Directory GENOM/

Directory Created:
2000-11-30 14:22
Total Files:
17
Deleted Files:
13
Lines of Code:
5521

[root]/GENOM

Lines of Code

GENOM/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 889 (100.0%) 15177 (100.0%) 17.0
westram 865 (97.3%) 14159 (93.3%) 16.3
meierh 17 (1.9%) 975 (6.4%) 57.3
baderk 2 (0.2%) 14 (0.1%) 7.0
spanfeln 1 (0.1%) 13 (0.1%) 13.0
aboeckma 2 (0.2%) 12 (0.1%) 6.0
epruesse 1 (0.1%) 3 (0.0%) 3.0
boehnel 1 (0.1%) 1 (0.0%) 1.0

Most Recent Commits

westram 2019-07-02 14:45 Rev.: 17944


* FIXES crash in RELEASE version (when invalid color group occurs in database).
* add assertions against
- invalid color_groups and
- invalid unshaded GCs.
* ARBDB color-group interface:
- define number of allowed color groups in ARBDB
- fix interface types (long->int)
- report error when color_group passed to {{{GBT_set_color_group}}} is out-of-range.
- {{{GBT_get_color_group}}} does range check. returns 0 if out-of-range.

2 lines of code changed in 2 files:

  • GENOM: GEN_graphic.cxx (-1), Makefile (+2)
westram 2019-05-14 13:59 Rev.: 17890


* reintegrates 'dbui' into 'trunk'
* adds: log:branches/dbui@17881:17889

2 lines of code changed in 2 files:

  • GENOM: EXP_interface.cxx (+1 -1), GEN_interface.cxx (+1 -1)
westram 2019-05-10 13:57 Rev.: 17877


* reintegrates 'gcc' into 'trunk'
* adds: log:branches/gcc@17850:17876

2 lines of code changed in 2 files:

  • GENOM: GEN_interface.cxx (+1 -1), GEN_nds.cxx (+1 -1)
westram 2019-04-29 14:44 Rev.: 17836


* reintegrates 'clone' into 'trunk'
* adds: log:branches/clone@17813:17835

2 lines of code changed in 2 files:

  • GENOM: EXP_interface.cxx (+1 -1), GEN_interface.cxx (+1 -1)
westram 2019-04-05 19:32 Rev.: 17748


* remove hardcoded 'markCreated==true' from
- GBT_find_or_create_species_rel_species_data and
- GBT_find_or_create_species.
* hardcode 'markCreated==false' in GBT_find_or_create_SAI.
- changes result DB.
- increase diff buf size (result DB has loooong lines).

1 lines of code changed in 1 file:

  • GENOM: GEN_map.cxx (+1 -1)
westram 2018-10-31 10:52 Rev.: 17593


* reintegrates 'fix' into 'trunk'
- performs #798
* adds genetic code tables (24-31)
* adds combined amino acid J (I or L)
* improved translate and/or realign
- handle optional start-/stop-codons
- improve recognition of nuc-triples containing IUPAC-codes
* error messages now always list EMBL table numbers
* adds:
- log:branches/fix@17480:17485,17491:17492,17494:17507,17509:17528,17534:17592
- log:branches/optional@17481:17568

1 lines of code changed in 1 file:

  • GENOM: GEN_translations.cxx (+1 -1)
westram 2018-10-23 10:36 Rev.: 17510


* partial merge from 'fix' into 'trunk'
* adds: [17508/branches/fix]

2 lines of code changed in 1 file:

  • GENOM: GEN_translations.cxx (+2 -2)
westram 2018-09-20 18:43 Rev.: 17396


* reintegrates 'fix' into 'trunk'
- elim dead code
- use const hash loop
* adds: log:branches/fix@17380,17388:17395

16 lines of code changed in 2 files:

  • GENOM: GEN_local.hxx (-1), GEN_map.cxx (+16 -19)
westram 2018-07-23 16:52 Rev.: 17262


* partial merge from 'group' into 'trunk'
- fixes to arb_progress
* adds:
- log:branches/group@17191:17218,17220:17260
- log:branches/progress@17195:17216,17218:17259

2 lines of code changed in 1 file:

  • GENOM: GEN_map.cxx (+2 -2)
westram 2018-05-02 11:32 Rev.: 16961


* partial merge from 'fix' into 'trunk'
- refactored {{{AW_device}}} text output
* reduces calls to strlen (using {{{SizedCstr}}})
* eliminated/modernized several parameters/functions (esp. in {{{TextOverlayCallback}}}s)
* adds: log:branches/fix@16939:16960

5 lines of code changed in 2 files:

  • GENOM: GEN_graphic.cxx (+3 -3), Makefile (+2)
westram 2018-04-30 18:27 Rev.: 16936


* reintegrates 'cleanup' into 'trunk'
- performs #762 (shrink 3.7 k)
* adds: log:branches/cleanup@16924:16935

0 lines of code changed in 1 file:

  • GENOM: GEN_map.cxx (-2)
westram 2017-11-28 19:22 Rev.: 16766


* reintegrates 'gcc' into 'trunk'
- mostly cosmetics changes
* adds: log:branches/gcc@16655,16741:16743,16752:16765

4 lines of code changed in 3 files:

  • GENOM: EXP_interface.cxx (+1 -1), GEN_interface.cxx (+2 -2), GEN_map.cxx (+1 -3)
westram 2017-11-28 18:09 Rev.: 16763


* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751

162 lines of code changed in 8 files:

  • GENOM: EXP_interface.cxx (+20 -20), EXP_main.cxx (+1 -1), GEN_gene.cxx (+13 -13), GEN_graphic.cxx (+4 -4), GEN_interface.cxx (+43 -43), GEN_map.cxx (+60 -61), GEN_nds.cxx (+13 -13), GEN_translations.cxx (+8 -8)
westram 2017-10-08 15:54 Rev.: 16508


* reintegrates 'macros' into 'trunk'
- introduce generic input prompt (related #179)
- use it instead of locally generated windows:
* species (rename + create)
* alignment (rename, copy + create)
* experiments (rename, copy + create)
* genes (rename, copy + extract)
* mergetool (rename SAI + configs)
* SAIviz color translation (copy + create)
- fixed bugs in mergetool ([16503],[16504])
* adds: log:branches/macros@16484:16507

129 lines of code changed in 8 files:

  • GENOM: EXP_interface.cxx (+49 -108), EXP_local.hxx (-3), EXP_main.cxx (-1), GEN.hxx (+1 -2), GEN_interface.cxx (+48 -84), GEN_local.hxx (-3), GEN_map.cxx (+28 -53), Makefile (+3)
westram 2017-09-23 14:03 Rev.: 16425


* reintegrates 'aci' into 'trunk'
- extends ACI language (implementing #707)
* boolean operators: {{{And}}},{{{Or}}},{{{Not}}}
* numeric comparison: {{{isAbove}}},{{{isBelow}}},{{{isEqual}}}
* floating point arithmetic: {{{fplus}}},{{{fminus}}},{{{fmult}}},{{{fdiv}}}
* misc: {{{round}}},{{{inRange}}},{{{isEmpty}}}
- enforce parameter checks in ACI function code
- case of commands completely ignored
* adds: log:branches/aci@16385,16391:16424

1 lines of code changed in 1 file:

  • GENOM: Makefile (+1)
westram 2017-09-18 15:23 Rev.: 16374


* reintegrates 'aci' into 'trunk'
- refactored wide parts of ACI code (incl. SRT+REG)
* added more test
* ACI tracing
- more complete and readable
- automatically turned off when done with expression
* improved error messages (esp. diagnostics)
* documentation (updated, added missing)
* fixed a bunch of bugs (incl. SEGV and deadlock)
* ACI now runs inside execution environment
- ACI language may be extended with custom commands (implements #756)
* added ACI extension for group-batch-rename
* adds:
- log:branches/aci@16170:16373
- log:branches/addtest@16193:16316

12 lines of code changed in 4 files:

  • GENOM: GEN_gene.cxx (+2 -2), GEN_nds.cxx (+5 -2), GEN_nds.hxx (+1 -1), Makefile (+4)
westram 2017-06-08 17:59 Rev.: 16021


* reintegrates 'fix' into 'trunk'
- refactors {{{DbScanner}}} -> OO + shrink 1.4k
- fixes #251 and #506
* adds: log:branches/fix@15975,15982:16020

10 lines of code changed in 2 files:

  • GENOM: EXP_interface.cxx (+5 -3), GEN_interface.cxx (+5 -3)
westram 2017-06-02 11:17 Rev.: 15982


* full update from child 'fix' into 'trunk'
- fixes #478
* adds: log:branches/fix@15976:15981

10 lines of code changed in 2 files:

  • GENOM: EXP_interface.cxx (+5 -3), GEN_interface.cxx (+5 -3)
westram 2017-05-21 17:59 Rev.: 15966


* reintegrates 'group' into 'trunk'
- implements #652 (group search)
* adds: log:branches/group@15733:15740,15743:15748,15750:15752,15754,15756,15758:15777,15781:15793,15796,15798:15806,15808:15817,15819:15965

2 lines of code changed in 2 files:

  • GENOM: EXP_interface.cxx (+1 -1), GEN_interface.cxx (+1 -1)
westram 2017-03-23 14:58 Rev.: 15665


* reintegrates 'refactor' into 'trunk'
- refactored AWT_graphic
* now have explicit states with different permissions
1. update model + request view/DB updates (AWT_auto_refresh)
- always preceeded by DB->model up-to-date-check
- automatically updates the view on destruction
2. update (DB and view) from model
3. neither
- benefits
* saves several view-updates
* unproblematic nesting of functions requesting view-updates
* will allow
- delayed view-updates and
- easier modification of update logic
- fixes a bunch of update-issues (found on the way)
* adds: log:branches/refactor@15613:15615,15627:15637,15639:15664

43 lines of code changed in 3 files:

  • GENOM: GEN_graphic.cxx (+8 -10), GEN_graphic.hxx (+2 -3), GEN_map.cxx (+33 -22)
westram 2016-10-06 12:52 Rev.: 15306


* derive {{{TREE_canvas}}} from {{{AWT_canvas}}}
- move {{{awar_tree}}} -> {{{TREE_canvas}}}
- use {{{TREE_canvas}}} where required
- remove dummy-param from {{{AWT_canvas}}}-ctor
* rename {{{NT_canvas_registry}}} -> {{{TREE_canvas_registry}}}
* remove unused param from {{{AP_user_push_cb}}}

1 lines of code changed in 1 file:

  • GENOM: GEN_map.cxx (+1 -1)
westram 2016-10-05 12:39 Rev.: 15301


* full update from child 'sync' into 'trunk'
- register all NTREE canvases
- provide canvas selection list
- pass awar to canvas (not its name; expect awar already exists); no awar for non-tree-canvases
* adds: log:branches/sync@15292:15300

1 lines of code changed in 1 file:

  • GENOM: GEN_map.cxx (+1 -1)
westram 2016-08-30 12:30 Rev.: 15254


* depends for [15253]

2 lines of code changed in 1 file:

  • GENOM: Makefile (+2)
westram 2016-08-17 20:39 Rev.: 15198


* remove {{{virtual}}} if {{{OVERRIDE}}} is present
- OVERRIDE implies 'implicit virtual' (if code compiles as C++11 <- tested on build server!)

13 lines of code changed in 3 files:

  • GENOM: EXP_main.cxx (+5 -5), GEN_graphic.hxx (+3 -3), GEN_map.cxx (+5 -5)
westram 2016-08-11 11:05 Rev.: 15176


* reintegrates 'fixres' into 'trunk'
- fixes #715
* adds: log:branches/fixres@15127:15175

41 lines of code changed in 6 files:

  • GENOM: EXP_interface.cxx (+2 -2), GEN_gene.cxx (+1 -1), GEN_interface.cxx (+6 -8), GEN_map.cxx (+4 -4), GEN_nds.cxx (+20 -23), Makefile (+8)
westram 2016-07-27 13:26 Rev.: 15096


* add scalers to genemap-options

50 lines of code changed in 1 file:

  • GENOM: GEN_map.cxx (+50 -38)
westram 2016-07-21 17:53 Rev.: 15082


* partial merge from 'fix' into 'trunk'
- default_copyability++
* adds: log:branches/fix@15072,15077:15081

24 lines of code changed in 3 files:

  • GENOM: GEN_gene.cxx (+12 -8), GEN_gene.hxx (+10 -21), GEN_map.cxx (+2 -7)
westram 2016-07-15 15:48 Rev.: 15064


* remove parameter {{{base_gc}}} from {{{AW_manage_GC}}} (always zero)

1 lines of code changed in 1 file:

  • GENOM: GEN_graphic.cxx (+1 -1)
westram 2016-06-15 13:35 Rev.: 14943


* merge 2 WINDOW-modifications from 'color' into 'trunk'
* adds: log:branches/color@14929,14940

8 lines of code changed in 2 files:

  • GENOM: GEN_graphic.cxx (+6 -3), Makefile (+2)
westram 2016-05-27 11:16 Rev.: 14866


* change names of GC-property-windows to reset stored window-user-sizes
- only done for "named" propery-windows (standard windows have already been reset with [14864])

1 lines of code changed in 1 file:

  • GENOM: GEN_map.cxx (+1 -1)
westram 2016-05-12 09:58 Rev.: 14838


* no longer pseudo-hide gc-manager-object
- {{{aw_gc_manager}}} -> {{{AW_gc_manager}}}
- use pointers to {{{AW_gc_manager}}} instead of pointer-typedef

19 lines of code changed in 3 files:

  • GENOM: GEN_graphic.cxx (+17 -14), GEN_graphic.hxx (+1 -1), GEN_map.cxx (+1 -1)
westram 2016-04-29 18:02 Rev.: 14786


* reintegrates 'gde' into 'trunk'
- fixes #695
* adds: log:branches/gde@14670:14675,14682:14785

22 lines of code changed in 3 files:

  • GENOM: EXP_interface.cxx (+3 -4), GEN_interface.cxx (+3 -4), GEN_nds.cxx (+16 -55)
westram 2016-01-29 09:35 Rev.: 14686


* change datatypes used in awar-access (only changed simple cases)

12 lines of code changed in 1 file:

  • GENOM: GEN_graphic.cxx (+12 -12)
westram 2015-11-11 13:40 Rev.: 14490


* change callbacktype used to trigger refresh after GCs changed
- pass what has been changed (font,color only,use of color groups)
* added standard callback ({{{AWT_GC_changed_cb}}})
* {{{AWAR_COLOR_GROUPS_USE}}}
- remove client callback triggering refresh (installed by TREEDISP)
- add general callback calling {{{GcChangedCallback}}} passed to {{{AW_manage_GC}}}
- hide awar inside {{{AW_preset.cxx}}}
* effects:
- EDIT4 does refresh now when toggling use of color groups
- (several) canvases just do "expose" in case of color change (instead of "resize/zoom reset" which is needed for font changes)

1 lines of code changed in 1 file:

  • GENOM: GEN_graphic.cxx (+1 -1)
westram 2015-11-04 11:43 Rev.: 14457


* few more callback fixes

3 lines of code changed in 1 file:

  • GENOM: EXP_main.cxx (+3 -6)
westram 2015-11-04 10:57 Rev.: 14453


* do not cast AW_POPDOWN

15 lines of code changed in 3 files:

  • GENOM: EXP_interface.cxx (+6 -5), GEN_interface.cxx (+6 -5), GEN_map.cxx (+3 -3)
westram 2015-10-30 18:12 Rev.: 14448


* remove impossible TODOs
* use DOWNCAST for expected dynamic type

2 lines of code changed in 1 file:

  • GENOM: GEN_map.cxx (+2 -5)
westram 2015-10-30 17:22 Rev.: 14445


* fix callback handling in genemap
- revert first attempt to fix ([14436])
- bind callbacks to '''correct''' {{{gene_data}}} if genemap is attached to an organism (was always bound to globally "selected organism")
- test whether organism still exists before removing callbacks (if not -> just forget callbacks)
- fixes
* crash at exit (as fixed by [14436])
* various crashes occurring while attaching, deleting and unattaching organisms from views

70 lines of code changed in 5 files:

  • GENOM: GEN.hxx (-2), GEN_graphic.cxx (+12 -4), GEN_graphic.hxx (+3 -2), GEN_local.hxx (+1), GEN_map.cxx (+54 -30)
westram 2015-10-30 17:20 Rev.: 14444


* clear unhandled error while extracting genes to a non-existing alignment

5 lines of code changed in 1 file:

  • GENOM: GEN_map.cxx (+5 -2)
westram 2015-10-30 13:07 Rev.: 14442


* fix genemap gc window
- id clashed with NTREE gc window. fixed by using named gc window
- created multiple gc windows for multiple genemaps

8 lines of code changed in 1 file:

  • GENOM: GEN_map.cxx (+8 -1)

(391 more)

Generated by StatSVN 0.7.0