July 2007 Commit Log

Number of Commits:

78

Number of Active Developers:

3

westram 2007-07-31 16:38 #78 Rev.: 4754

- simpler and straight-forward error handling for AW_xfig-ctor
- sometimes xfig-files are stored with magnification != 100.00
Now xfig-reader ignores the magnification (previously it expected '100.00'),
does not seem to make any difference!
- fixed AWUSE

251 lines of code changed in 1 file:

• WINDOW: AW_xfig.cxx (+251 -252)

westram 2007-07-31 16:36 #77 Rev.: 4753

- changed several prototypes (AWUSE/statics/etc.)

27 lines of code changed in 1 file:

• NTREE: AP_cprofile.cxx (+27 -41)

westram 2007-07-31 16:36 #76 Rev.: 4752

- note about AWUSE
- warnings4me

9 lines of code changed in 1 file:

• WINDOW: aw_root.hxx (+9 -1)

westram 2007-07-31 16:36 #75 Rev.: 4751

- __attribute__((noreturn)) for throw_IO_error()

1 lines of code changed in 1 file:

• RNA3D: RNA3D_StructureData.cxx (+1)

westram 2007-07-31 16:36 #74 Rev.: 4750

- added color toggle

21 lines of code changed in 1 file:

• lib/pictures/awt: secExport.fig (+21 -21)

westram 2007-07-31 16:35 #73 Rev.: 4749

- Note about influence of current physical zoom

5 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: tree2prt.hlp (+5 -2)

westram 2007-07-31 16:35 #72 Rev.: 4748

- AWT_create_print_window -> AWT_popup_print_window

1 lines of code changed in 1 file:

• TEST: D_main.cxx (+1 -1)

westram 2007-07-31 16:35 #71 Rev.: 4747

- popup now done by AWT_popup_sec_export_window()
- fixed AWUSE

5 lines of code changed in 1 file:

• SECEDIT: SEC_main.cxx (+5 -7)

westram 2007-07-31 16:34 #70 Rev.: 4746

- popup now done by AWT_popup_tree_export_window()
- fixed AWUSE

19 lines of code changed in 1 file:

• PARSIMONY: PARS_main.cxx (+19 -39)

westram 2007-07-31 16:34 #69 Rev.: 4745

- popup now done by AWT_popup_tree_export_window()

2 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+2 -2)

westram 2007-07-31 16:34 #68 Rev.: 4744

- awar creation now done by functions
- since print and export use the same file awar,
rewrite filename+filter everytime a window is opened.
- AWT_create..._window changed into AWT_popup_...__window
They popup the window.

322 lines of code changed in 1 file:

• AWT: AWT_canio.cxx (+322 -280)

westram 2007-07-31 16:34 #67 Rev.: 4743

- AWT_create..._window changed into AWT_popup_...__window

3 lines of code changed in 1 file:

• AWT: awt_canvas.hxx (+3 -5)

yadhu 2007-07-31 12:50 #66 Rev.: 4742

removed AWUSE()

19 lines of code changed in 5 files:

• RNA3D: RNA3D_Graphics.cxx (+4 -11), RNA3D_Interface.cxx (+11 -22), RNA3D_OpenGLGraphics.cxx (+2 -4), RNA3D_Renderer.cxx (+1 -2), RNA3D_StructureData.cxx (+1 -2)

yadhu 2007-07-30 12:15 #65 Rev.: 4741

Removed unnessasary warnings!

18 lines of code changed in 4 files:

• RNA3D: RNA3D_Interface.cxx (+12 -3), RNA3D_OpenGLEngine.cxx (+2 -1), RNA3D_OpenGLGraphics.cxx (+2), RNA3D_Renderer.cxx (+2 -1)

westram 2007-07-29 18:12 #64 Rev.: 4740

- attached things to correct border

30 lines of code changed in 1 file:

• lib/pictures/edit4: save_search.fig (+30 -25)

westram 2007-07-29 18:12 #63 Rev.: 4739

- don't try to create dir ''

1 lines of code changed in 1 file:

• WINDOW: AW_nawar.cxx (+1 -1)

westram 2007-07-29 15:27 #62 Rev.: 4738

- really perform fallback in case of non-existing directory (only told it does, but it didn't)
- ask to create default directory, if it doesn't exist

13 lines of code changed in 1 file:

• WINDOW: AW_nawar.cxx (+13 -2)

westram 2007-07-29 15:27 #61 Rev.: 4737

- renamed AWAR_SECEDIT_IMEXPORT_BASE -> AWAR_SECEDIT_SAVEDIR

3 lines of code changed in 1 file:

• SECEDIT: SEC_main.cxx (+3 -3)

westram 2007-07-29 15:27 #60 Rev.: 4736

- default directory to save secondary structure changed into .arb_prop/secondary_structure
- renamed AWAR_SECEDIT_IMEXPORT_BASE -> AWAR_SECEDIT_SAVEDIR

2 lines of code changed in 1 file:

• SECEDIT: SEC_graphic.cxx (+2 -2)

westram 2007-07-29 15:27 #59 Rev.: 4735

- renamed AWAR_SECEDIT_IMEXPORT_BASE -> AWAR_SECEDIT_SAVEDIR
changed internal awarpath as well to force reinitialization

2 lines of code changed in 1 file:

• SECEDIT: sec_graphic.hxx (+2 -2)

westram 2007-07-29 15:27 #58 Rev.: 4734

- default save directory for search settings changed to .arb_prop/search_settings

1 lines of code changed in 1 file:

• EDIT4: ED4_search.cxx (+1 -1)

westram 2007-07-29 14:46 #57 Rev.: 4733

- added target 'sec'

3 lines of code changed in 1 file:

• Makefile (+3 -1)

westram 2007-07-26 17:01 #56 Rev.: 4732

- fixed indentation

64 lines of code changed in 1 file:

• WINDOW: aw_device.hxx (+64 -64)

westram 2007-07-12 17:32 #55 Rev.: 4731

- typo

1 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+1 -1)

westram 2007-07-12 17:32 #54 Rev.: 4730

- missing default selection

1 lines of code changed in 1 file:

• NTREE: AP_csp_2_gnuplot.cxx (+1)

westram 2007-07-12 17:32 #53 Rev.: 4729

*** empty log message ***

0 lines of code changed in 1 file:

• lib/BUGS: known_bugs.txt (-1)

westram 2007-07-12 17:31 #52 Rev.: 4728

- indented, untabified

40 lines of code changed in 1 file:

• TOOLS: arb_count_chars.cxx (+40 -40)

westram 2007-07-12 17:27 #51 Rev.: 4727

- save result as 'data' containing '0-9A-P'

16 lines of code changed in 1 file:

• TOOLS: arb_count_chars.cxx (+16 -22)

westram 2007-07-12 10:26 #50 Rev.: 4726

*** empty log message ***

13 lines of code changed in 1 file:

• lib/pictures/awt: print.fig (+13 -17)

westram 2007-07-11 15:25 #49 Rev.: 4725

- hotkeys fixed

2 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+2 -2)

westram 2007-07-11 15:24 #48 Rev.: 4724

- overlap toggle + overlap amount definition
- input field for page count
- input fields resize with window
- layout

54 lines of code changed in 1 file:

• lib/pictures/awt: print.fig (+54 -40)

westram 2007-07-11 15:24 #47 Rev.: 4723

- added paper sizes in inches
- note about border
- help for 'overlap' and 'fit pages'

19 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: tree2prt.hlp (+19 -2)

westram 2007-07-11 15:24 #46 Rev.: 4722

- added awars for overlap and fit-to-pages

12 lines of code changed in 1 file:

• AWT: awt_canvas.hxx (+12 -9)

westram 2007-07-11 15:24 #45 Rev.: 4721

- AWAR_PRINT_TREE_ORIENTATION (containing fig2dev-flag) changed
into AWAR_PRINT_TREE_LANDSCAPE (1=landscape, 0=portrait)
- several debugging prints
- added overlap toggle and call fig2dev appropriate
- changed forward and backward calculation of resulting pages
when overlap is used
- can calc fit onto any number of pages

183 lines of code changed in 1 file:

• AWT: AWT_canio.cxx (+183 -75)

westram 2007-07-10 11:34 #44 Rev.: 4720

- renamed AWARs
- beautified code
- reduced button size to 6 (show gfx size)

175 lines of code changed in 1 file:

• AWT: AWT_canio.cxx (+175 -182)

westram 2007-07-10 11:34 #43 Rev.: 4719

- renamed AWARs + made several saveable to preferences
- beautified code

91 lines of code changed in 1 file:

• AWT: awt_canvas.hxx (+91 -87)

westram 2007-07-09 14:41 #42 Rev.: 4718

- updated

5 lines of code changed in 1 file:

• ARBDB: ad_prot.h (+5 -7)

westram 2007-07-09 14:41 #41 Rev.: 4717

- renamed create-hash functions

15 lines of code changed in 8 files:

• ARBDB: adtools.c (+2 -3)
• AWT: AWT_query_and_functions.cxx (+2 -2), AWT_tree_cb.cxx (+2 -2)
• GENOM: GEN_map.cxx (+1 -1)
• MERGE: MG_preserves.cxx (+3 -3), MG_species.cxx (+2 -2)
• NTREE: NT_extern.cxx (+2 -2)
• PARSIMONY: PARS_main.cxx (+1 -1)

westram 2007-07-09 14:40 #40 Rev.: 4716

- simplified hash generators
- removed duplicate functions
- use similar names for all create-hash functions

27 lines of code changed in 1 file:

• ARBDB: adhashtools.c (+27 -77)

westram 2007-07-09 14:40 #39 Rev.: 4715

- moved organism hash functions to adhashtools.c
- added GEN_get_organism_count() - slow

14 lines of code changed in 1 file:

• ARBDB: adGene.c (+14 -26)

westram 2007-07-09 14:39 #38 Rev.: 4714

- removed prototypes (they are already in ad_prot.h)

2 lines of code changed in 1 file:

• ARBDB: adGene.h (+2 -80)

westram 2007-07-09 14:39 #37 Rev.: 4713

- don't use adGene.h for prototyping (ad_prot.h contains enough)

0 lines of code changed in 1 file:

• PERL2ARB: Makefile.main (-1)

westram 2007-07-06 14:03 #36 Rev.: 4712

- enabled chimere_check in NDEBUG VERSION

2 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+2 -8)

westram 2007-07-06 12:08 #35 Rev.: 4711

- added target 'clean' (did never occur here)

3 lines of code changed in 1 file:

• GDE/CORE: Makefile (+3)

westram 2007-07-06 11:48 #34 Rev.: 4710

- vertical merge-button

58 lines of code changed in 1 file:

• lib/pixmaps/merge: icon_vertical.bitmap (new 58)

westram 2007-07-06 11:48 #33 Rev.: 4709

- vertical layout

45 lines of code changed in 1 file:

• lib/pictures/merge: startup.fig (+45 -42)

westram 2007-07-06 11:48 #32 Rev.: 4708

- new layout with add.fields and indicators

29 lines of code changed in 1 file:

• lib/pictures/merge: names.fig (+29 -17)

westram 2007-07-06 11:47 #31 Rev.: 4707

- added adhashtools.c

3 lines of code changed in 1 file:

• SOURCE_TOOLS: generate_all_links.sh (+3 -2)

westram 2007-07-06 11:47 #30 Rev.: 4706

- added AWTC_create_numbered_suffix()
- AWTC_pars_names() got extra result-parameter indicating duplicated species
- function renamed

38 lines of code changed in 2 files:

• SL/AW_NAME: AW_rename.cxx (+33 -16), AW_rename.hxx (+5 -4)

westram 2007-07-06 11:47 #29 Rev.: 4705

- updated

39 lines of code changed in 2 files:

• HELP_SOURCE/oldhelp: mg_names.hlp (+28 -13)
• MERGE: merge.hxx (+11 -4)

westram 2007-07-06 11:47 #28 Rev.: 4704

- depends updated

34 lines of code changed in 4 files:

• ARBDB: Makefile (+11)
• ARBDB2: Makefile (+11)
• ARBDBS: Makefile (+11)
• MERGE: Makefile (+1)

westram 2007-07-06 11:46 #27 Rev.: 4703

- function renamed
- MG_simple_merge: when species are present in destination DB, new
answer possibility to auto-rename all (= insert as duplicates)
- Uses species-hash to find/avoid target species.
- Handle DB errors during simple merge (ignored before)

87 lines of code changed in 1 file:

• MERGE: MG_species.cxx (+87 -24)

westram 2007-07-06 11:46 #26 Rev.: 4702

- additional fields for nameserver displayed in rename window
- only one button to rename both DBs (renaming is mandatory now)
- display rename-status
- option to allow merging when duplicates are present

184 lines of code changed in 1 file:

• MERGE: MG_names.cxx (+184 -24)

westram 2007-07-06 11:46 #25 Rev.: 4701

- create DB dependent awars (when DBs are available)
- added MG_popup_if_renamed (to enforce renaming before merging species,
trees or configs)
- init renamed-state
- redesigned startup window (vertical instead of horizontal layout)

36 lines of code changed in 1 file:

• MERGE: MG_main.cxx (+36 -12)

westram 2007-07-06 11:46 #24 Rev.: 4700

- function renamed

3 lines of code changed in 3 files:

• MERGE: MG_alignment.cxx (+1 -1), MG_extendeds.cxx (+1 -1)
• NTREE: NT_extern.cxx (+1 -1)

westram 2007-07-06 11:45 #23 Rev.: 4699

- ignore case when building hash in find_species_candidates()

2 lines of code changed in 1 file:

• MERGE: MG_preserves.cxx (+2 -2)

westram 2007-07-06 11:45 #22 Rev.: 4698

- ignore case when building hash in NT_mark_nontree_cb()

2 lines of code changed in 1 file:

• AWT: AWT_tree_cb.cxx (+2 -1)

westram 2007-07-06 11:44 #21 Rev.: 4697

- prototypes updated

15 lines of code changed in 3 files:

• ARBDB: ad_lpro.h (+2), ad_prot.h (+10), ad_t_prot.h (+3 -6)

westram 2007-07-06 11:42 #20 Rev.: 4696

- added item-count functions: GBT_get_species_count + GBT_get_SAI_count
- moved hash-generating functions to adhashtools.c

22 lines of code changed in 1 file:

• ARBDB: adtools.c (+22 -83)

westram 2007-07-06 11:41 #19 Rev.: 4695

- moved hash-generating functions to here

123 lines of code changed in 1 file:

• ARBDB: adhashtools.c (new 123)

westram 2007-07-06 11:41 #18 Rev.: 4694

- added adhashtools.o

1 lines of code changed in 1 file:

• ARBDB: AD_MOBJECTS.h (+1 -1)

westram 2007-07-06 11:41 #17 Rev.: 4693

- added target 'mg' (MERGE)

1 lines of code changed in 1 file:

• Makefile (+1)

westram 2007-07-05 15:17 #16 Rev.: 4692

- mention SUBDIR clean

1 lines of code changed in 1 file:

• Makefile (+1 -1)

westram 2007-07-05 15:04 #15 Rev.: 4691

- expand LD_LIBRARY_PATH before calling arb_proto_2_xsub

1 lines of code changed in 1 file:

• PERL2ARB: Makefile.main (+1 -5)

westram 2007-07-05 15:04 #14 Rev.: 4690

- target dball builds libARBDPP as well

4 lines of code changed in 1 file:

• Makefile (+4 -4)

baderk 2007-07-05 14:02 #13 Rev.: 4689

Changed nomenclature for the quality data entries: Now stored in its own container 'quality' instead of the alignment. Avoids incompatibilities with EDIT4.

149 lines of code changed in 2 files:

• SEQ_QUALITY: SQ_functions.cxx (+141 -92), SQ_physical_layout.h (+8 -5)

baderk 2007-07-03 14:11 #12 Rev.: 4688

Added "unmark rest" comment to clearify marking scheme.

11 lines of code changed in 1 file:

• lib/pictures: seq_quality.fig (+11 -12)

baderk 2007-07-03 13:41 #11 Rev.: 4687

Fixed a segfault which sometimes occured when marked parts of a tree were evaluated.

0 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_main.cxx (-2)

baderk 2007-07-02 13:04 #10 Rev.: 4686

Fixed wrong aw_status timer output when computing a list of species without tree information.

8 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_functions.cxx (+8 -8)

baderk 2007-07-02 13:02 #9 Rev.: 4685

Fixed an error which occured when analysing marked parts of a tree.

13 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_main.cxx (+13 -5)

baderk 2007-07-02 13:01 #8 Rev.: 4684

Fixed ill-formatted code.

6 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_helix.h (+6 -3)

westram 2007-07-02 11:41 #7 Rev.: 4683

- skip: TAGS, GDE/CORE/functions.h, PERL2ARB/perlmain.c, PERL2ARB/Makefile.PL
- added: PERL2ARB/Makefile.main

5 lines of code changed in 1 file:

• util: arb_srclst.pl (+5)

westram 2007-07-01 01:11 #6 Rev.: 4682

- depends updated

14 lines of code changed in 1 file:

• NTREE: Makefile (+14)

westram 2007-07-01 01:10 #5 Rev.: 4681

- updated

4 lines of code changed in 1 file:

• NTREE: nt_internal.h (+4)

westram 2007-07-01 01:10 #4 Rev.: 4680

- proto depends on arb_replace (in TOOLS)

1 lines of code changed in 1 file:

• Makefile (+1 -1)

westram 2007-07-01 01:09 #3 Rev.: 4679

- ignore Makefile.PL

1 lines of code changed in 1 file:

• PERL2ARB: .cvsignore (+1)

westram 2007-07-01 00:57 #2 Rev.: 4678

- missing \

1 lines of code changed in 1 file:

• PROBE_DESIGN: probe_design.cxx (+1 -1)

westram 2007-07-01 00:57 #1 Rev.: 4677

- removed generated file

0 lines of code changed in 1 file:

• PERL2ARB: Makefile.PL (del)

June 2007 »