March 2007 Commit Log

Number of Commits:
127
Number of Active Developers:
3
westram 2007-03-29 20:24 Rev.: 4457

- added missing -fstart

2 lines of code changed in 1 file:

westram 2007-03-29 19:42 Rev.: 4456

- removed -x

1 lines of code changed in 1 file:

westram 2007-03-29 19:41 Rev.: 4455

- removed evil trailing space

3 lines of code changed in 1 file:

westram 2007-03-29 19:37 Rev.: 4454

- skip arbsrc.lst.tmp
- skip arb_build.h

3 lines of code changed in 1 file:

westram 2007-03-29 19:37 Rev.: 4453

- reports errors by exitcode (to make make fail)

11 lines of code changed in 1 file:

westram 2007-03-29 19:13 Rev.: 4452

- dump PATH and ARBHOME when building release

3 lines of code changed in 1 file:

westram 2007-03-29 18:30 Rev.: 4451

- reduced height of mode help-line in top-area

7 lines of code changed in 1 file:

westram 2007-03-29 17:55 Rev.: 4450

- removed transparency, less height

227 lines of code changed in 2 files:

westram 2007-03-29 17:55 Rev.: 4449

- less height

36 lines of code changed in 2 files:

westram 2007-03-29 17:55 Rev.: 4448

- 3<->5 toggle (was 5to3.xpm before)

9 lines of code changed in 1 file:

westram 2007-03-29 17:55 Rev.: 4447

- 3<->5 toggle (was 3to5.xpm before)

9 lines of code changed in 1 file:

westram 2007-03-29 17:55 Rev.: 4446

- undo icon (was undo.xpm before)

7 lines of code changed in 1 file:

westram 2007-03-29 17:55 Rev.: 4445

- redo icon (was redo.xpm before)

7 lines of code changed in 1 file:

westram 2007-03-29 17:55 Rev.: 4444

- tree view icon (was radial.xpm before)

8 lines of code changed in 1 file:

westram 2007-03-29 17:55 Rev.: 4443

- removed smooting with grey (doesn't work with non-default background color)

67 lines of code changed in 1 file:

westram 2007-03-29 17:55 Rev.: 4442

- more/less-toggle (was more.xpm before)

6 lines of code changed in 1 file:

westram 2007-03-29 17:55 Rev.: 4441

- new icon for list display mode

9 lines of code changed in 1 file:

westram 2007-03-29 17:54 Rev.: 4440

- more/less-toggle (was less.xpm before)

6 lines of code changed in 1 file:

westram 2007-03-29 17:54 Rev.: 4439

- new icon for genome map

138 lines of code changed in 1 file:

westram 2007-03-29 17:54 Rev.: 4438

- removed transparency

30 lines of code changed in 1 file:

westram 2007-03-29 17:54 Rev.: 4437

- tree view icon (was dendroIrs.xpm before)

9 lines of code changed in 1 file:

westram 2007-03-29 17:54 Rev.: 4436

- tree view icon (was dendro.xpm before)

9 lines of code changed in 1 file:

westram 2007-03-29 17:54 Rev.: 4435

- some positions fixes

72 lines of code changed in 1 file:

westram 2007-03-29 17:54 Rev.: 4434

- relayout

99 lines of code changed in 1 file:

westram 2007-03-29 17:54 Rev.: 4433

- renamed $filter -> $seqfilter

2 lines of code changed in 1 file:

westram 2007-03-29 17:54 Rev.: 4432

- XFIG_DEFAULT_FONT_SIZE -> XFIG_DEFAULT_FONT_WIDTH / XFIG_DEFAULT_FONT_HEIGHT
- added private ctor-helper calc_scaling
- changed ctor-prototypes of AW_xfig

15 lines of code changed in 1 file:

westram 2007-03-29 17:53 Rev.: 4431

- added get_at_xposition / get_at_yposition
- added/changed create_text_toggle / create_toggle
- added private helper function create_toggle

10 lines of code changed in 1 file:

westram 2007-03-29 17:53 Rev.: 4430

- changed prototype of aw_create_selection_box_awars

4 lines of code changed in 1 file:

westram 2007-03-29 17:53 Rev.: 4429

- renamed tmp awar for species button

1 lines of code changed in 1 file:

westram 2007-03-29 17:53 Rev.: 4428

- changed call of AW_xfig

4 lines of code changed in 1 file:

westram 2007-03-29 17:53 Rev.: 4427

- use both font dimensions to calculate scaling factor
- added function calc_scaling() and removed dup-code

31 lines of code changed in 1 file:

westram 2007-03-29 17:53 Rev.: 4426

- force reset of vectorfont-selection-box awars
- cosmetics

10 lines of code changed in 1 file:

westram 2007-03-29 17:53 Rev.: 4425

- aw_create_selection_box_awars:
. new parameter resetValues, to force reset of awars
. if directory was stored in properties -> auto-reset if it
does not exist
. DEBUG code: warn about saving $ARBHOME-relative directories

48 lines of code changed in 1 file:

westram 2007-03-29 17:53 Rev.: 4424

- rewrote parts of create_button:
. more obvious test, whether button size is caused by xfig,
by button_length() or autodetected.
. graphical buttons w/o callback (aka labels) use less space
. mheight is calculated now as well (and passed to Motif)
- added create_text_toggle()
- new parameter buttonWidth for toggles
- fixed width calculation of input_fields

151 lines of code changed in 1 file:

westram 2007-03-29 17:53 Rev.: 4423

- added get_at_xposition / get_at_yposition
- use defines XFIG_DEFAULT_FONT_WIDTH / XFIG_DEFAULT_FONT_HEIGHT

7 lines of code changed in 1 file:

westram 2007-03-29 17:53 Rev.: 4422

- redesigned top-area
. more compact layout
. moved list-mode back to tree-display modes
. marked-species button calls 'Species/Configurations'

141 lines of code changed in 1 file:

westram 2007-03-29 17:53 Rev.: 4421

- force reinit of ED4_AWAR_NDS_ECOLI_NAME

1 lines of code changed in 1 file:

westram 2007-03-29 17:53 Rev.: 4420

- call AW_init_color_group_defaults only for first window
- redesigned top-area
. more compact layout
. added aligner button
. buttons work with changed frame color (e.g. with dark color)
- 'Ecoli' in top area uses ED4_AWAR_NDS_ECOLI_NAME

138 lines of code changed in 1 file:

westram 2007-03-29 17:53 Rev.: 4419

- changed default for ED4_AWAR_NDS_ECOLI_NAME

1 lines of code changed in 1 file:

westram 2007-03-29 17:53 Rev.: 4418

- force reset of eft-selection-box awars.
It was possible, that they pointed to an old or non-existing
directory - in the latter case no efts were selectable
- replaced at-pos $filter by $seqfilter (clashed with selection box)

2 lines of code changed in 1 file:

westram 2007-03-29 17:53 Rev.: 4417

- reverted search button to text

3 lines of code changed in 1 file:

westram 2007-03-29 17:53 Rev.: 4416

- use PATH_MAX instead of FILENAME_MAX

2 lines of code changed in 1 file:

westram 2007-03-21 01:08 Rev.: 4415

- removed 'AW_window::' prefix

1 lines of code changed in 1 file:

westram 2007-03-21 01:03 Rev.: 4414

*** empty log message ***

3 lines of code changed in 1 file:

westram 2007-03-21 01:02 Rev.: 4413

- added missing swap template for gcc 2.95.3 or below

5 lines of code changed in 1 file:

westram 2007-03-21 01:02 Rev.: 4412

- C variable fix

4 lines of code changed in 1 file:

westram 2007-03-21 01:02 Rev.: 4411

- gcc 2.95.3 needs memory.h for memcpy

4 lines of code changed in 1 file:

westram 2007-03-21 01:02 Rev.: 4410

- C variable fixes

32 lines of code changed in 1 file:

westram 2007-03-20 13:58 Rev.: 4409

- depends updated

4 lines of code changed in 2 files:

westram 2007-03-20 13:57 Rev.: 4408

- crashed when using an non-string add.field for name-generation

8 lines of code changed in 1 file:

westram 2007-03-20 13:57 Rev.: 4407

- defines ARB_VERSION from build info

46 lines of code changed in 1 file:

westram 2007-03-20 13:57 Rev.: 4406

- create arb_build.h

12 lines of code changed in 1 file:

westram 2007-03-20 13:57 Rev.: 4405

- added arb_build.h

1 lines of code changed in 1 file:

westram 2007-03-20 13:57 Rev.: 4404

- link arb_version.h and arb_build.h

2 lines of code changed in 1 file:

westram 2007-03-20 13:57 Rev.: 4403

- use ARB_VERSION
- eventually show build information with command line help

6 lines of code changed in 1 file:

westram 2007-03-20 13:57 Rev.: 4402

- use ARB_VERSION
- eventually put build information into support mails

6 lines of code changed in 1 file:

westram 2007-03-20 13:56 Rev.: 4401

- removed nt_date.h generation

6 lines of code changed in 1 file:

westram 2007-03-20 13:56 Rev.: 4400

- use ARB_VERSION

2 lines of code changed in 1 file:

westram 2007-03-20 13:56 Rev.: 4399

- call Makefile in TEMPLATES (generates ARB_VERSION)

2 lines of code changed in 1 file:

westram 2007-03-20 13:11 Rev.: 4398

- as long as possible use wanted modification direction

2 lines of code changed in 1 file:

westram 2007-03-20 12:57 Rev.: 4397

- removed TuneBackground(..,0) calls
- rewrote TuneBackground, now change only brightness, not color
- added TuneOrSetBackground (supports special 'colors' "+" and "-")
- moved AW_window::set_background from AW_at.cxx.
Instantly allocates color and stores X11-Pixel
- removed duplicated color allocation code (now done in set_background)

143 lines of code changed in 1 file:

westram 2007-03-20 12:57 Rev.: 4396

- removed button color code for closed radio button (only
working together with label)
- fixed button color for opened radio button
- code for special button 'colors' "+" and "-" moved to TuneOrSetBackground
- removed duplicated color allocation code (now done in set_background)

48 lines of code changed in 1 file:

westram 2007-03-20 12:56 Rev.: 4395

- removed several unneeded calls to set_background
- fixed memleak

6 lines of code changed in 1 file:

westram 2007-03-20 12:56 Rev.: 4394

- added TuneOrSetBackground
- added TUNE_INPUT (for input fields and selection lists)
- set_background now private

17 lines of code changed in 1 file:

westram 2007-03-20 12:56 Rev.: 4393

- AW_at does no longer store the background color NAME, but the X11-Pixel itself

2 lines of code changed in 1 file:

westram 2007-03-20 12:56 Rev.: 4392

- AW_at does no longer store the background color NAME, but the X11-Pixel itself
- replaced several deletes by free

12 lines of code changed in 1 file:

westram 2007-03-20 12:56 Rev.: 4391

- instead of using set_background, pass color to button

1 lines of code changed in 1 file:

westram 2007-03-20 12:55 Rev.: 4390

- added $help

12 lines of code changed in 1 file:

westram 2007-03-20 12:55 Rev.: 4389

*** empty log message ***

5 lines of code changed in 1 file:

westram 2007-03-20 12:55 Rev.: 4388

- added HELP to REORDER FIELDS window

4 lines of code changed in 1 file:

yadhu 2007-03-15 16:17 Rev.: 4387

Added warnings for testing!

2 lines of code changed in 1 file:

yadhu 2007-03-15 16:10 Rev.: 4386

Added warnings for testing!

6 lines of code changed in 1 file:

yadhu 2007-03-15 16:04 Rev.: 4385

Changes to Background Color Tuning!
Increased the color modification to 50. Now works with the darker and lighter background as well.
Changed the 3-5' button.

157 lines of code changed in 6 files:

westram 2007-03-13 20:16 Rev.: 4384

- added 'Mark' button

38 lines of code changed in 1 file:

westram 2007-03-13 20:16 Rev.: 4383

- help for mark matching

6 lines of code changed in 1 file:

westram 2007-03-13 20:16 Rev.: 4382

- added ED4_mark_matching_species() + button in all search windows

41 lines of code changed in 1 file:

westram 2007-03-13 17:57 Rev.: 4381

- inserted include wrapper, header
- beautified

36 lines of code changed in 1 file:

westram 2007-03-13 17:48 Rev.: 4380

- untabified, removed some dead code

73 lines of code changed in 1 file:

westram 2007-03-13 17:40 Rev.: 4379

- changed T-as-U-label

1 lines of code changed in 1 file:

westram 2007-03-13 17:40 Rev.: 4378

- non-exact search for complement failed whenever reverse was marked
- when "T matches U" was checked, DNA search reported T as mismatch
to A for complement searches
- allow up to 33% of mismatches (was 25%) relative to pattern length.
This slows down search a bit.
- cosmetics

46 lines of code changed in 1 file:

westram 2007-03-13 15:38 Rev.: 4377

- cleanup

1 lines of code changed in 1 file:

westram 2007-03-13 15:37 Rev.: 4376

- wrong assertion in NT_fix_gene_data()

1 lines of code changed in 1 file:

westram 2007-03-13 15:36 Rev.: 4375

- fixed warning in ValidSearchColor
- made function static and non-class

10 lines of code changed in 2 files:

westram 2007-03-09 21:40 Rev.: 4374

*** empty log message ***

3 lines of code changed in 1 file:

westram 2007-03-09 21:32 Rev.: 4373

*** empty log message ***

3 lines of code changed in 2 files:

westram 2007-03-09 21:32 Rev.: 4372

- workaround for multiple equal-named sourcefiles

154 lines of code changed in 1 file:

westram 2007-03-09 21:32 Rev.: 4371

- added add. nameserver field

20 lines of code changed in 1 file:

westram 2007-03-09 21:31 Rev.: 4370

- added new nameserver for additional field 'start'

11 lines of code changed in 1 file:

westram 2007-03-09 21:31 Rev.: 4369

- removed NAMES_FILE_LOCATION (now we got multiple nameservers)
- added AWAR_NAMESERVER_ADDID
- added prototypes for new functions

12 lines of code changed in 1 file:

westram 2007-03-09 21:31 Rev.: 4368

- added AW_get_nameserver_addid (reads used add. field from current DB)
- when establishing a nameserver connection, test field used by DB
matches field used by server. Enforce reconnect on mismatch.
- changed AWTC_generate_one_name to use add. field

115 lines of code changed in 1 file:

westram 2007-03-09 21:31 Rev.: 4367

- added namesFilename(): give the name of the current names.dat
- use namesFilename
- config field for additional nameserver field.
On change -> instantly test nameserver

51 lines of code changed in 1 file:

westram 2007-03-09 21:31 Rev.: 4366

- added field to arb_params

2 lines of code changed in 1 file:

westram 2007-03-09 21:31 Rev.: 4365

- when starting servers pass more than one parameter from arb_tcp.dat
- arb_look_and_start_server uses GBS_scan_arb_tcp_param()
- added arb_print_server_params() - shows general server
parameters for command line
- added general switch -f (used to pass the name of a database field)

127 lines of code changed in 1 file:

westram 2007-03-09 21:31 Rev.: 4364

- use GBS_scan_arb_tcp_param()

8 lines of code changed in 1 file:

westram 2007-03-09 21:30 Rev.: 4363

- create AWARs for names admin
- changed name and interface of names admin

3 lines of code changed in 1 file:

westram 2007-03-09 21:30 Rev.: 4362

- changed concatenateFieldsCreateNewSpecies() to use
add.field with nameserver

76 lines of code changed in 1 file:

westram 2007-03-09 21:30 Rev.: 4361

- added 'add_id' to AN_LOCAL, AN_SHORTS and AN_REVERS
- added 'add_field' to AN_MAIN

24 lines of code changed in 1 file:

westram 2007-03-09 21:30 Rev.: 4360

dead code removed

0 lines of code changed in 2 files:

westram 2007-03-09 21:30 Rev.: 4359

- raised SERVER_VERSION to 4
- use additional fields value
- added case check for additional field
- reforce case-error checks for all versions < 4
- command line help
- show timeout message only if a timeout occurred
- added new AISC method 'get_field' (ask nameserver which add. field it uses)
- when the nameserver is started up on the newly copied names.dat-template,
it stores the name of the field passed as parameter in it's database.
On further startups it checks whether field stored in DB and field passed
by param match -> otherwise error.

107 lines of code changed in 1 file:

westram 2007-03-09 21:30 Rev.: 4358

- help for names admin window

76 lines of code changed in 1 file:

westram 2007-03-09 21:29 Rev.: 4357

- pass NULL (instead of additional field) to AWTC_generate_one_name

1 lines of code changed in 1 file:

westram 2007-03-09 21:29 Rev.: 4356

- pass additional field to AWTC_generate_one_name

17 lines of code changed in 1 file:

westram 2007-03-09 21:29 Rev.: 4355

- cleanup

0 lines of code changed in 1 file:

westram 2007-03-09 21:29 Rev.: 4354

updated

2 lines of code changed in 2 files:

westram 2007-03-09 21:29 Rev.: 4353

- GBS_read_arb_tcp
. adds a 2nd delimiter at EOL
. commented return value
- added gbs_strnicmp
- rewrote GBS_ptserver_id_to_choice
- added GBS_scan_arb_tcp_param
All together needed to allow more than one real parameter in arb_tcp.dat.

80 lines of code changed in 1 file:

westram 2007-03-09 21:23 Rev.: 4352

- in ARB mode descent into GENC/GENH directories

8 lines of code changed in 1 file:

baderk 2007-03-09 19:03 Rev.: 4351

A segfault, occasionally appearing during export when "remove all' is selected, removed.

8 lines of code changed in 1 file:

westram 2007-03-09 11:49 Rev.: 4350

- renamed toggle

3 lines of code changed in 1 file:

westram 2007-03-09 11:32 Rev.: 4349

- cleaned developers

2 lines of code changed in 1 file:

westram 2007-03-09 11:32 Rev.: 4348

- fixed text layout in bottom area
- added AP_display_status::writePadded

27 lines of code changed in 1 file:

westram 2007-03-09 11:32 Rev.: 4347

- beautified
- added writePadded

60 lines of code changed in 1 file:

westram 2007-03-09 11:32 Rev.: 4346

- renamed toggle

1 lines of code changed in 1 file:

westram 2007-03-09 10:53 Rev.: 4345

- cosmetics

6 lines of code changed in 1 file:

westram 2007-03-09 10:53 Rev.: 4344

- added enum for toggle values
- removed duplicate of class PH_filter; include PH_filter.hxx

60 lines of code changed in 1 file:

westram 2007-03-09 10:53 Rev.: 4343

- unused warning

7 lines of code changed in 1 file:

westram 2007-03-09 10:53 Rev.: 4342

- more descriptive names for handling of non-regular sequence characters
- new method 'treat as regular char' for ambiguity codes

32 lines of code changed in 1 file:

westram 2007-03-09 10:53 Rev.: 4341

- enumerated PH_filter::options_vector
- use the PH_filter version defined here

31 lines of code changed in 1 file:

westram 2007-03-09 10:53 Rev.: 4340

- use enum values instead of hardcoded numbers
- lowercase as well for proteins
- new methods to handle characters:
. COUNT_DONT_USE_MAX for '.'
. TREAT_AS_REGULAR for ambiguity codes
. COUNT_DONT_USE_MAX for lower case chars
- cosmetics

247 lines of code changed in 1 file:

westram 2007-03-09 10:52 Rev.: 4339

- depends updated

6 lines of code changed in 1 file:

westram 2007-03-09 10:52 Rev.: 4338

- wrote help for ARB_PHYLO

74 lines of code changed in 1 file:

westram 2007-03-09 10:52 Rev.: 4337

- labels were duplicated in code and xfig (removed here)

26 lines of code changed in 1 file:

westram 2007-03-09 10:52 Rev.: 4336

- depends updated
@kai: einfach bei bedarf make depends in $ARBHOME aufrufen oder
in deinem Fall: make SEQ_QUALITY/SEQ_QUALITY.depends

7 lines of code changed in 1 file:

baderk 2007-03-08 16:59 Rev.: 4335

Added zombie-detection. (Quality check now stops the computation if zombies are detected.)

42 lines of code changed in 4 files:

baderk 2007-03-07 19:37 Rev.: 4334

Added filter support to the sequence quality tool resulting in a speedup and far less memory consumption. This check-in still has issues (zombies).

234 lines of code changed in 4 files:

baderk 2007-03-07 19:23 Rev.: 4333

Revised sequence quality GUI - button for filter selection added

36 lines of code changed in 1 file:

baderk 2007-03-05 13:51 Rev.: 4332

Sequence-quality tool with processing speedup and less memory consumption (still not enough for a full tree).

339 lines of code changed in 5 files:

baderk 2007-03-05 12:04 Rev.: 4331

Sequence-quality sourcecode reformatted (tabs and brackets fixed) - needed for further checkin

1253 lines of code changed in 10 files:

February 2007 »

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