Lines of Code
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| westram | 74 (100.0%) | 2110 (100.0%) | 28.5 |
* introduce {{{onlyC_flags}}}
- flags used for C compilation only.
- similar to {{{cxxflags}}} (references added).
- pass down onlyC_flags into AxML, CLUSTAL, CLUSTALW, FASTDNAML, FASTTREE, GL, MrBAYES, PHYLIP, PHYML*, RAxML, SINA(unused), SOURCE_TOOLS, SUPPORT, TOOLS, TREEGEN + TREEPUZZLE.
- set flags to {{{-Werror-implicit-function-declaration}}}
* error is only effective in a small part of these modules.
* TODO: need to activate warnings -> will activate the error as well.
1 lines of code changed in 1 file:
* remove trailing whitespace from c source.
1 lines of code changed in 1 file:
* partial merge from 'fix' into 'trunk'
- refactored {{{AW_device}}} text output
* reduces calls to strlen (using {{{SizedCstr}}})
* eliminated/modernized several parameters/functions (esp. in {{{TextOverlayCallback}}}s)
* adds: log:branches/fix@16939:16960
1 lines of code changed in 1 file:
* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751
17 lines of code changed in 1 file:
* depends for [15253]
1 lines of code changed in 1 file:
* reintegrates 'fixres' into 'trunk'
- fixes #715
* adds: log:branches/fixres@15127:15175
1 lines of code changed in 1 file:
* fix area-management for opengl code
21 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
2 lines of code changed in 1 file:
* depends for [11033]
1 lines of code changed in 1 file:
* fixed unused private members reported by clang
* turned off 'unused private members'-warnings (2 of 3 were false positives)
1 lines of code changed in 1 file:
* use cflags before cxxflags
1 lines of code changed in 1 file:
* renamed include variables
2 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)
2 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:
* depends for recent patches
3 lines of code changed in 1 file:
* removed default entries (see [9703]) from ARB_NT and ARB_PARSIMONY
* harmonized main help entries for each executable
1 lines of code changed in 1 file:
- effect of [9574] (comments only)
1 lines of code changed in 1 file:
- updated depends for [9520]
1 lines of code changed in 1 file:
- reintegrated branch 'cxx11'
1 lines of code changed in 1 file:
* [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:
- fixed incomplete dependencies for AW_window_ogl.o
8 lines of code changed in 1 file:
- compile on suse 12.1
13 lines of code changed in 1 file:
merge from dev [7748] [7749] [7750]
* comments (C->C++ style)
* fixed umlauts in TREEGEN
57 lines of code changed in 4 files:
* merge from dev [7539] [7541] [7543] [7544] [7548] [7549] [7550] [7552] [7553] [7554] [7555] [7556] [7557] [7558] [7559] [7561] [7562] [7563] [7564] [7565] [7566] [7567] [7568] [7569] [7570] [7571] [7572] [7574] [7575]
- behavioral changes
* when jumping to gene the text will also move into viewport
* this slightly changed the zoom used in IRS tree
* dont try to draw clipped bracket
* arcs were not drawn if NW-quadrant was not fully visible
* fixed '~'-bond (SECEDIT): use constants; fixed a small gap sometimes visible; reduced OUTSIDE overhang of arcs by 15 degrees
* reset disp_device after show()
- use new type AW_rgb for colors
- removed old-style enum typedefs
- refactored
* AW_GC
* DRYed AWT_graphic_tree::show() vs fake_AWT_graphic_tree::test_show_tree()
* AW_clipable
* moved font_overlap values into AW_font_overlap
* AW_device
- removed transform/rtransform flavors using ints (replaced usages by Position/Rectangle transformations)
- added get_rtransformed_cliprect
- pass radius as Vector (circle/arc)
- fixed degrees chaos in arc params: arc_degrees now also is clockwise (like start_degrees) - both are clockwise cause ARBs y-coordinate grows downwards
- invisible_impl uses Position as param
- fixed return type of draw functions
- fixed a bug in pop_clip_scale
* push+pop did not restore scale and offset properly (only if zoom was not 1.0)
* reset AW_zoomable before restoring and restore offset before scale
- AW_device_Xm
* refactored arc_impl
- AW_device_print
* refactored circle_impl
- added assertion against drawing zero-sized circles
- test for positive radius before drawing bootstrap circles (e.g. if branchlength is zero)
- "fix" clipping of circles on AW_device_print (only affects printing when "screen only" is selected)
* if more than half of circle gets clipped -> skip circle
* otherwise force circle into clipped bounding rectangle (i.e. print a smaller circle, that fits on the screen)
* basic implementation of AW_device_print::arc_impl
- arcs based on circles are drawn using xfigs ARC command
- arcs based on ellipses are interpolated using splines
- clipping does some as with circles (clip bounding-box and draw arc inside; if less than half of arc is inside clipping area, skip arc completely)
* separated fprintf into single lines for better documentation of single xfig parameters
* AW_area_management (made member variables private + split up with useless friends)
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
1 lines of code changed in 1 file:
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)
2 lines of code changed in 1 file:
- updated prototypes and dependencies
2 lines of code changed in 1 file:
* ARB GUI (merges [6844] [6845] [6847] [6858] [6861] from refactor)
* new central header cb.h (planned to define ALL callbacks used in ARB here later)
* refactored callback handling for some AW_root callbacks
- AW_root_callback hides function ptr + arguments
- AW_root_cblist hides lists of AW_root_callback
* DRYed AW_RCB
* reduced tight coupling between some of WINDOW/*.hxx (omg)
* removed AWUSE
1 lines of code changed in 1 file:
- depends for [6816]
1 lines of code changed in 1 file:
* depends updated for [6812] + [6813]
1 lines of code changed in 1 file:
* moved a few types to arbdb_base.h
* only use arbdb_base.h or arbdb.h where possible
* global included cleanup
* added MBI headers to many files
* moved SQ_ambiguities.SQ_count_ambiguities() to separate object
2 lines of code changed in 1 file:
- added library dependency declarations
7 lines of code changed in 1 file:
- removed trailing whitespace
62 lines of code changed in 7 files:
- removed void
4 lines of code changed in 2 files:
* fixed doxygen-alike comments
- either use explicit qt-style triggers (/*! and //!)
- or made them simple comments
* converted several "normal" comments into doxygen-comments
* moved many comments inside the function/struct to which they (seemed) to belong (otherwise function and comments tend to get separated over the years)
* deleted several comments
- obvious things like paraphrases of the function name
- spammy things like repeating the function prototype
* reduced comments for vertical seperation
4 lines of code changed in 2 files:
* fixed whitespace (scripted)
164 lines of code changed in 5 files:
- changed very uncommon multiline-string format (never seen that :)
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
7 lines of code changed in 2 files:
- fixed hard readable '} else {'
2 lines of code changed in 1 file:
(9 more)