June 2009 Commit Log

Number of Commits:
121
Number of Active Developers:
5
westram 2009-06-30 12:10 Rev.: 6090


* new ift-command INCLUDE

69 lines of code changed in 1 file:

westram 2009-06-30 07:37 Rev.: 6089


- move PARS/kernlin.fig -> pars/kernlin.fig (fixes problems on case-insensitive filesystems)

115 lines of code changed in 3 files:

westram 2009-06-29 13:14 Rev.: 6088


* store line number of NEW_FORMAT
* more detailed error messages for nested formats
* cosmetics

24 lines of code changed in 3 files:

westram 2009-06-29 12:43 Rev.: 6087


* changed order of commands (often used commands first)
* GLOBAL_COMMAND has to test 'error' (set as side-effect of MATCH_COMMAND)

31 lines of code changed in 1 file:

westram 2009-06-29 12:31 Rev.: 6086


* improved handling of errors in import filters
- if no format selected, give a hint
- changed message for misplaced MATCH-commands
- print line number of error
- show only filename of filter in error
* 'TAG ""' does an error now
* command matching done by two macros now (for global and match-local commands)

56 lines of code changed in 1 file:

arb_build 2009-06-26 08:35 Rev.: 6085

Auto version upgrade to 4.38 by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2009-06-26 08:18 Rev.: 6084


* name servers with add.field have to be started with '-fFIELD=DEFAULT' instead of '-fFIELD' only.
* convert existing nameserver-DBs on the fly
* increased namesDB version to 5
* added a version check (too late - as always)
* nameserver sends fatal errors to running ARB (using arb_message)
* fixed nameserver definitions in arb_tcp_org.dat (arb_tcp.dat needs to be updated manually by users)

137 lines of code changed in 6 files:

westram 2009-06-25 11:07 Rev.: 6083


* do not raise error in ED4_init_faligner_data if no helix is found (only needed by islandhopper if 'use 2nd structure' is selected)
* check helix-existance in AWTC_start_faligning instead
* fixed wrong error message in GBT_expect_item_rel_item_data ("Could not find name with name 'HELIX'" :)

91 lines of code changed in 3 files:

westram 2009-06-25 08:21 Rev.: 6082


* import/export filter (and similar) selection fileboxes clashed with filebox search.
- if 'cbs->show_dir' is true, search is used now (recurses subdirs)
- otherwise does a non-recursive match for "name*filter" (fixed #198)
* skip "Dot files/dirs" from filter selection
* cosmetics

(partly reverted by [6096])

16 lines of code changed in 1 file:

westram 2009-06-24 16:34 Rev.: 6081

* removed modulo calculation from GBCONTAINER_MAIN. Seems not necessary and costs about 1% of overall DB performance. Added assertions where GBDATA::main_idx is set.
* gb_write_index_key - get Main only in condition

13 lines of code changed in 3 files:

westram 2009-06-24 16:24 Rev.: 6080

* quark 0 is not illegal - it's the quark of the main db entry

2 lines of code changed in 1 file:

westram 2009-06-24 16:22 Rev.: 6079


* avoid crash during deletion of main db entry (delete {{{__SYSTEM__}}} container '''after''' other containers)

31 lines of code changed in 3 files:

westram 2009-06-23 15:14 Rev.: 6078


* reduced shutdown time for nameserver to 2 min (hack around #192)

2 lines of code changed in 1 file:

westram 2009-06-23 14:58 Rev.: 6077


* fix #186 + #34
- added GBT_create_sequence_data (as replacement for GBT_add_data). Sets protection level of created 'species/ali_xxx/element' to passed value
- added GB_copy_with_protection (after release GB_copy should generally behave like that)
- pass write-protection selected in import-window to awtc_read_data (and removed hard-coded protection 4)
- MG_simple_merge uses GB_copy_with_protection to copy imported species into main DB

57 lines of code changed in 9 files:

westram 2009-06-18 12:27 Rev.: 6076


* changed Protection error message
* print it to console in debug mode (to detect unhandled security errors)

10 lines of code changed in 1 file:

westram 2009-06-18 10:44 Rev.: 6075


* new database can be added to already running DB browser (happens if you browse first and then import data)

20 lines of code changed in 1 file:

westram 2009-06-18 10:42 Rev.: 6074


* removed invalid assertion (since [5948] button list only contains sensitive widgets)

1 lines of code changed in 1 file:

westram 2009-06-18 09:22 Rev.: 6073


* if NUMLOCK is on and user presses an 'ALT-a .. ALT-z'-key, warn once about NUMLOCK

16 lines of code changed in 1 file:

westram 2009-06-18 09:21 Rev.: 6072


* added missing and fixed broken hotkeys

125 lines of code changed in 9 files:

westram 2009-06-17 13:54 Rev.: 6071


* full -> complete sequences (mark)

2 lines of code changed in 1 file:

westram 2009-06-17 13:35 Rev.: 6070


* moved 'Mark species in (NOT) Tree' to separate sub-menus

47 lines of code changed in 1 file:

westram 2009-06-17 12:55 Rev.: 6069


* changed GDE menu names
* added hotkeys
* GDE_load_menu now warns if requested to load an unknown menu or topic (console)

72 lines of code changed in 7 files:

westram 2009-06-17 08:37 Rev.: 6068


- fixed some console messages

8 lines of code changed in 4 files:

arb_build 2009-06-16 15:40 Rev.: 6067

Auto version upgrade to 4.37 by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2009-06-16 15:20 Rev.: 6066


* Added two options to Tree-Exporter
- quoting style (none/single/double)
- replace problem chars, currently "()[]:;," plus used quote
* added quote-mode to TREE_write_Newick()
* changes to previous behavior
- if a label (e.g. from NDS) contains a single quote (') it now gets replaced by '_'. Before ARB wrote two single quotes.

63 lines of code changed in 3 files:

westram 2009-06-16 13:26 Rev.: 6065


* moved GBT_export_tree (ARBDB) -> TREE_export_tree (SL/TREE_WRITE).
* arb_export_tree
- added command line switches --bifurcated, --nobranchlens and --doublequotes
* beautifyNewick.pl - formats newick tree using BioPerl

(this are just some coproducts of my RAxML tests)

256 lines of code changed in 11 files:

westram 2009-06-16 12:40 Rev.: 6064


- added RAxML bug to help

11 lines of code changed in 2 files:

westram 2009-06-15 18:59 Rev.: 6063


- enabled PGT for DEBUG version

2 lines of code changed in 1 file:

westram 2009-06-15 16:56 Rev.: 6062


* AWT_date_string -> GB_date_string
* separated SL/TREE_WRITE from AWT

78 lines of code changed in 11 files:

westram 2009-06-15 14:09 Rev.: 6061


* open transaction in unlink_awars_from_DB in transaction (callback rely on that)
* GLOBAL_gb_main is already NULL, when gde_filter_weights is called (from unlink_awars_from_DB).

3 lines of code changed in 2 files:

westram 2009-06-15 13:17 Rev.: 6060


* Translate (fixes #187)
- raise security in GBT_check_alignment
- removed "Database corrupted" message, simply show the error
- warn if no species were marked

38 lines of code changed in 2 files:

westram 2009-06-15 13:07 Rev.: 6059


- added treetool to dependencies

3 lines of code changed in 3 files:

westram 2009-06-15 11:24 Rev.: 6058


* suppress known mem-leaks in system libs

20 lines of code changed in 1 file:

westram 2009-06-15 11:22 Rev.: 6057


* use dynaval hash for cached taxonomies
* fixed macros GB_TYPE and GB_TYPE_TS
* GB_get_db_path works w/o transaction
* removed useless return value from GB_disable_path

9 lines of code changed in 5 files:

westram 2009-06-14 18:30 Rev.: 6056


- removed useless return value

6 lines of code changed in 2 files:

westram 2009-06-14 13:20 Rev.: 6055


* flush_taxonomy_cb() does NOT remove callbacks, if inside delete callback (illegal memaccess - at least during GB_close)
* GB_close expects that no transaction is running (assertion only)
* changed callback type in delete-callback-list from (undefined) to GB_CB_DELETE
* set g_b_old_main to NULL, when finished with callbacks (in gb_do_callback_list)
* added GB_inside_callback() and GB_get_gb_main_during_cb()
* comment about restrictions in delete-callbacks
* added assertion to gb_remove_callback + GB_add_priority_callback (refuses to modify callbacks of already deleted element)

116 lines of code changed in 11 files:

westram 2009-06-13 14:16 Rev.: 6054


* store DB-browser singleton in SmartPtr (automatically freed on exit)

16 lines of code changed in 1 file:

westram 2009-06-13 13:49 Rev.: 6053


* Errors about undefined variables in inport-formats had some meaning for the writer of the input-format, but none for the user of the format.
* new command IFNOTSET for ift
- each 'SETVAR x' expects a corresponding 'IFNOTSET x msg' (and vv.)
* undef error prints reason defined by IFNOTSET
* fixed import filters
* checked feature table sections in longebi.ift and longgenbank.ift for similarity
- typo 'secimen_voucher'
* updated help

199 lines of code changed in 7 files:

westram 2009-06-13 13:46 Rev.: 6052


* ignore errors from XtOpenApplication and XmIsMotifWMRunning

6 lines of code changed in 1 file:

westram 2009-06-13 10:19 Rev.: 6051


* RN entry was missing

1 lines of code changed in 1 file:

westram 2009-06-13 10:17 Rev.: 6050


* removed frame from status window (use 2 points to set size). ARB often printed over frame.

16 lines of code changed in 1 file:

westram 2009-06-13 10:16 Rev.: 6049


* increment status during export

11 lines of code changed in 1 file:

westram 2009-06-13 09:09 Rev.: 6048


produced wrong feature table when exporting field 'strain'

previous output:
{{{
FT strain=abcd
}}}

current output:
{{{
FT source 1..1188
FT /strain=DSM 2039
}}}

or
{{{
FT source 1..1188
}}}

if no strain present (hope a single source line is ok)

2 lines of code changed in 1 file:

westram 2009-06-13 09:09 Rev.: 6047


* crashed when called-back from GB_close. Now only open transaction if needed

4 lines of code changed in 1 file:

westram 2009-06-13 08:50 Rev.: 6046


* use faster method reading input

1 lines of code changed in 1 file:

westram 2009-06-12 19:55 Rev.: 6045


* increased number of GBL_MAX_ARGUMENTS (50->500). overflow caused by data.

14 lines of code changed in 2 files:

westram 2009-06-12 19:47 Rev.: 6044


* use unsigned to print 1 (first line of formatted sequence data)
* warning fix

3 lines of code changed in 1 file:

westram 2009-06-12 19:41 Rev.: 6043


* Several export filters wrote a 'u' at start of sequence, due to wrong format string (re-introduced in revocation [6026])

7 lines of code changed in 1 file:

westram 2009-06-12 17:37 Rev.: 6042


- use gunzip instead of zcat

2 lines of code changed in 5 files:

arb_build 2009-06-10 16:55 Rev.: 6041

Auto version upgrade to 4.36 by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2009-06-10 16:18 Rev.: 6040


- don't pack provided libs into arbsrc.tgz

1 lines of code changed in 1 file:

westram 2009-06-10 16:11 Rev.: 6039


- possibility to provide libXm.so as well (commented out)

3 lines of code changed in 1 file:

westram 2009-06-10 15:52 Rev.: 6038


* new make target 'addlibs' (used by tarfile)
- uses SOURCE_TOOLS/provide_libs.pl to copy some shared libs to lib/addlibs (they will be packed into binary)
* removed lib/addlibs/install_libs.sh and libGLEW.so.1.3.5

183 lines of code changed in 6 files:

westram 2009-06-10 15:41 Rev.: 6037


* search for any arb.32.*.tgz or arb.64.*.tgz
* do not call install_libs.sh

9 lines of code changed in 1 file:

arb_build 2009-06-09 18:25 Rev.: 6036

Auto version upgrade to 4.35 by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2009-06-09 17:26 Rev.: 6035


- get arb version from arbsrc.tgz

32 lines of code changed in 1 file:

westram 2009-06-08 14:56 Rev.: 6034


- compile fix (ubuntu 64bit)

1 lines of code changed in 1 file:

westram 2009-06-08 13:31 Rev.: 6033


* DB browser now is only included in DEBUG mode
* include wrappers for ad_spec.hxx + ad_trees.hxx

105 lines of code changed in 19 files:

westram 2009-06-08 12:33 Rev.: 6032


- wrong entry-count in AWT_reactivate_all_advices

1 lines of code changed in 1 file:

westram 2009-06-07 11:36 Rev.: 6031


* separated internal and external input-mask-interface

615 lines of code changed in 7 files:

westram 2009-06-06 14:53 Rev.: 6030


* renamed defines

12 lines of code changed in 3 files:

westram 2009-06-06 14:48 Rev.: 6029


* compile error, aisc_mkpt arguments in wrong order

2 lines of code changed in 1 file:

westram 2009-06-06 14:31 Rev.: 6028


* fixed handling of newick comments (see #153 3.)
- comments need to be well-formed (contain the same number of opening and closing brackets). Tree writer forces well-formed comments by adding brackets. Tree reader expects well-formed comments now.
- no longer use escaping of [ and ] in comments (that is not newick format)
- new reader error (EOF reached in comment)
* if tree-reader has an error, delete tree and report error
* Tree reader and writer log to comment (what was loaded or saved)

138 lines of code changed in 6 files:

westram 2009-06-06 14:28 Rev.: 6027


* fixed illegal memory access

5 lines of code changed in 2 files:

westram 2009-06-06 13:47 Rev.: 6026


* revoke changes done by [5938] and [5966]
* fix #167

17 lines of code changed in 1 file:

westram 2009-06-06 09:04 Rev.: 6025


* swapped name suffixes for NDS- and normal tree
- NDS-tree uses '.ntree' now, because it is not meant to be reloaded
- Normal tree (using species names as node names) uses '.tree' now (as Tree/Import does)

2 lines of code changed in 1 file:

westram 2009-06-06 08:56 Rev.: 6024


* renamed tree IO functions

48 lines of code changed in 8 files:

westram 2009-06-05 20:02 Rev.: 6023


* moved tree I/O functions to separate libraries (TREE_READ.a and TREE_WRITE.a)
* link only with ARB_NTREE and arb_read_tree (before they were linked everywhere)

1055 lines of code changed in 20 files:

westram 2009-06-05 19:50 Rev.: 6022


* missing transaction

1 lines of code changed in 1 file:

westram 2009-06-05 19:24 Rev.: 6021


* complete revoke of [6000] see http://bugs.arb-home.de/changeset?new=PROBE%2FPT_match.cxx%406002&old=PROBE%2FPT_match.cxx%405918

1 lines of code changed in 1 file:

westram 2009-06-05 18:18 Rev.: 6020


* splitted adtools.c into multiple files (no code change)

3523 lines of code changed in 13 files:

westram 2009-06-05 18:09 Rev.: 6019


* NT_remove_dup_colors -> static remove_dup_colors

8 lines of code changed in 2 files:

westram 2009-06-05 18:04 Rev.: 6018


depends + proto

5 lines of code changed in 2 files:

westram 2009-06-05 14:02 Rev.: 6017


* do not insert \n into error (\n will not display in secedit main window)
* rename (SEC_root) get_helix -> get_helixDef (get_helix is duplicated in SEC_helix_strand)

15 lines of code changed in 7 files:

meierh 2009-06-05 13:13 Rev.: 6016

mesaglw und mesaglw-devel added to list of packages to install for
compiling ARB with OpenGL=1 under OpenSuSE

5 lines of code changed in 1 file:

meierh 2009-06-05 10:03 Rev.: 6015

added gcc 4.3 to Makefile-->supported compiler versions
added mesa and freeglut to list of packages to install for compiling
arb with OpenGL=1 in arb_INSTALL.txt

4 lines of code changed in 2 files:

westram 2009-06-04 14:59 Rev.: 6014


* changed authors
* added citation

33 lines of code changed in 1 file:

westram 2009-06-04 14:15 Rev.: 6013


* compile fix (NDEBUG)

2 lines of code changed in 1 file:

arb_build 2009-06-04 13:55 Rev.: 6012

Auto version upgrade to 4.34 by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2009-06-04 12:22 Rev.: 6011


* added (AW_window) force_expose()
* added (AW_root) process_pending_events()
* debug module
- forces exposure of window generator functions (maybe superfluous)
- processes pending events after callbacks, exposures and popdowns
- callallcallbacks counts called callbacks

55 lines of code changed in 5 files:

westram 2009-06-04 12:13 Rev.: 6010


* ST_ML
* in case of error (while loading tree), set tree variables to NULL
* dont try to free NULL-tree in dtor

8 lines of code changed in 1 file:

westram 2009-06-04 12:11 Rev.: 6009


* avoid call of calc_color if no tree exists

3 lines of code changed in 1 file:

westram 2009-06-04 12:10 Rev.: 6008


* set gb_tree_gone zero after tree has been deleted (avoids double GB_delete)

2 lines of code changed in 1 file:

westram 2009-06-04 09:47 Rev.: 6007


* fixed sensitivity masks

5 lines of code changed in 3 files:

westram 2009-06-03 19:53 Rev.: 6006


* [debug] more exclusions

58 lines of code changed in 1 file:

westram 2009-06-03 19:52 Rev.: 6005


* added checks performed with all items (species, genes, experiments, ...)
* silently remove duplicated 'ARB_color' entries

131 lines of code changed in 5 files:

westram 2009-06-03 19:00 Rev.: 6004


* added message (see #75)

19 lines of code changed in 1 file:

baderk 2009-06-03 16:33 Rev.: 6003

Fixed ambiguous button functionalities.
Removed file selection dialog from quick-save functionality.
Removed unnecessary whitespaces.

19 lines of code changed in 1 file:

eissler 2009-06-03 15:35 Rev.: 6002

revoke patch 6000

2 lines of code changed in 1 file:

westram 2009-06-03 15:26 Rev.: 6001


* ensure that automatic organism-marking is undone in EXP_get_first_experiment_data and GEN_get_first_gene_data
* note about when AW_root argument of get_first_item_container may be NULL

44 lines of code changed in 3 files:

eissler 2009-06-03 14:17 Rev.: 6000

Fixed bug #106: probe_match and editor have been showing different positions for specific probe
(difference was 1).

4 lines of code changed in 1 file:

westram 2009-06-03 14:00 Rev.: 5999


* reuse colorset save/load window for identical item selectors
* unique window-IDs for colorize windows
* unique window-IDs for submission text-edit

70 lines of code changed in 2 files:

baderk 2009-06-03 12:56 Rev.: 5998

Upper limit check (sequence length) in the editor. Removed unneeded whitespaces.

9 lines of code changed in 1 file:

meierh 2009-06-03 11:08 Rev.: 5997

xterm added to list of packages to install

2 lines of code changed in 2 files:

westram 2009-06-03 10:53 Rev.: 5996


* removed 'Tools/WL specials/Check GCG list' (unused, we got SILVA now)

1 lines of code changed in 5 files:

baderk 2009-06-03 10:17 Rev.: 5995

Fixed popdown params.

1 lines of code changed in 1 file:

westram 2009-06-03 10:04 Rev.: 5994


* fixed id and popdown params

2 lines of code changed in 1 file:

westram 2009-06-03 09:48 Rev.: 5993


* fixed sens masks

3 lines of code changed in 1 file:

westram 2009-06-03 09:03 Rev.: 5992


* new commands for import filters (WRITE_INT, WRITE_FLOAT)
* Silva-Import-Filters write start, stop, insdc, version as ints
* see ticket #44

thx to fog and elmar


50 lines of code changed in 4 files:

westram 2009-06-03 06:55 Rev.: 5991


* fixed include path (thx elmar). See #178

1 lines of code changed in 1 file:

westram 2009-06-02 14:26 Rev.: 5990


* AW_POPDOWN expects params 0,0

1 lines of code changed in 1 file:

westram 2009-06-02 14:25 Rev.: 5989


* do not macro record user mask 'EDIT' and 'RELOAD'

2 lines of code changed in 1 file:

westram 2009-06-02 14:24 Rev.: 5988


* use AWM_ALL instead of -1

28 lines of code changed in 4 files:

westram 2009-06-02 13:30 Rev.: 5987


* print a space in prefixSSH (instead of a zero char)
* avoid that assertions overwrite internal buffers
* note about printing zero chars

16 lines of code changed in 3 files:

westram 2009-06-02 12:12 Rev.: 5986


* expect correct mask (no longer allow -1 as alias for AWM_ALL)

39 lines of code changed in 3 files:

westram 2009-06-02 11:58 Rev.: 5985


* set sensitivity in make_sensitive(). That functionality was dropped with [5948]

1 lines of code changed in 1 file:

westram 2009-06-02 10:48 Rev.: 5984


* menu entry in debug menu to mark all callbacks as called

36 lines of code changed in 2 files:

westram 2009-06-02 10:41 Rev.: 5983


* reloaded masks no longer use callback ids, only initially loaded mask does
* notes about user masks and macro recording

21 lines of code changed in 2 files:

westram 2009-06-02 10:24 Rev.: 5982


* made window-IDs and awar-names determininistic and dependent on base-awar-name in
- mp_create_load_box_for_selection_lists
- create_save_box_for_selection_lists
- awt_create_select_filt
* use one filter for all gde calls

55 lines of code changed in 4 files:

westram 2009-06-02 10:14 Rev.: 5981


* insert default selection when creating probe design result list (ARB crashed on ProbeDesign+Result(w/o designing)+Match)

3 lines of code changed in 1 file:

westram 2009-06-01 11:37 Rev.: 5980


* fixed formatting in filter window for filters with multiple sequences (e.g. MAX_FREQUENCY)

2 lines of code changed in 1 file:

westram 2009-06-01 11:33 Rev.: 5979


* debug module calls each callback only once
- added 'Forget called'
- automatically forbid functions for clone window, if forbidden in main window

80 lines of code changed in 3 files:

westram 2009-06-01 11:30 Rev.: 5978


* store created windows statically inside window-factory-functions
- CPRO_savestatisticwindow_cb
- CPRO_loadstatisticwindow_cb
- NT_createMergeSimilarSpeciesWindow
- NT_createMergeSimilarSpeciesAndConcatenateWindow

63 lines of code changed in 2 files:

westram 2009-06-01 11:29 Rev.: 5977


* "Change pseudo species to organisms in tree" now only appears in genome DB
* typo

7 lines of code changed in 1 file:

westram 2009-06-01 11:29 Rev.: 5976


* awtc_read_export_format tried to close non-open file

1 lines of code changed in 1 file:

westram 2009-06-01 11:27 Rev.: 5975


* advices are no longer modal windows

38 lines of code changed in 1 file:

westram 2009-06-01 11:18 Rev.: 5974


* reuse already created filter selection window (the window was already stored in adfiltercbstruct)

50 lines of code changed in 2 files:

westram 2009-06-01 11:13 Rev.: 5973


* seems i used perl too much

1 lines of code changed in 1 file:

westram 2009-06-01 11:09 Rev.: 5972


* cosmetics

23 lines of code changed in 2 files:

westram 2009-06-01 11:09 Rev.: 5971


* GB_dump_indices (dump indices attached to a container; intended use is from gdb: p GB_dump_indices(gbc))

77 lines of code changed in 1 file:

westram 2009-06-01 11:07 Rev.: 5970


* silently create $(HOME)/.arb_prop/macros if it does not exist

7 lines of code changed in 1 file:

May 2009 »

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