August 2004 Commit Log

Number of Commits:

81

Number of Active Developers:

2

meierh 2004-08-25 17:11 #81 Rev.: 3119

import locations with ^ too

55 lines of code changed in 1 file:

• GENOM: GEN_read.cxx (+55 -40)

westram 2004-08-25 16:14 #80 Rev.: 3118

debug helpers

14 lines of code changed in 2 files:

• ARBDB: ad_core.c (+7)
• AWT: AWT_tree.cxx (+7 -1)

westram 2004-08-25 10:33 #79 Rev.: 3117

- cleanup
- gb_save_dictionary -> gb_save_dictionary_data
- added gb_load_dictionary_data + gb_read_dict_data
- gb_save_dictionary_data deletes existing dictionary if parameter 'dict' is NULL

85 lines of code changed in 1 file:

• ARBDB: adsystem.c (+85 -33)

westram 2004-08-25 10:30 #78 Rev.: 3116

- readAndWrite forwards error
- rescue old dictionary data and restore it in case of an error during re-compression
- GB_optimize does no longer open transactions
- gb_create_dictionaries creates single transactions for each dictionary generation
and does proper abort (including restore of old dictionary) in error-case

95 lines of code changed in 1 file:

• ARBDB: adoptimize.c (+95 -76)

westram 2004-08-25 10:23 #77 Rev.: 3115

- spelling

1 lines of code changed in 1 file:

• ARBDB: admalloc.c (+1 -1)

westram 2004-08-25 10:23 #76 Rev.: 3114

updated

3 lines of code changed in 1 file:

• ARBDB: ad_lpro.h (+3 -1)

westram 2004-08-25 10:23 #75 Rev.: 3113

minor change

1 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+1 -1)

westram 2004-08-24 12:54 #74 Rev.: 3112

- added taxonomy(1)

5 lines of code changed in 1 file:

• lib/sellists: srt_aci.sellst (+5 -4)

westram 2004-08-24 12:54 #73 Rev.: 3111

- corrected description for binary operators with 2 arguments
- added description+examples for 'select'
- corrected description for 'contains' and 'partof'

39 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: commands.hlp (+39 -10)

westram 2004-08-24 12:54 #72 Rev.: 3110

- fixed a bug in make_node_text_struct.append()

12 lines of code changed in 1 file:

• AWT: AWT_nds.cxx (+12 -4)

westram 2004-08-24 12:53 #71 Rev.: 3109

- implemented toback + tofront
- binary operators with 2 arguments interpret their arguments as escaped ACI commands
- added command 'select'

75 lines of code changed in 1 file:

• ARBDB: adlang1.c (+75 -17)

westram 2004-08-19 17:13 #70 Rev.: 3108

- added reverse to input_format_per_line

6 lines of code changed in 1 file:

• AWTI: awti_imp_local.hxx (+6)

westram 2004-08-19 17:13 #69 Rev.: 3107

- reverses match list after reading IFT

4 lines of code changed in 1 file:

• AWTI: AWTI_import.cxx (+4 -1)

westram 2004-08-19 14:30 #68 Rev.: 3106

- awt_create_query_box tried to read a awar w/o having its name (fixed)

1 lines of code changed in 1 file:

• AWT: AWT_query_and_functions.cxx (+1 -1)

westram 2004-08-19 11:54 #67 Rev.: 3105

- description of binary operators
- description of string compare/find functions
- description of dropempty, dropzero and merge

68 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: commands.hlp (+68 -15)

westram 2004-08-19 11:54 #66 Rev.: 3104

- uses nested callbacks for numeric binary operators (plus, minus, ...)
- added 'rest' (aka modulo)
- implemented gbl_apply_binary_operator()
- made contains, partof, equals and compare binary operators
- added case insensitive versions (icontains, ipartof, iequals and icompare)
- fixed bugs in 'command', 'eval' + 'origin' (in case of X input streams the
ACI-command has been applied X times to the first input stream)
- added merge, drop, rot, swap
- added dropempty + dropzero

332 lines of code changed in 1 file:

• ARBDB: adlang1.c (+332 -170)

westram 2004-08-19 11:51 #65 Rev.: 3103

*** empty log message ***

2 lines of code changed in 1 file:

• ARBDB: adlocal.h (+2 -2)

westram 2004-08-19 11:51 #64 Rev.: 3102

- GB_command_interpreter errors are more verbose

37 lines of code changed in 1 file:

• ARBDB: adquery.c (+37 -10)

westram 2004-08-19 11:50 #63 Rev.: 3101

- dont expand error from GB_command_interpreter (now it's descriptive enough)

2 lines of code changed in 1 file:

• AWT: AWT_nds.cxx (+2 -4)

westram 2004-08-18 12:01 #62 Rev.: 3100

- hint how one can write NDS content into DB
- describes new NDS window behavior

21 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: props_nds.hlp (+21 -25)

westram 2004-08-18 12:00 #61 Rev.: 3099

- added description for 'compare'
- added description for 'taxonomy'

20 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: commands.hlp (+20 -1)

westram 2004-08-18 11:33 #60 Rev.: 3098

- change tree-sort-type to AP_NO_NDS during startup

8 lines of code changed in 1 file:

• PARSIMONY: PARS_main.cxx (+8 -1)

westram 2004-08-18 11:33 #59 Rev.: 3097

- minor change

7 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+7 -6)

westram 2004-08-18 11:33 #58 Rev.: 3096

- added GB_add_priority_callback
- GB_add_callback uses default priority 5

50 lines of code changed in 1 file:

• ARBDB: arbdb.c (+50 -12)

westram 2004-08-18 11:33 #57 Rev.: 3095

- added 'priority' member to 'struct gb_callback'

1 lines of code changed in 1 file:

• ARBDB: adlocal.h (+1)

westram 2004-08-18 11:33 #56 Rev.: 3094

- adds callbacks to tree-containers, which deletes the taxonomy cache

82 lines of code changed in 1 file:

• ARBDB: adlang1.c (+82 -14)

westram 2004-08-18 11:33 #55 Rev.: 3093

- spelling

1 lines of code changed in 1 file:

• ARBDB: adhash.c (+1 -1)

westram 2004-08-18 11:32 #54 Rev.: 3092

- updated

1 lines of code changed in 1 file:

• ARBDB: ad_prot.h (+1)

westram 2004-08-17 13:41 #53 Rev.: 3091

- fixed AWAR_CHANGE_DUMP

7 lines of code changed in 1 file:

• WINDOW: AW_nawar.cxx (+7 -4)

westram 2004-08-17 13:40 #52 Rev.: 3090

- changed AWT_config_manager callbacks

105 lines of code changed in 6 files:

• AWT: AWT_query_and_functions.cxx (+14 -23), AWT_www.cxx (+11 -11)
• EDIT4: ED4_search.cxx (+20 -22)
• PRIMER_DESIGN: primer_design.cxx (+24 -33)
• PROBE_DESIGN: SaiProbeVisualization.cxx (+9 -10), probe_design.cxx (+27 -25)

westram 2004-08-17 13:37 #51 Rev.: 3089

- changed AWT_config_manager callbacks (puh!)

35 lines of code changed in 1 file:

• MERGE: MG_gene_species.cxx (+35 -38)

westram 2004-08-17 13:35 #50 Rev.: 3088

- changed AWT_config_manager callbacks
- conversion from old->new NDS config (for stored configs)

104 lines of code changed in 1 file:

• AWT: AWT_nds.cxx (+104 -12)

westram 2004-08-17 13:34 #49 Rev.: 3087

- moved class AWT_config_definition to header
- defined AWT_config_mapping global
- added 2nd ctor to AWT_config_definition (allows initialization from table)
- added AWT_config

170 lines of code changed in 1 file:

• AWT: AWT_config_manager.cxx (+170 -97)

westram 2004-08-17 13:34 #48 Rev.: 3086

- predeclares AWT_config_mapping
- moved class AWT_config_definition to header
- removed config def interface functions (done by class AWT_config_definition itself)
- added AWT_config (helper class - stores configname->awar or configname->value mapping)
- added methods to parse, modify and rebuild a config string

70 lines of code changed in 1 file:

• AWT: awt_config_manager.hxx (+70 -8)

westram 2004-08-13 14:06 #47 Rev.: 3085

- updated

1 lines of code changed in 2 files:

• ARBDB: ad_lpro.h (+1), ad_prot.h (-1)

westram 2004-08-13 14:06 #46 Rev.: 3084

- moved some ACI related types to adlocal.h

1 lines of code changed in 1 file:

• ARBDB: arbdb.h (+1 -39)

westram 2004-08-13 14:06 #45 Rev.: 3083

- GB_install_command_table -> gb_install_command_table (visibility now arbdb local)
- uses GBL_command_arguments in calls to ACI commands

13 lines of code changed in 1 file:

• ARBDB: adquery.c (+13 -4)

westram 2004-08-13 14:05 #44 Rev.: 3082

- moved GBL, GBL_COMMAND and GBL_command_table here (were in arbdb.h)
- GBL_COMMAND: uses GBL_command_arguments instead of looong parameter list

36 lines of code changed in 1 file:

• ARBDB: adlocal.h (+36)

westram 2004-08-13 14:05 #43 Rev.: 3081

- started to make binary functions a generalized concept [unused yet]
- converted all ACI-command-functions (using struct instead of long parameter list)
- general cleanup

615 lines of code changed in 1 file:

• ARBDB: adlang1.c (+615 -696)

westram 2004-08-13 14:04 #42 Rev.: 3080

- removed debug output

2 lines of code changed in 1 file:

• WINDOW: AW_button.cxx (+2 -2)

westram 2004-08-12 13:35 #41 Rev.: 3079

- fixed group_key bug

7 lines of code changed in 1 file:

• ARBDB: adlang1.c (+7 -7)

westram 2004-08-12 12:20 #40 Rev.: 3078

- sets tree awar-name

1 lines of code changed in 1 file:

• NTREE: ad_spec.cxx (+1)

westram 2004-08-12 12:20 #39 Rev.: 3077

- pass name of current tree to make_node_text_nds in export_nds_cb()
- changes tree display type for first refresh (does not use NDS)

22 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+22 -13)

westram 2004-08-12 12:18 #38 Rev.: 3076

- set tree awar-name to 0

1 lines of code changed in 1 file:

• MERGE: MG_species.cxx (+1)

westram 2004-08-12 12:17 #37 Rev.: 3075

- set tree awar-name

5 lines of code changed in 2 files:

• GENOM: EXP_interface.cxx (+2 -1), GEN_interface.cxx (+3 -2)

westram 2004-08-12 12:17 #36 Rev.: 3074

- fixed call to make_node_text_nds

3 lines of code changed in 1 file:

• DIST: DI_save_matr.cxx (+3 -3)

westram 2004-08-12 12:16 #35 Rev.: 3073

- reads the current tree from configured awar (normally points to AWAR_TREE)
- query functions pass tree_name down into ACI calls

32 lines of code changed in 1 file:

• AWT: AWT_query_and_functions.cxx (+32 -31)

westram 2004-08-12 12:16 #34 Rev.: 3072

- new parameter 'tree_name' for make_node_text_nds()
- rewrote create_nds_var (converts old NDS style [inherit] to new style [group|leaf|taxonomy])
- make_node_text_struct modified (- 'inherit' + 'at_group' and 'at_leaf')
+ added some methods to fill NDS buffer w/o overflow
- make_node_text_init() expects 'group' and 'leaf' instead of 'inherit' and 'flag1'
- fixed elements in NDS window
- fixed name of awars (tmp/viewkeys/key_text_select)
- saving NDS config is currently broken

468 lines of code changed in 1 file:

• AWT: AWT_nds.cxx (+468 -286)

westram 2004-08-12 12:12 #33 Rev.: 3071

- calls to make_node_text_nds pass 'tree_name'
- changed calls to NT_scalebox

4 lines of code changed in 1 file:

• AWT: AWT_irstree.cxx (+4 -4)

westram 2004-08-12 12:12 #32 Rev.: 3070

- calls to make_node_text_nds pass 'tree_name'

21 lines of code changed in 1 file:

• AWT: AWT_imp_exp.cxx (+21 -23)

westram 2004-08-12 12:11 #31 Rev.: 3069

- added member variable 'tree_name' to AWT_graphic_tree
- calls to make_node_text_nds pass 'tree_name'
- added bool 'use_nds' to show_nds_list_rek (if false -> simply show name)
- changed calls to NT_scalebox / NT_emptybox / NT_rotbox

88 lines of code changed in 1 file:

• AWT: AWT_dtree.cxx (+88 -59)

westram 2004-08-12 12:09 #30 Rev.: 3068

- changed call to GB_command_interpreter

3 lines of code changed in 2 files:

• AWT: AWT_input_mask.cxx (+2 -2), AWT_www.cxx (+1 -1)

westram 2004-08-12 12:07 #29 Rev.: 3067

- added member 'tree_name' to awt_query_struct

1 lines of code changed in 1 file:

• AWT: awt.hxx (+1)

westram 2004-08-12 12:06 #28 Rev.: 3066

- added member 'tree_name' to struct adaqbsstruct

1 lines of code changed in 1 file:

• AWT: awtlocal.hxx (+1)

westram 2004-08-12 12:05 #27 Rev.: 3065

- new parameter 'tree_name' for make_node_text_nds()

1 lines of code changed in 1 file:

• AWT: awt_nds.hxx (+1 -1)

westram 2004-08-12 12:05 #26 Rev.: 3064

- added member variable 'tree_name' to AWT_graphic_tree
- added bool 'use_nds' to show_nds_list_rek (allows to toggle NDS-use)
- NT_scalebox, NT_emptybox, NT_rotbox: width passed as double

20 lines of code changed in 1 file:

• AWT: awt_dtree.hxx (+20 -18)

westram 2004-08-12 12:05 #25 Rev.: 3063

- added member 'gc_manager' to AWT_canvas
- beautified

41 lines of code changed in 1 file:

• AWT: awt_canvas.hxx (+41 -39)

westram 2004-08-12 12:04 #24 Rev.: 3062

- init 'gc_manager' member in ctor

1 lines of code changed in 1 file:

• AWT: AWT_canvas.cxx (+1)

westram 2004-08-12 12:03 #23 Rev.: 3061

- fixed calls to GB_command_interpreter

8 lines of code changed in 5 files:

• AWTC: AWTC_next_neighbours.cxx (+1 -1)
• AWTI: AWTI_import.cxx (+2 -3)
• EDIT4: ED4_nds.cxx (+1 -1)
• GENOM: GEN_nds.cxx (+1 -1)
• MERGE: MG_gene_species.cxx (+3 -3)

westram 2004-08-12 12:01 #22 Rev.: 3060

- beautified

119 lines of code changed in 1 file:

• WINDOW: AW_Xm.cxx (+119 -119)

westram 2004-08-12 11:58 #21 Rev.: 3059

improved help

3 lines of code changed in 1 file:

• SOURCE_TOOLS: mv_if_diff (+3 -2)

westram 2004-08-12 11:58 #20 Rev.: 3058

don't remember where this came from

78 lines of code changed in 1 file:

• lib/import: bergey.ift (new 78)

westram 2004-08-12 11:56 #19 Rev.: 3057

- changed type of GBL_COMMAND

7 lines of code changed in 1 file:

• ARBDB: arbdb.h (+7 -1)

westram 2004-08-12 11:56 #18 Rev.: 3056

- changed call to GB_command_interpreter

2 lines of code changed in 1 file:

• ARBDB: adstring.c (+2 -4)

westram 2004-08-12 11:56 #17 Rev.: 3055

- made ACI commands static (they are exported by hash)
- added 'equals', 'contains' and 'partof'
- skips internal numbers from taxonomy hash
- added ACI functions 'compare' + 'taxonomy'
- changed calls to GB_command_interpreter

653 lines of code changed in 1 file:

• ARBDB: adlang1.c (+653 -175)

westram 2004-08-12 11:53 #16 Rev.: 3054

cleanup

1 lines of code changed in 1 file:

• ARBDB: adsocket.c (+1 -4)

westram 2004-08-12 11:52 #15 Rev.: 3053

- GB_command_interpreter inserts default_tree_name into client data, which is now
passed to all commands

16 lines of code changed in 1 file:

• ARBDB: adquery.c (+16 -13)

westram 2004-08-12 11:49 #14 Rev.: 3052

updated

1 lines of code changed in 1 file:

• ARBDB: ad_prot.h (+1 -1)

westram 2004-08-12 11:49 #13 Rev.: 3051

- updated (gbl functions made static)

0 lines of code changed in 1 file:

• ARBDB: ad_lpro.h (-35)

westram 2004-08-12 11:48 #12 Rev.: 3050

- make 'proto' uses mv_if_diff to keep untouched as many headers as possible.

9 lines of code changed in 1 file:

• ARBDB: Makefile (+9 -9)

westram 2004-08-06 14:40 #11 Rev.: 3049

- sort_selection_list may sort case sensitive or not.
till now it always did it sensitive

26 lines of code changed in 1 file:

• WINDOW: AW_button.cxx (+26 -12)

westram 2004-08-06 14:40 #10 Rev.: 3048

- sort_selection_list prototype changed

1 lines of code changed in 1 file:

• WINDOW: aw_window.hxx (+1 -1)

westram 2004-08-06 14:37 #9 Rev.: 3047

- automatically sorts SAI selections lists
- prefixes SAIs with their group
- cleanup

41 lines of code changed in 1 file:

• AWT: AWT_sel_boxes.cxx (+41 -26)

westram 2004-08-06 14:37 #8 Rev.: 3046

- call to sort_selection_list changed

22 lines of code changed in 4 files:

• AWT: AWT_file_selection.cxx (+3 -3)
• MULTI_PROBE: MP_noclass.cxx (+8 -8)
• NTREE: NT_validManual.cxx (+2 -2)
• PROBE_DESIGN: probe_design.cxx (+9 -9)

westram 2004-08-06 13:31 #7 Rev.: 3045

- preserve -> adapt

21 lines of code changed in 6 files:

• HELP_SOURCE/oldhelp: mg_preserve.hlp (+5 -5), mg_species.hlp (+2 -2)
• MERGE: MG_preserves.cxx (+6 -6), MG_species.cxx (+3 -3)
• lib/pictures/merge: preserves.fig (+3 -3), species.fig (+2 -2)

westram 2004-08-05 14:50 #6 Rev.: 3044

uses ARB

3 lines of code changed in 1 file:

• PERL_SCRIPTS/GENOME: GI.pm (+3 -1)

westram 2004-08-05 14:50 #5 Rev.: 3043

- changed method to push include paths

10 lines of code changed in 1 file:

• PERL_SCRIPTS/GENOME: import_proteomdata.pl (+10 -4)

westram 2004-08-05 13:28 #4 Rev.: 3042

- fixed include path

1 lines of code changed in 1 file:

• PERL_SCRIPTS/GENOME: import_proteomdata.pl (+1 -1)

westram 2004-08-05 10:03 #3 Rev.: 3041

- added AW_window::GC_to_RGB
- GC_to_RGB maps ARB-gc into Xm-gc

23 lines of code changed in 1 file:

• WINDOW: AW_window.cxx (+23)

westram 2004-08-05 10:03 #2 Rev.: 3040

- added AW_window::GC_to_RGB

7 lines of code changed in 1 file:

• WINDOW: aw_window.hxx (+7 -6)

westram 2004-08-05 10:03 #1 Rev.: 3039

- added NT_dump_gcs

15 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+15)

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