May 2005 Commit Log

Number of Commits:
134
Number of Active Developers:
2
westram 2005-05-25 23:28 Rev.: 3916

- do not set cursor after block operation if not has been set before
- fixed gap-usage for unalign block and shift block

39 lines of code changed in 1 file:

westram 2005-05-25 22:33 Rev.: 3915

- recreate short-prefixes via list (avoids deadlock)

39 lines of code changed in 1 file:

westram 2005-05-25 21:34 Rev.: 3914

- rewrote GetDisplayInfo
. field content now input for ACI (as everywhere in ARB)
. fixed some mem leaks
- SAI_graphic::paint()
. fixed some mem leaks
. pass default tree name to GetDisplayInfo
. better sizing for different font sizes
- create GC window with different name (otherwise it always has the same size as
the one in ARB_NTREE)

77 lines of code changed in 1 file:

westram 2005-05-25 21:33 Rev.: 3913

- added AW_create_gc_window_named()

15 lines of code changed in 2 files:

westram 2005-05-25 21:32 Rev.: 3912

- missing transactions

34 lines of code changed in 2 files:

westram 2005-05-25 21:32 Rev.: 3911

- missing transaction

8 lines of code changed in 2 files:

westram 2005-05-25 19:04 Rev.: 3910

- added awt_macro.hxx

1 lines of code changed in 1 file:

westram 2005-05-25 19:04 Rev.: 3909

- include fix (gcc 2.95.x)

1 lines of code changed in 1 file:

westram 2005-05-25 19:00 Rev.: 3908

- store AWAR_SPV_DB_FIELD_NAME with database (everything else is also stored with db)
- changed AWAR_... to AWAR_SPV_...
- touch AWAR_SPV_DB_FIELD_NAME to refresh probe list
- cleanup

9 lines of code changed in 1 file:

westram 2005-05-25 19:00 Rev.: 3907

- changed AWAR_... to AWAR_SPV_... (some of the names were to general)
- removed AWAR_SPV_PROBE_LIST (only used to refresh probe list, now done via AWAR_SPV_DB_FIELD_NAME)

7 lines of code changed in 1 file:

westram 2005-05-25 19:00 Rev.: 3906

- changed AWAR_... to AWAR_SPV_...
- use AWT_popup_select_species_field_window

26 lines of code changed in 1 file:

westram 2005-05-25 18:55 Rev.: 3905

- fixed error handling

16 lines of code changed in 1 file:

westram 2005-05-25 18:53 Rev.: 3904

- DEBIAN made no difference

0 lines of code changed in 1 file:

westram 2005-05-25 18:19 Rev.: 3903

- includes fixed

55 lines of code changed in 40 files:

westram 2005-05-25 18:17 Rev.: 3902

- depends updated

42 lines of code changed in 14 files:

westram 2005-05-25 18:11 Rev.: 3901

- removed AWT_create_select_nds_window
- uses AWT_popup_select_species_field_window

5 lines of code changed in 1 file:

westram 2005-05-25 18:10 Rev.: 3900

- added AWT_popup_select_species_field_window (former AWT_create_select_nds_window)
- moved macro recording functions to AWT_macro.cxx

25 lines of code changed in 1 file:

westram 2005-05-25 18:09 Rev.: 3899

- removed AWT_create_select_nds_window

0 lines of code changed in 1 file:

westram 2005-05-25 18:08 Rev.: 3898

- moved prototypes to awt_sel_boxes.hxx / awt_macro.hxx

0 lines of code changed in 1 file:

westram 2005-05-25 18:07 Rev.: 3897

- added AWT_macro.o
- depends updated

19 lines of code changed in 1 file:

westram 2005-05-25 18:06 Rev.: 3896

- macro recording functions

162 lines of code changed in 2 files:

westram 2005-05-25 18:06 Rev.: 3895

- moved several prototype from awt.hxx here

98 lines of code changed in 1 file:

westram 2005-05-25 18:04 Rev.: 3894

- added awt_sel_boxes.hxx
- removed PH_phylo.hxx

2 lines of code changed in 1 file:

westram 2005-05-25 17:55 Rev.: 3893

- headers fixed

54 lines of code changed in 9 files:

westram 2005-05-25 17:55 Rev.: 3892

- depends updated

1 lines of code changed in 1 file:

westram 2005-05-25 17:55 Rev.: 3891

- another dont-bother-me-header -- removed

0 lines of code changed in 1 file:

westram 2005-05-25 14:09 Rev.: 3890

- better error messages (grep-like)
- automatically removes symlinks to nowhere
- tests whether target of symlink exists

253 lines of code changed in 1 file:

westram 2005-05-25 13:29 Rev.: 3889

- spelling error

1 lines of code changed in 1 file:

westram 2005-05-25 12:55 Rev.: 3888

- AWTC_recreate_name: fix for parameter 'update_status' (had no effect)

9 lines of code changed in 1 file:

westram 2005-05-25 12:49 Rev.: 3887

- added some options from removed sec_layout.fig

21 lines of code changed in 1 file:

westram 2005-05-25 12:49 Rev.: 3886

- now called sec_bonddef.fig

0 lines of code changed in 1 file:

westram 2005-05-25 12:49 Rev.: 3885

- created from sec_layout.fig - now only contains bond definitions

26 lines of code changed in 1 file:

westram 2005-05-25 12:49 Rev.: 3884

- ::read() members return an GB_ERROR
- added SEC_helix_strand::is_rootside_fixpoint, isRootsideFixpoint()
- removed set_fixpoint_x/y, set_fixpoints() -> set_fixpoint(,rootside)
- added SEC_loop::get_rootside_loop()
- added SEC_helix_strand::change_angle()

82 lines of code changed in 1 file:

westram 2005-05-25 12:49 Rev.: 3883

- changed error messages
- implemented error-handling which reaches the user, instead of locking the application
- SEC_read_line -> static sec_read_line, const result
- SEC_make_numbers -> static sec_scan_doubles / sec_scan_ints, const char *arg
- warn once about missing DELTA_IN entries, in that case set them all to 0.0

261 lines of code changed in 1 file:

westram 2005-05-25 12:49 Rev.: 3882

- compute_length() also sets base-length
- paint constrainst on top of structure
- SEC_root::show_constraints takes different values (bits 0 and 1) for loops and strands
- removed old code (paint_other_strand, paint_this_strand)
- SEC_helix_strand::update(), new parameter is_rootside_fixpoint_
- use set_fixpoint()
- SEC_helix_strand::update uses set_fixpoint instead of setting members directly
- test that is_rootside_fixpoint differs between opposite strands in SEC_helix_strand::paint_strands
- implemented SEC_loop::get_rootside_loop()
- added SEC_helix_strand::change_angle(), implemented SEC_helix_strand::update() using change_angle()
- paint skeleton for empty segments
- speeded up segment paint (reuse results from sin/cos)
- smaller debug info circles

148 lines of code changed in 1 file:

westram 2005-05-25 12:48 Rev.: 3881

- added RIGHT click in stretch mode
- show_constraints changed meaning
- hotkey fix
- Layout window is now bond definition window (reachable from display options window)
- Display options window now contains all other display toggles

73 lines of code changed in 1 file:

westram 2005-05-25 12:48 Rev.: 3880

- bug fixed in ~SEC_helix_strand (if strand got deleted, which had no loop yet)
- added SEC_helix_strand::is_rootside_fixpoint

28 lines of code changed in 1 file:

westram 2005-05-25 12:48 Rev.: 3879

- changed choices when error occurs reading sec structure
- simplified stretch calculation, added reset (right click) and definition of max value
- show_constraints changed meaning
- do not draw structure if no species is selected (show message instead)
- renamed some locals (fixpoint_x,fixpoint_y) - already used as members
- uses fixpoint of rootside strand when zooming loops (or loop-center for root-loop)
- use change_angle() instead of update in rotate mode
- made variables more local - some were re-used un-initialized

143 lines of code changed in 1 file:

westram 2005-05-25 12:48 Rev.: 3878

- short description of options

47 lines of code changed in 1 file:

westram 2005-05-25 12:48 Rev.: 3877

- added AW_window::create_inverse_toggle

11 lines of code changed in 2 files:

westram 2005-05-24 18:05 Rev.: 3876

- depends updated

38 lines of code changed in 8 files:

westram 2005-05-24 18:05 Rev.: 3875

- header fixes

20 lines of code changed in 16 files:

westram 2005-05-24 18:04 Rev.: 3874

- warning added

3 lines of code changed in 1 file:

westram 2005-05-24 18:03 Rev.: 3873

- added modify_input_cb

1 lines of code changed in 1 file:

westram 2005-05-24 18:03 Rev.: 3872

- warning removed

1 lines of code changed in 1 file:

westram 2005-05-24 18:02 Rev.: 3871

- replaced GBS_SPECIES_HASH_SIZE by GBT_get_species_hash_size()

2 lines of code changed in 2 files:

westram 2005-05-24 18:02 Rev.: 3870

- removed generate_GBT_TREE_hash(_rek)
- cleaned

2 lines of code changed in 1 file:

westram 2005-05-24 17:59 Rev.: 3869

- uses aisc_server_shutdown_and_exit

4 lines of code changed in 1 file:

westram 2005-05-24 17:59 Rev.: 3868

- uses aisc_server_shutdown_and_exit
- untabified

162 lines of code changed in 1 file:

westram 2005-05-24 17:57 Rev.: 3867

- header fixes

5 lines of code changed in 2 files:

westram 2005-05-24 17:57 Rev.: 3866

- deactivated test code

2 lines of code changed in 1 file:

westram 2005-05-24 17:56 Rev.: 3865

- header fix

3 lines of code changed in 2 files:

westram 2005-05-24 17:55 Rev.: 3864

- changed names in GEN_PERFORM_MODE (SPECIES->ORGANISM)
- GEN_perform_command only acts on organisms

38 lines of code changed in 1 file:

westram 2005-05-24 17:55 Rev.: 3863

- fixed error in GEN_get_first_gene_data / GEN_get_next_gene_data (did access normal species)
- removed GEN_is_genome_db (went to ARBDB)
- init 'parent_selector' in GEN_item_selector

18 lines of code changed in 1 file:

westram 2005-05-24 17:55 Rev.: 3862

- init 'parent_selector' in EXP_item_selector
- header fixes

5 lines of code changed in 1 file:

westram 2005-05-24 17:54 Rev.: 3861

- removed GEN_is_genome_db (went to ARBDB)

0 lines of code changed in 1 file:

westram 2005-05-24 17:52 Rev.: 3860

- removed use of GBS_SPECIES_HASH_SIZE

1 lines of code changed in 1 file:

westram 2005-05-24 17:52 Rev.: 3859

- use GBT_count_species()

1 lines of code changed in 1 file:

westram 2005-05-24 17:51 Rev.: 3858

- added AWT_changekey.o + AWT_item_sel_list.o
- removed AWT_species_sel_box.o
- depends updated

31 lines of code changed in 1 file:

westram 2005-05-24 17:50 Rev.: 3857

- added 'parent_selector' to ad_item_selector
- some parts moved to AWT_item_sel_list.hxx and SL/DB_SCANNER/db_scanner.hxx

2 lines of code changed in 1 file:

westram 2005-05-24 17:50 Rev.: 3856

- moved awt_map_arbdb_edit_box to SL/DB_SCANNER/db_scanner.hxx

0 lines of code changed in 1 file:

westram 2005-05-24 17:47 Rev.: 3855

- replaced GBS_SPECIES_HASH_SIZE by GBT_get_species_hash_size()
- init 'parent_selector' in selector instances

8 lines of code changed in 1 file:

westram 2005-05-24 17:46 Rev.: 3854

- init all instances of adawcbstruct with zero + init member 'awr'

36 lines of code changed in 2 files:

westram 2005-05-24 17:45 Rev.: 3853

- include fix

3 lines of code changed in 2 files:

westram 2005-05-24 17:44 Rev.: 3852

- part of code from AWT_species_sel_box.cxx

191 lines of code changed in 2 files:

westram 2005-05-24 17:42 Rev.: 3851

- corrected new timings/behavior
- note about acc-generation
- what to do with duplicated species

19 lines of code changed in 1 file:

westram 2005-05-24 17:41 Rev.: 3850

- added function DEL_SHORT
- added variable AN_main.server_filedate

4 lines of code changed in 1 file:

westram 2005-05-24 17:40 Rev.: 3849

- fixed call to GBT_commit_rename_session()

1 lines of code changed in 1 file:

westram 2005-05-24 17:40 Rev.: 3848

- defined 2 different timeouts: one for each accept-call and a global timeout for the nameserver
- defined RETRY_SLEEP time

7 lines of code changed in 1 file:

westram 2005-05-24 17:39 Rev.: 3847

- made most functions static
- use case-insensitive compare for name parts
- automatically checks and removes name parts only differing in case
- capitalizes names that are completely in upper or lower case
- automatically corrects case of old all-upper-or-lower-case names
- improved error handling
- store filetime for automatic shutdown
- instantly shuts down when names.dat changes on disc
- use lower case for identifiers ('*acc' or 'name1*name2*S'), automatically make them lower-case
- added class NameInformation (helper to create shortname and its ID)
- reacts on deleted names.dat

509 lines of code changed in 1 file:

westram 2005-05-24 17:36 Rev.: 3846

- replaced GBS_SPECIES_HASH_SIZE by GBT_get_species_hash_size()
- spelling

6 lines of code changed in 1 file:

westram 2005-05-24 17:34 Rev.: 3845

- fixed call to GBT_commit_rename_session()
- ad_species_delete_cb: first search species, then ask to delete
- added ad_species_rename_cb
- added ad_species_copy_cb
- removed old rename/copy code
- made all local functions static

113 lines of code changed in 1 file:

westram 2005-05-24 17:08 Rev.: 3844

- allow modify_input_cb

1 lines of code changed in 1 file:

westram 2005-05-24 17:07 Rev.: 3843

- if aw_message is called with empty button string -> abort
- added input modifiers

83 lines of code changed in 1 file:

westram 2005-05-24 17:06 Rev.: 3842

- use GB_number_of_subentries()

3 lines of code changed in 2 files:

westram 2005-05-24 17:05 Rev.: 3841

- changekey management

370 lines of code changed in 2 files:

westram 2005-05-24 17:05 Rev.: 3840

- splitted into AWT_item_sel_list and SL/DB_SCANNER

0 lines of code changed in 1 file:

westram 2005-05-24 17:04 Rev.: 3839

- fixed calls to GEN_is_genome_db

4 lines of code changed in 2 files:

westram 2005-05-24 17:02 Rev.: 3838

- prototypes updated

5 lines of code changed in 2 files:

westram 2005-05-24 17:02 Rev.: 3837

- moved AWAR_CONFIG* to ad_config.h

0 lines of code changed in 1 file:

westram 2005-05-24 17:02 Rev.: 3836

- removed GBS_SPECIES_HASH_SIZE

1 lines of code changed in 1 file:

westram 2005-05-24 17:01 Rev.: 3835

- added $(GB_X) to objects

18 lines of code changed in 2 files:

westram 2005-05-24 17:00 Rev.: 3834

- GB_number_of_subentries() now works in server AND client
- removed GB_rescan_number_of_subentries()

18 lines of code changed in 1 file:

westram 2005-05-24 17:00 Rev.: 3833

- renames ARB_origin_species
- increased hash sizes used by rename session
- added GBT_get_species_hash_size()
- added GBT_get_tree_names_and_count()
- replaced GBS_SPECIES_HASH_SIZE by GBT_get_species_hash_size()
- assert GB_is_server in GBT_count_species
- removed GBT_recount_species (GBT_count_species now also works in client)
- moved duplicated code to gbt_free_rename_session_data()
- GBT_link_tree shows status message
- pass show_status_text() to GBT_commit_rename_session
- GBT_commit_rename_session: show status messages, rename species in configs
- GBT_rename_species stops early, if not a "real" rename
- removed gbt_rename_struct.new_species_hash (senseless!)

224 lines of code changed in 1 file:

westram 2005-05-24 16:58 Rev.: 3832

- uses GB_is_server()

3 lines of code changed in 1 file:

westram 2005-05-24 16:58 Rev.: 3831

- added GB_is_server() / GB_is_client()

17 lines of code changed in 1 file:

westram 2005-05-24 16:56 Rev.: 3830

- GEN_is_genome_db() moved here

29 lines of code changed in 2 files:

westram 2005-05-24 16:56 Rev.: 3829

- added $(GB_X) to objects
- uncommented strange targets

13 lines of code changed in 1 file:

westram 2005-05-24 16:55 Rev.: 3828

- added ad_config.o
- added new section for modules with separate headers
- commented sections

17 lines of code changed in 1 file:

westram 2005-05-24 12:40 Rev.: 3827

- objects fixed, depends updated

7 lines of code changed in 1 file:

westram 2005-05-24 12:39 Rev.: 3826

- moved to SL/AW_NAME

0 lines of code changed in 3 files:

westram 2005-05-24 12:38 Rev.: 3825

- handle editor configurations
- moved AWAR_CONFIG* here

83 lines of code changed in 1 file:

westram 2005-05-24 12:38 Rev.: 3824

- handle editor configurations
- added GBT_get_configuration_names()
- added save/load functions for config data

355 lines of code changed in 1 file:

westram 2005-05-24 12:37 Rev.: 3823

- changed hash table sizes

4 lines of code changed in 1 file:

westram 2005-05-24 12:36 Rev.: 3822

- aisc_server_shutdown -> aisc_server_shutdown_and_exit

7 lines of code changed in 2 files:

westram 2005-05-24 12:35 Rev.: 3821

- added AW_NAME.a to some exes
- several other lib fixes

16 lines of code changed in 1 file:

westram 2005-05-24 12:33 Rev.: 3820

* SL/Makefile: - added AW_NAME.a and DB_SCANNER.a

2 lines of code changed in 1 file:

westram 2005-05-24 12:32 Rev.: 3819

- former AWTC code

159 lines of code changed in 3 files:

westram 2005-05-24 12:32 Rev.: 3818

- separated from AWTC lib
- uses hashes to generate random names
- AWTC_makeUniqueShortName accepts long prefixes (cuts them)

474 lines of code changed in 1 file:

westram 2005-05-24 12:31 Rev.: 3817

- ARB database scanner (former AWT code)

707 lines of code changed in 3 files:

westram 2005-05-24 12:28 Rev.: 3816

- added ad_config.*
- added and use function arbdb_symlink
- added SL/AW_NAME/AW_rename.hxx
- added SL/DB_SCANNER/db_scanner.hxx
- added AWT/awt_changekey.hxx

56 lines of code changed in 1 file:

baderk 2005-05-22 13:54 Rev.: 3815

Added gcc version 3.3.6 to the list of working compilers.

1 lines of code changed in 1 file:

westram 2005-05-20 16:42 Rev.: 3814

- show more awars

9 lines of code changed in 1 file:

westram 2005-05-20 14:26 Rev.: 3813

- removed AWAR_EXPERIMENT_NAME (went to EXP.hxx)

1 lines of code changed in 1 file:

westram 2005-05-20 14:26 Rev.: 3812

- initialize AWAR_PROTEOM_NAME, AWAR_PROTEIN_NAME

3 lines of code changed in 1 file:

westram 2005-05-20 14:26 Rev.: 3811

- added AWAR_EXPERIMENT_NAME and proteom/protein awars

6 lines of code changed in 1 file:

westram 2005-05-06 15:28 Rev.: 3810

- fixed calls to ED4_cursor::set_to_terminal

6 lines of code changed in 1 file:

westram 2005-05-06 15:28 Rev.: 3809

- new parameter 'center_cursor' to ED4_cursor::set_to_terminal

48 lines of code changed in 2 files:

westram 2005-05-06 15:01 Rev.: 3808

- small fix; but failed to fix listbox display bug on menuett

16 lines of code changed in 1 file:

westram 2005-05-06 13:47 Rev.: 3807

- fixed a bug in AWT_embl_transl_table_2_arb_code_nr

10 lines of code changed in 1 file:

westram 2005-05-06 11:15 Rev.: 3806

- ED4_consensus_sequence_terminal::draw:
. avoids position overflow at right end
. fixed length of text passed to AW_device::text() from
- ED4_sequence_terminal::draw():
. fixed semantic of variable right (now it's the last position which is drawn)

27 lines of code changed in 1 file:

westram 2005-05-06 11:14 Rev.: 3805

- added ED4_expose_all_windows()

10 lines of code changed in 1 file:

westram 2005-05-06 11:14 Rev.: 3804

- HOME/END also work on empty consensus sequence (like '????')

5 lines of code changed in 1 file:

westram 2005-05-06 11:13 Rev.: 3803

- block operations restore cursor position

12 lines of code changed in 1 file:

westram 2005-05-06 11:13 Rev.: 3802

- invalidate cursors base_position before deleting managers (because it refers to managers callback list)
- if remapping is recalculated in expose callback -> detect changed screenwidth
and re-init depending variables
- actively re-set the cursor in expose callback
- quit: invalidate cursor (to unbind callbacks) before deleting internal data structures
- call species manager callbacks when rebuilding consensus

30 lines of code changed in 1 file:

westram 2005-05-06 11:08 Rev.: 3801

- added non-inline ED4_base_position-ctor/dtor
- bound invalidation callbacks to corresponding ED4_species_manager
- remove callback before adding new one in calc4base

35 lines of code changed in 1 file:

westram 2005-05-06 11:07 Rev.: 3800

- call remove_all_callbacks in kill_object

28 lines of code changed in 1 file:

westram 2005-05-06 11:06 Rev.: 3799

- added ED4_cursor::sequence2base_position(), ::get_base_position(), ::set_to_base_position(), ::jump_left_right_cursor_to_base_pos()
- added ED4_base_position::invalidate, made ctor/dtor non-inline
- added callback capability to ED4_species_manager
- added ED4_expose_all_windows
- bugfix: remap: hiding columns with less than x% nucleotides did not work

53 lines of code changed in 1 file:

westram 2005-05-06 11:04 Rev.: 3798

- added callback capability to ED4_species_manager

57 lines of code changed in 1 file:

westram 2005-05-06 11:00 Rev.: 3797

- ED4_sequence_terminal::calc_update_intervall() now clips right range to MAXSEQUENCECHARACTERLENGTH-1
- run ED4_species_manager callbacks

7 lines of code changed in 1 file:

westram 2005-05-06 10:58 Rev.: 3796

- assert right index inside alignment range in build_consensus_string()
- build_consensus_string:
. always uses '=' if no base present (even if count gaps is disabled)
. use '-' (instead of '=') when gap count is above limit
Now behavior is same as CON_evaluatestatistic()

15 lines of code changed in 1 file:

westram 2005-05-06 10:58 Rev.: 3795

- layout changed

58 lines of code changed in 1 file:

westram 2005-05-06 10:57 Rev.: 3794

- shows behavior for 100% gaps, sync with consensus/expert.fig

878 lines of code changed in 1 file:

westram 2005-05-06 10:57 Rev.: 3793

- shows behavior for 100% gaps, sync with edit4/consensus.fig

739 lines of code changed in 1 file:

westram 2005-05-06 10:56 Rev.: 3792

- note added

5 lines of code changed in 1 file:

westram 2005-05-06 10:54 Rev.: 3791

- saved (deleting empty gene_data containers)

0 lines of code changed in 1 file:

westram 2005-05-06 10:53 Rev.: 3790

- note

2 lines of code changed in 1 file:

westram 2005-05-06 10:53 Rev.: 3789

- updated

52 lines of code changed in 2 files:

westram 2005-05-06 08:35 Rev.: 3788

- gcc 4.0.0 fix (extern variable was declared static later)

1 lines of code changed in 2 files:

westram 2005-05-06 08:34 Rev.: 3787

- added virtual dtor to SEC_base

1 lines of code changed in 1 file:

westram 2005-05-06 08:34 Rev.: 3786

- added virtual dtor to PS_Callback

2 lines of code changed in 1 file:

westram 2005-05-06 08:34 Rev.: 3785

- gcc 4.0.0 fix (undefined behavior)

9 lines of code changed in 2 files:

westram 2005-05-06 08:34 Rev.: 3784

- gcc 4.0.0 fix

3 lines of code changed in 3 files:

westram 2005-05-06 08:33 Rev.: 3783

- added gcc 4.0.0

2 lines of code changed in 1 file:

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