Directory SL/AW_HELIX/

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

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

1 lines of code changed in 1 file:

• SL/AW_HELIX: Makefile (+1)

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

* remove trailing whitespace from c source.

1 lines of code changed in 1 file:

• SL/AW_HELIX: AW_helix.cxx (+1 -1)

westram 2021-09-15 12:37 Rev.: 18724

* directly use {{{OBJECTS}}}.

1 lines of code changed in 1 file:

• SL/AW_HELIX: Makefile (+1 -2)

westram 2021-09-15 12:31 Rev.: 18723

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

1 lines of code changed in 1 file:

• SL/AW_HELIX: Makefile (+1 -4)

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

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

1 lines of code changed in 1 file:

• SL/AW_HELIX: Makefile (+1 -1)

westram 2021-09-15 11:53 Rev.: 18718

* eliminate unused {{{C_OBJECTS}}}.

1 lines of code changed in 1 file:

• SL/AW_HELIX: Makefile (+1 -2)

westram 2019-04-01 16:41 Rev.: 17724

* partial merge from 'fts' into 'trunk'
- {{{ConfigMapping}}}:
* cleanup
* add missing tests
* fix config bug: trailing backslash at end of values did cause wrong read of data
* adds: log:branches/fts@17718:17723

2 lines of code changed in 1 file:

• SL/AW_HELIX: Makefile (+2)

westram 2018-09-20 17:43 Rev.: 17396

* reintegrates 'fix' into 'trunk'
- elim dead code
- use const hash loop
* adds: log:branches/fix@17380,17388:17395

1 lines of code changed in 1 file:

• SL/AW_HELIX: AW_helix.cxx (+1 -1)

westram 2018-05-02 10:32 Rev.: 16961

* 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 3 files:

• SL/AW_HELIX: AW_helix.cxx (-30), AW_helix.hxx (-1), Makefile (+1)

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

3 lines of code changed in 1 file:

• SL/AW_HELIX: AW_helix.cxx (+3 -3)

westram 2016-08-30 11:30 Rev.: 15254

* depends for [15253]

1 lines of code changed in 1 file:

• SL/AW_HELIX: Makefile (+1)

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

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

2 lines of code changed in 2 files:

• SL/AW_HELIX: AW_helix.cxx (+1 -1), Makefile (+1)

westram 2016-04-16 13:52 Rev.: 14731

* mark code binding callbacks to non-button-widgets (probably incomplete; see #559 for details)

3 lines of code changed in 1 file:

• SL/AW_HELIX: AW_helix.cxx (+3 -3)

westram 2015-12-17 17:11 Rev.: 14626

* sync gtk and motif versions

0 lines of code changed in 1 file:

• SL/AW_HELIX: AW_helix.hxx (-2)

westram 2015-09-08 12:45 Rev.: 14273

* pass refresh callback as typed callback
- Note: IIRC this is the first use of a (pointer to a static) typed callback as parameter of another typed callback

12 lines of code changed in 2 files:

• SL/AW_HELIX: AW_helix.cxx (+8 -8), AW_helix.hxx (+4 -1)

westram 2015-04-16 16:30 Rev.: 13735

* add config manager to helix properties

19 lines of code changed in 2 files:

• SL/AW_HELIX: AW_helix.cxx (+18), Makefile (+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

2 lines of code changed in 1 file:

• SL/AW_HELIX: Makefile (+2 -2)

westram 2013-11-02 16:41 Rev.: 11034

* depends for [11033]

1 lines of code changed in 1 file:

• SL/AW_HELIX: Makefile (+1)

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

* use cflags before cxxflags

1 lines of code changed in 1 file:

• SL/AW_HELIX: Makefile (+1 -1)

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

* renamed include variables

2 lines of code changed in 1 file:

• SL/AW_HELIX: Makefile (+2 -2)

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:

• SL/AW_HELIX: 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)

2 lines of code changed in 1 file:

• SL/AW_HELIX: Makefile (+2 -2)

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:

• SL/AW_HELIX: Makefile (+1 -1)

westram 2013-10-21 13:16 Rev.: 10863

* replaced usage of untyped AW_POPUP_HELP

1 lines of code changed in 1 file:

• SL/AW_HELIX: AW_helix.cxx (+1 -1)

epruesse 2013-10-06 11:27 Rev.: 10745

remove use of AW_cb outside of WINDOW (scheduled for removal in gtkport).
this is a hack, I know. I'm open to suggestions.

7 lines of code changed in 2 files:

• SL/AW_HELIX: AW_helix.cxx (+6 -7), AW_helix.hxx (+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)

1 lines of code changed in 1 file:

• SL/AW_HELIX: Makefile (+1)

westram 2013-07-04 15:49 Rev.: 10212

* depends for recent patches

3 lines of code changed in 1 file:

• SL/AW_HELIX: Makefile (+3)

westram 2013-07-04 15:22 Rev.: 10209

* reintegrate branch 'bpcb' (examples; non-WINDOW)

5 lines of code changed in 2 files:

• SL/AW_HELIX: AW_helix.cxx (+4 -4), AW_helix.hxx (+1 -1)

westram 2013-07-04 14:59 Rev.: 10206

* merge from bpcb [10181] [10186] (renames in WINDOW)

5 lines of code changed in 2 files:

• SL/AW_HELIX: AW_helix.cxx (+3 -3), AW_helix.hxx (+2 -2)

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

- effect of [9574] (comments only)

1 lines of code changed in 1 file:

• SL/AW_HELIX: Makefile (+1 -1)

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

- updated depends for [9520]

1 lines of code changed in 1 file:

• SL/AW_HELIX: Makefile (+1)

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

- reintegrated branch 'cxx11'

1 lines of code changed in 1 file:

• SL/AW_HELIX: Makefile (+1)

westram 2012-04-11 12:19 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/AW_HELIX: needs_libs (+1 -1)

westram 2012-02-18 16:43 Rev.: 8423

* use !LocallyModify for several flags

34 lines of code changed in 1 file:

• SL/AW_HELIX: AW_helix.cxx (+34 -34)

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

* moved much code into static scope

(partly reverted by [8310])

1 lines of code changed in 1 file:

• SL/AW_HELIX: AW_helix.cxx (+1 -1)

westram 2011-06-16 19:16 Rev.: 7666

* 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)

2 lines of code changed in 1 file:

• SL/AW_HELIX: AW_helix.cxx (+2 -2)

westram 2011-06-10 14:24 Rev.: 7622

* merge from dev [7434] [7435] [7436] [7437] [7438] [7439] [7440] [7441] [7442] [7443] [7444]
- AW_device
* removed some derived-class-specific functions
* virtual functions
- removed default parameters, renamed them to XXX_impl, made them private and added missing variants to replace direct calls to renamed functions
* added AW_simple_device as base for AW_device_click and AW_device_size
* do not pass AW_CL/AW_CL for AW_device_click down through all paint functions, instead create instances of AW_click_cd
* devirtualized ready_to_draw + cursor
* added default for filter to all paint functions (removed default from calls)
* XXX_impl functions use Position, Rectangle, Vector etc. instead of AW_pos
- AW_common
* removed unneccessary members; made members private
* moved some code between AW_gc, AW_GC_Xm and AW_common
* global data (color tables) now referenced by references instead of pointers
* made independent member function x_alignment() global
* no longer install resize callback from ctor
- AW_clicked_line (renamed some members; removed distanceTo)
- fixed possible return of temporaries
- AW_root
* made independent member functions font_2_ascii() and font_2_xfig() global (AW_font_2_ascii AW_font_2_xfig)
- Tree display
* client data changed (bootstrap text and vertical lines starting at bifurcation belong to son now)

6 lines of code changed in 2 files:

• SL/AW_HELIX: AW_helix.cxx (+5 -11), AW_helix.hxx (+1 -5)

westram 2011-03-16 12:04 Rev.: 7272

merged from dev [7244] [7250] [7251] [7252] [7253] [7254] [7255] [7257] [7258] [7259] [7260] [7261] [7271]
* extracted conversion logic of absolute <-> relative position into !BasePosition
- refactored BI_ecoli_ref and ED4_base_position (using !BasePosition)
- corrected input range of abs_2_rel ([0..N-1] -> [0..N])
* clean up chaos caused by different semantics of positions (biological[1..N] vs informational[0..N-1])
- commented (hopefully) all AWARs and variables which use biological positions
- made semantic changes explicit by using bio2info() and info2bio()
* positions passed to/reported by PTserver are now biological positions. Affects
- probe design (absolute position, ecoli range restriction)
- probe match (absolute position, ecoli position (bugfix see below)).
- !ProbeMatchParser does not change semantics
* fix several bugs
- ED4_jump_to_cursor_position limited position to screen before converting from relative to absolute position
- SEC_root::paintEcoliPositions added 1 to relative pos (instead of including position at cursor)
- ecoli position in probe match/PTserver (did not include ecoli-base at match position)
- ecoli range restriction in probe design/PTserver (check was broken, see [7261])
- base position for consensus terminals

3 lines of code changed in 2 files:

• SL/AW_HELIX: AW_helix.cxx (+1), Makefile (+2)

westram 2011-02-23 13:37 Rev.: 7183

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:

• SL/AW_HELIX: Makefile (+2 -1)

westram 2010-09-18 16:39 Rev.: 6868

- updated prototypes and dependencies

3 lines of code changed in 1 file:

• SL/AW_HELIX: Makefile (+3)

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