (too many; version in trunk is outdated)
1 lines of code changed in 1 file:
- depends for [6816]
10 lines of code changed in 1 file:
* depends updated for [6812] + [6813]
10 lines of code changed in 1 file:
- added library dependency declarations
5 lines of code changed in 1 file:
Moved a lot of dead code to where it belongs: into the depths of SVN.
I didn't care much: If there was no obvious reason (e.g. some coment explaining why it's still there), it has been deleted
62 lines of code changed in 17 files:
* removed GB_strdup
* moved freeset, nulldup, etc to own header (dupstr.h)
* added freenull
- replacement for freeset(var,NULL)
- freeset is a template now and does no longer work with NULL/0
- replaced all occurrances
11 lines of code changed in 2 files:
* ARBDB
- compiles as C++ (no longer compiled as plain C)
- removed ARBDB2 + ARBDBS
- removed rotten C++-wrappers (ARBDBPP)
- generates special header for perl-interface to reduce dependencies (ad_p_prot.h)
* removed (ARBDB)
- gb_search_enum (merged with GB_TYPES)
* renamed (ARBDB)
- gbs_malloc_copy -> GB_memdup
- gb_search_types -> GB_SEARCH_TYPE + renamed enum-members
* tweaked perl interface
- code in ARBDB is now able to 'die' correctly (see GBP_croak_function)
- compiles as C++
- wrote generic functions for enum <-> string conversion (perl uses strings for enum values)
- added needed conversion functions
- removed handcoded xsubs (now all are generated by arb_proto_2_xsub - nevertheless, it's still possible to define xsubs manually)
- ARB::find and ARB::find_string (3rd parameter needs different values, only one file affected: PERL_SCRIPTS/GENOME/GI.pm - fixed)
- removed all functions using GBQUARK from perl interface
* perl interface generator (arb_proto_2_xsub)
- completely rewritten
- does automatic type conversion (expecting that the needed functions are defined in ARBDB/adperl.c)
* prototype generator
- compiles as C++
- switch -F accept's '!^' as beginning-of-name expression
* removed ARB_EDIT
- moved naligner interface code to EDIT4
29 lines of code changed in 2 files:
* ARB_ERROR (drop-in replacement for GB_ERROR)
- checks for unused and overwritten errors in DEBUG mode
- nearly no overhead in NDEBUG mode
* added some error-delivery wrappers
- aw_message_if()
- GB_end_transaction_show_error()
- GB_end_transaction()
- GB_transaction.close()
* updated dependencies - majority of code depends on ARB_ERROR
2 lines of code changed in 1 file:
- dependencies updated
1 lines of code changed in 1 file:
* spellchecked all (phew)
24 lines of code changed in 6 files:
* replaced GB_entry/GB_create/GB_search+GB_read_XXX by GBT_read_XXX
* improved error handling in many functions
30 lines of code changed in 5 files:
* removed useless macros:
- GB_STRDUP (easily taken for GB_strdup)
- GB_MEMCPY + GB_MEMSET + GB_FREE
- GB_DELETE (replaced by freeset(xx,NULL))
* added macros:
- freeset (= free + assign)
- freedup (= free + assign strdup'ed)
- reassign (= free + assign + clear source var)
- nulldup (=strdup accepting NULL; replacement for GB_strdup in C++ code)
* use these macros where applicable
32 lines of code changed in 5 files:
- made depends for [5708]
20 lines of code changed in 1 file:
- removed automatic timestamps (the best they were good for, were vc-conflicts)
0 lines of code changed in 1 file:
- generally use GBT_read_name() where possible
- recoded several functions
26 lines of code changed in 2 files:
* moved AWT_get_full_path() + AWT_concat_full_path() to ARBDB
* rewrote GBS_read_dir() using opendir/readdir (instead of calling 'ls')
* changed result of GB_is_...(): int -> GB_BOOL, added GB_is_readablefile()
* added GB_path_in_ARBLIB() + GB_path_in_ARBHOME()
* removed GBS_free_names() (same as GBT_free_names())
* Pressing 'Auto detect' again, selects next matching import filter. added some advices
1 lines of code changed in 1 file:
- replaced calls to GB_find with new find-functions
99 lines of code changed in 3 files:
(20 more)