March 2005 Commit Log

Number of Commits:
123
Number of Active Developers:
2
westram 2005-03-31 15:29 Rev.: 3777

- prepared for RAxML

1 lines of code changed in 1 file:

westram 2005-03-30 10:31 Rev.: 3776

- removed

0 lines of code changed in 1 file:

westram 2005-03-30 10:31 Rev.: 3775

- removed GEN_read.o

0 lines of code changed in 1 file:

westram 2005-03-30 10:31 Rev.: 3774

- removed old import functions

0 lines of code changed in 1 file:

westram 2005-03-30 10:31 Rev.: 3773

- activated ARTEMs genome flatfile importer - removed old import code

1 lines of code changed in 3 files:

westram 2005-03-18 15:28 Rev.: 3772

- fix for feature names (may also contain non-identifier characters)

8 lines of code changed in 2 files:

westram 2005-03-17 16:29 Rev.: 3771

- new version; runs after embl_gen_long_features.pl; will be modified by WL

356 lines of code changed in 1 file:

westram 2005-03-17 16:29 Rev.: 3770

- old version of ebi.ift

3 lines of code changed in 1 file:

westram 2005-03-17 16:29 Rev.: 3769

- prefilter input through embl_gen_long_features.pl and pass to nonformats/longebi.ift

4 lines of code changed in 2 files:

westram 2005-03-17 16:28 Rev.: 3768

- perl script to change embl feature table for more simple
ift-parsing

67 lines of code changed in 2 files:

westram 2005-03-17 13:23 Rev.: 3767

- replaced 'char error[]' by 'char *error'

16 lines of code changed in 2 files:

westram 2005-03-17 13:23 Rev.: 3766

- fixed IS_NUCLEOTIDE/IS_AMINO occurrances
- DNA alignment uses T in consensus

10 lines of code changed in 1 file:

westram 2005-03-17 13:23 Rev.: 3765

- fixed IS_NUCLEOTIDE/IS_AMINO occurrances

2 lines of code changed in 1 file:

westram 2005-03-17 13:23 Rev.: 3764

- minor bugfix (allocated 1 byte too much)
- added some asserts to resolve_pointer_to_char_pntr (something goes wrong with length reported by database)

36 lines of code changed in 1 file:

westram 2005-03-17 13:22 Rev.: 3763

- changed alignment detection macros

7 lines of code changed in 1 file:

westram 2005-03-17 13:22 Rev.: 3762

- detected unfixed error in database - added assertion to be able to fix it

18 lines of code changed in 1 file:

westram 2005-03-17 09:15 Rev.: 3761

- dependencies updated

19 lines of code changed in 6 files:

westram 2005-03-17 09:14 Rev.: 3760

- prototypes updated

2 lines of code changed in 2 files:

westram 2005-03-17 09:14 Rev.: 3759

- added 'Quit & Start'

19 lines of code changed in 1 file:

westram 2005-03-17 09:14 Rev.: 3758

- some code cleanup in MG_equal_alignments
- case-insensitive compare of alignment names in MG_equal_alignments

72 lines of code changed in 1 file:

westram 2005-03-17 09:12 Rev.: 3757

- include arbdbt.h

1 lines of code changed in 1 file:

westram 2005-03-17 09:12 Rev.: 3756

- GBT_rename_alignment:
. rewrote
. comprehensive error messages
- added gbt_nonexisting_alignment()

131 lines of code changed in 1 file:

westram 2005-03-17 09:11 Rev.: 3755

- added gbs_stricmp()

13 lines of code changed in 1 file:

westram 2005-03-17 09:10 Rev.: 3754

- removed old code

0 lines of code changed in 1 file:

westram 2005-03-17 09:10 Rev.: 3753

- calc_cursor_position -> pixel2pos

1 lines of code changed in 1 file:

westram 2005-03-17 09:09 Rev.: 3752

- warning fix

1 lines of code changed in 1 file:

westram 2005-03-17 09:09 Rev.: 3751

- added ED4_root::pixel2pos() (replacement for calc_cursor_position)

12 lines of code changed in 1 file:

westram 2005-03-17 09:09 Rev.: 3750

- changed call to show_clicked_cursor()

1 lines of code changed in 1 file:

westram 2005-03-17 09:09 Rev.: 3749

- added ED4_cursor::show_cursor_at()
- re-implemented show_clicked_cursor() using show_cursor_at()
- move_cursor() uses show_cursor_at() instead of show_clicked_cursor()
- removed calc_cursor_position()
- jump_centered_cursor_to_seq_pos() respects edit direction

36 lines of code changed in 1 file:

westram 2005-03-17 09:09 Rev.: 3748

- added ED4_root::pixel2pos()
- added ED4_cursor::show_cursor_at()
- don't pass terminal to draw_cursor()

9 lines of code changed in 1 file:

westram 2005-03-17 09:07 Rev.: 3747

- set-cursor always set wrong position

2 lines of code changed in 1 file:

yadhu 2005-03-16 18:30 Rev.: 3746

Changes to RNA3D Module:
Feature to shift the "Molecule View" by pressing arrow keys(left/right/up/down) has been added.

49 lines of code changed in 4 files:

westram 2005-03-16 12:35 Rev.: 3745

- changed answers in 'Generate new names' prompt

1 lines of code changed in 1 file:

westram 2005-03-16 12:29 Rev.: 3744

- shows globals in all libs

14 lines of code changed in 1 file:

westram 2005-03-16 12:26 Rev.: 3743

- alpha_Size_Supported -> AW_alpha_Size_Supported
- untabified

81 lines of code changed in 1 file:

westram 2005-03-16 12:26 Rev.: 3742

- declare 'AW_alpha_Size_Supported' in header

5 lines of code changed in 1 file:

westram 2005-03-16 12:25 Rev.: 3741

- fixed error messages in detect_bitmap_size()

15 lines of code changed in 1 file:

westram 2005-03-16 12:24 Rev.: 3740

- removed globals (ApplicationBGColor + G)
- changed name of global instance of RNA3D_Global
- removed extern declarations

17 lines of code changed in 1 file:

westram 2005-03-16 12:23 Rev.: 3739

- fixes for new member ApplicationBGColor
- changed name of global instance of RNA3D_Global

9 lines of code changed in 1 file:

westram 2005-03-16 12:22 Rev.: 3738

- made module-globals static
- changed name of global instance of RNA3D_Global
- call RNA3D_init_global_data()

56 lines of code changed in 1 file:

westram 2005-03-16 12:20 Rev.: 3737

- changed name of global instance of RNA3D_Global

1 lines of code changed in 1 file:

westram 2005-03-16 12:20 Rev.: 3736

- made GRAPHICS member of Structure3D
- collected module-globals at top, made them static
- changed name of global instance of RNA3D_Global
- removed extern declarations

49 lines of code changed in 1 file:

westram 2005-03-16 12:18 Rev.: 3735

- removed extern declarations

0 lines of code changed in 2 files:

westram 2005-03-16 12:17 Rev.: 3734

- made several variables const or static
- moved ctor/dtor of RNA3D_Global here
- untabified
- changed name of global instance of RNA3D_Global

169 lines of code changed in 1 file:

westram 2005-03-16 12:14 Rev.: 3733

- added GRAPHICS to Structure3D (not really a good place)

3 lines of code changed in 1 file:

westram 2005-03-16 12:14 Rev.: 3732

- made G member of GLRenderer
- pass Structure3D to TexturizeStructure

4 lines of code changed in 1 file:

westram 2005-03-16 12:14 Rev.: 3731

- made ApplicationBGColor member of OpenGLGraphics

3 lines of code changed in 1 file:

westram 2005-03-16 12:14 Rev.: 3730

- added rest of globals
- removed inlined code
- declare globals

19 lines of code changed in 1 file:

yadhu 2005-03-15 17:58 Rev.: 3729

Changes to RNA3D Module:
1.Feature to rotate molecule by pressing arrow keys(left/right/up/down) has been added.
2.Replaced extern variable declaration to Global Class members.

221 lines of code changed in 8 files:

westram 2005-03-15 10:08 Rev.: 3728

- fixed SIGSEGV

9 lines of code changed in 1 file:

westram 2005-03-11 19:21 Rev.: 3727

- disabled font debugs - finally its working! :-)

2 lines of code changed in 1 file:

westram 2005-03-11 19:14 Rev.: 3726

- added 3 directories to generate

4 lines of code changed in 1 file:

westram 2005-03-11 19:14 Rev.: 3725

- fixed todays date generation

1 lines of code changed in 1 file:

westram 2005-03-11 19:13 Rev.: 3724

- removed ldd calls

2 lines of code changed in 1 file:

yadhu 2005-03-11 18:57 Rev.: 3723

Changes to RNA3D Module:
1.Feature to display Insertions in the Mapped 3D structure has been added.
2.Updated images and xfigs.

229 lines of code changed in 13 files:

westram 2005-03-11 14:11 Rev.: 3722

DEBIAN OPENGL patch

4 lines of code changed in 1 file:

westram 2005-03-11 13:46 Rev.: 3721

- use tar instead of cpio|gzip-queue, because many file dates
where reset to 197x - looks like a Y2K bug
- exclude directories from file list
- exclude .cvsignore + ChangeLog

6 lines of code changed in 1 file:

westram 2005-03-11 12:10 Rev.: 3720

file has been added to release tree in 2001, but never was added to cvs

2 lines of code changed in 1 file:

westram 2005-03-10 19:21 Rev.: 3719

- valgrind fixes_

7 lines of code changed in 2 files:

westram 2005-03-10 19:21 Rev.: 3718

* adstring.c: - GBS_chrcat uses gbs_strensure_mem
- assertion

3 lines of code changed in 1 file:

westram 2005-03-10 12:50 Rev.: 3717

- activated font debug output

8 lines of code changed in 1 file:

westram 2005-03-10 12:40 Rev.: 3716

- crash fix

4 lines of code changed in 1 file:

westram 2005-03-10 12:22 Rev.: 3715

- lookfont now able to query only (instead of always loading the font)

97 lines of code changed in 1 file:

westram 2005-03-09 16:06 Rev.: 3714

- warning fix

22 lines of code changed in 3 files:

westram 2005-03-09 16:06 Rev.: 3713

- warning fix
- fixed broken if-clause (was only working in DEBUG mode)

12 lines of code changed in 1 file:

westram 2005-03-09 16:05 Rev.: 3712

- gcc 2.95 fixes

48 lines of code changed in 1 file:

yadhu 2005-03-09 13:58 Rev.: 3711

Changes to RNA3D Module:
1. Fixed Missing Red Channel when queried from OpenGL WIndow.
2. Fixed Text Rasterization on systems running ATI graphics card.
3. Added RGBA size initialization during OpenGL specific window creation (AW_window.cxx)

148 lines of code changed in 8 files:

westram 2005-03-08 20:26 Rev.: 3710

- updated

4 lines of code changed in 2 files:

westram 2005-03-08 20:26 Rev.: 3709

- comment

1 lines of code changed in 1 file:

westram 2005-03-08 20:26 Rev.: 3708

- added AWAR_ERROR_CONTAINER

2 lines of code changed in 1 file:

westram 2005-03-08 20:26 Rev.: 3707

- cosmetics

2 lines of code changed in 1 file:

westram 2005-03-08 20:25 Rev.: 3706

- removed NT_show_message()

1 lines of code changed in 2 files:

westram 2005-03-08 20:24 Rev.: 3705

- removed NT_show_message() - now handled by ARBDB (see GBT_install_message_handler)

0 lines of code changed in 1 file:

westram 2005-03-08 20:24 Rev.: 3704

- include nt_cb.hxx - because it contains some prototypes for functions from here

1 lines of code changed in 1 file:

westram 2005-03-08 20:06 Rev.: 3703

- GBT_check_alignment:
. better error handling, meaningful messages
. invisible from perl
. new parameter 'species_name_hash'
. if 'data' is missing -> fill with error message, raise error message, but continue
. better error message, if 'data' has wrong DB-type
- GBT_check_data warns if a species has no data in any alignment
- added GBT_install_message_handler()
needed because GBT_message was sometimes silenly swallowed
- rewrote GBT_message (now uses single DB entries for each message)

277 lines of code changed in 1 file:

westram 2005-03-08 20:03 Rev.: 3702

- GBS_create_hash: upper_case -> ignore_case (naming only)

6 lines of code changed in 1 file:

westram 2005-03-08 20:02 Rev.: 3701

- GB_login installs message handler in server

5 lines of code changed in 1 file:

westram 2005-03-08 20:01 Rev.: 3700

- comment

1 lines of code changed in 1 file:

westram 2005-03-08 20:01 Rev.: 3699

- changed location of AWAR_ERROR_MESSAGES

3 lines of code changed in 1 file:

westram 2005-03-08 20:00 Rev.: 3698

- changed location of AW_MESSAGE_AWAR
- changed some functions names

9 lines of code changed in 1 file:

westram 2005-03-08 19:59 Rev.: 3697

- fixed bug in AW_device_Xm::box causing BIG mark-boxes in ARB_NTREE

2 lines of code changed in 1 file:

westram 2005-03-08 19:58 Rev.: 3696

- IRS tree always uses tree_name for NDS at root level

6 lines of code changed in 1 file:

westram 2005-03-08 16:44 Rev.: 3695

- GEN_is_organism now returns true, if GENOM_ALIGNMENT exists

7 lines of code changed in 1 file:

westram 2005-03-08 16:44 Rev.: 3694

- NT_fix_empty_gene_data -> NT_fix_gene_data (re-creates needed gene_data containers)
- changed name of check-routine (forces new check for each DB)
- error if non-organism has non-empty gene_data

31 lines of code changed in 1 file:

westram 2005-03-05 21:27 Rev.: 3693

- devides between consensus-relevant and consensus-irrelevant "sequence"-entries

20 lines of code changed in 1 file:

westram 2005-03-05 21:27 Rev.: 3692

- fixed calls to AW_device::clear/clear_part
- cleanups

31 lines of code changed in 1 file:

westram 2005-03-05 21:27 Rev.: 3691

- fixed calls to AW_device::clear/clear_part
- cleanup
- allow top/bottom font overlap on all terminals
- use SEQ_TERM_TEXT_YOFFSET / INFO_TERM_TEXT_YOFFSET

92 lines of code changed in 1 file:

westram 2005-03-05 21:27 Rev.: 3690

- ED4_spacer_terminal gets drawn as well, to reduce text clipping
problems between top and middle area
- cleanup
- rewrote ED4_line_terminal::draw
- some optimizations using result of reduceClipBorders/adjust_clipping_rectangle

47 lines of code changed in 1 file:

westram 2005-03-05 21:27 Rev.: 3689

- store pointer to top_mid_spacer/line_terminal into main_manager for direct access
- Helix changes cause ED4_expose_cb
- added ED4_root::recalc_font_group()

23 lines of code changed in 1 file:

westram 2005-03-05 21:26 Rev.: 3688

- use info font height to calculate global TERMINALHEIGHT
- input fields for AWAR_EDIT_..._SPACING
- dynamically set top_middle_spacer height

64 lines of code changed in 1 file:

westram 2005-03-05 21:26 Rev.: 3687

- to avoid text-clipping problems between top and middle area, the
top-middle-spacer gets redrawn with increased clipping area after
everything has been updated
- changed method to detect whether a managers child shall be drawn.
Childs were not drawn, if only 1 pixel of child overlapped with
clipping area, thus causing empty lines during scrolling
- dont recalculate font-limits in ED4_main_manager::Show (done by callers now)
- use return value of reduceClipBorders/adjust_clipping_rectangle to avoid unnecessary drawing
- always redraw visible cursor at end of Show

42 lines of code changed in 1 file:

westram 2005-03-05 21:26 Rev.: 3686

- callback redraws cursor on direction change
- define AWAR_EDIT_..._SPACING + bind them to ED4_root members + callback
- added 2 globals (..._TERM_TEXT_YOFFSET) for drawing
- first init helix, then create editor window

19 lines of code changed in 1 file:

westram 2005-03-05 21:26 Rev.: 3685

- fixed calls to AW_device::clear/clear_part
- use return value of reduceClipBorders to avoid unnecessary drawing
- force redraw when redrawing area where cursor moved away
- changed cursor shape of ED4_TRADITIONAL_CURSOR
- added more cursor types
- cursor reflects editing direction
- CursorShape is position independent now, instead draw() and get_bounding_box() get a position
- renamed CursorShape -> ED4_CursorShape (CursorShape is defined elsewhere)
- renamed ED4_cursor::abs_x to cursor_abs_x
- renamed is_visible() to is_partly_visible()

150 lines of code changed in 1 file:

westram 2005-03-05 21:26 Rev.: 3684

- changed ED4_base::is_visible (case ED4_D_ALL_DIRECTION)
- added 2nd flavour of is_visible() to ED4_base
- when a sequence was deleted by database, it's data wasn't removed from consensus tables
- get_consensus_relevant_terminal() checks for uniqueness (only 1 terminal allowed to be consensus relevant)
- fixed calls to AW_device::clear/clear_part
- adjust_clipping_rectangle returns 0 if no clipping area is left
- use return value of adjust_clipping_rectangle to avoid unnecessary drawing

102 lines of code changed in 1 file:

westram 2005-03-05 21:25 Rev.: 3683

- reformatted

168 lines of code changed in 1 file:

westram 2005-03-05 21:25 Rev.: 3682

- added more cursor types
- added ED4_Cursor::redraw()
- added 2nd flavour of is_visible() to ED4_base
- added new members to ED4_root: helix_add_spacing + terminal_add_spacing

61 lines of code changed in 1 file:

westram 2005-03-05 21:25 Rev.: 3681

- added new property flag ED4_P_ALIGNMENT_DATA
- added/changed AWAR_EDIT_..._SPACING

22 lines of code changed in 1 file:

westram 2005-03-05 20:45 Rev.: 3680

- GBT_check_alignment counted length of secondary structure description
while testing alignment length
- if a SAI is not aligned -> count all sequences as not aligned

9 lines of code changed in 1 file:

westram 2005-03-05 00:39 Rev.: 3679

*** empty log message ***

3 lines of code changed in 1 file:

westram 2005-03-05 00:38 Rev.: 3678

- standart->standard

3 lines of code changed in 1 file:

westram 2005-03-05 00:37 Rev.: 3677

- standart->standard
- added HELIX_AWAR_ENABLE

11 lines of code changed in 1 file:

westram 2005-03-05 00:37 Rev.: 3676

- added enabled-flag to AW_helix (toggle by switch in config-window)

4 lines of code changed in 1 file:

westram 2005-03-05 00:37 Rev.: 3675

- standart->standard
- added global enable toggle for helix display
- use autosize button for default entries

29 lines of code changed in 1 file:

westram 2005-03-05 00:34 Rev.: 3674

- updated

4 lines of code changed in 3 files:

westram 2005-03-05 00:34 Rev.: 3673

- added -g3

1 lines of code changed in 1 file:

westram 2005-03-05 00:34 Rev.: 3672

- remove 'name width' (wasn't used)
- spelling

36 lines of code changed in 1 file:

westram 2005-03-05 00:33 Rev.: 3671

- fixed calls to AW_device::clear/clear_part

31 lines of code changed in 6 files:

westram 2005-03-05 00:33 Rev.: 3670

- fixed calls to AW_device::clear/clear_part
- displayed garbage if scrolling rightwards behind sequence end

23 lines of code changed in 1 file:

westram 2005-03-05 00:33 Rev.: 3669

- rewritten

64 lines of code changed in 2 files:

westram 2005-03-05 00:14 Rev.: 3668

- fixed calls to AW_device::clear/clear_part

5 lines of code changed in 2 files:

westram 2005-03-05 00:14 Rev.: 3667

- changed prototypes of AW_device::clear/clear_part

2 lines of code changed in 1 file:

westram 2005-03-05 00:13 Rev.: 3666

- removed biwidth font
- changed prototypes of AW_device::clear and ::clear_part

6 lines of code changed in 1 file:

westram 2005-03-05 00:13 Rev.: 3665

- removed biwidth font
- replaced macro-shit by inline functions
- again using CI_GetRowzeroCharInfo_2D() for ISO10646 fonts

92 lines of code changed in 1 file:

westram 2005-03-05 00:13 Rev.: 3664

- debugging code to dump changes to cliping area
- changed AW_device::clear and ::clear_part
- reduceClipBorders returns 0 if everything is clipped away
- rewrote box_clip()

32 lines of code changed in 1 file:

westram 2005-03-05 00:13 Rev.: 3663

- rewrote AW_device_Xm::clear_part
- AUTO_FLUSH skipped if no draw command has been called
- AW_device_Xm::clear respects filter
- ::box and ::clear_part draw 1 pixel too much in both directions
- ::clear_part rewritten (uses box_clip())

31 lines of code changed in 1 file:

westram 2005-03-04 11:23 Rev.: 3662

- again OPENGL header issues (testing)

6 lines of code changed in 3 files:

westram 2005-03-04 11:23 Rev.: 3661

- debugging code to dump changes to cliping area

41 lines of code changed in 1 file:

westram 2005-03-03 13:18 Rev.: 3660

- only if OPENGL

3 lines of code changed in 1 file:

westram 2005-03-03 13:14 Rev.: 3659

- use way #3

1 lines of code changed in 1 file:

yadhu 2005-03-02 17:23 Rev.: 3658

Changes to RNA3D Module:
1. Coments on Include Files.
2. Fixed Unnecessary calls to Mapping Species.
3. Enhanced display with depth buffer.

79 lines of code changed in 6 files:

yadhu 2005-03-02 17:20 Rev.: 3657

OpenGL Window Creation: Enabled depth buffer and stensil buffer for OpenGL Rendering.

2 lines of code changed in 1 file:

westram 2005-03-02 13:25 Rev.: 3656

- crash, if ECOLI does not contain data for loaded alignment
- changed gbAliName to ali_name, since variable names with
prefix 'gb' should be restricted to type GBDATA*
- commented out some unused variables

42 lines of code changed in 1 file:

westram 2005-03-02 11:50 Rev.: 3655

- added 3 different ways to include GL headers - @yadhu: please test them

36 lines of code changed in 1 file:

February 2005 »

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