Directory MERGE/

Directory Created:
2000-11-23 11:41
Total Files:
16
Deleted Files:
1
Lines of Code:
5910

[root]/MERGE

Lines of Code

MERGE/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 740 (100.0%) 17232 (100.0%) 23.2
westram 723 (97.7%) 14002 (81.3%) 19.3
oldcode 10 (1.4%) 3016 (17.5%) 301.6
meierh 1 (0.1%) 156 (0.9%) 156.0
yadhu 2 (0.3%) 34 (0.2%) 17.0
baderk 2 (0.3%) 19 (0.1%) 9.5
boehnel 1 (0.1%) 4 (0.0%) 4.0
epruesse 1 (0.1%) 1 (0.0%) 1.0

Most Recent Commits

westram 2022-06-20 12:12 Rev.: 19063


* fixed LOOP_VECTORIZED expressions that used '*'-count (for gcc 10.x-series).

1 lines of code changed in 1 file:

  • MERGE: MG_preserves.cxx (+1 -1)
westram 2022-03-30 17:36 Rev.: 18979


* fix use of empty labels:
- {{{AW_window::label}}} no longer
* accepts empty labels.
* allows to overwrite existing labels (assume this happens by mistake).
- {{{create_toggle_field}}}:
* assert label is used (in flavor with label-parameter)
* remove empty and NULp labels passed (from callers).

1 lines of code changed in 1 file:

  • MERGE: MG_gene_species.cxx (+1 -1)
westram 2022-03-30 17:31 Rev.: 18978


* remove unused mnemonic parameter to 'create_toggle_field'
- makes no sense anyway: having mnemonic for each toggle is sufficient (hence not implemented).

1 lines of code changed in 1 file:

  • MERGE: MG_gene_species.cxx (+1 -1)
westram 2022-03-04 16:20 Rev.: 18964


* remove parameter {{{fallback2default}}} from
- {{{create_selection_list}}}
- {{{create_list}}}
- {{{awt_create_TREE_selection_list}}}
- {{{awt_create_CONFIG_selection_list}}}
- {{{awt_create_SAI_selection_list}}}
* remove some - now unused - locals.

10 lines of code changed in 5 files:

  • MERGE: MG_configs.cxx (+2 -2), MG_extendeds.cxx (+2 -2), MG_gene_species.cxx (+1 -1), MG_preserves.cxx (+3 -3), MG_trees.cxx (+2 -2)
westram 2022-03-04 16:13 Rev.: 18962


* eliminate unused parameter {{{fallback2default}}} from {{{create_option_menu}}}.

3 lines of code changed in 2 files:

  • MERGE: MG_species.cxx (+2 -2), MG_trees.cxx (+1 -1)
westram 2022-03-04 12:26 Rev.: 18959


* reintegrates 'progress' into 'trunk'
- implements #789
* adds: log:branches/progress@18885:18958

11 lines of code changed in 1 file:

  • MERGE: Makefile (+11)
westram 2021-11-05 15:15 Rev.: 18827


* cleanup merge selectors.

20 lines of code changed in 2 files:

  • MERGE: MG_extendeds.cxx (+8 -20), MG_species.cxx (+12 -18)
westram 2021-11-05 12:35 Rev.: 18826


* add SAI selectors for both databases
- fixes crash when opening SAI transfer

64 lines of code changed in 1 file:

  • MERGE: MG_extendeds.cxx (+64 -2)
westram 2021-11-05 12:33 Rev.: 18825


* merging via FTS into new database did not copy alignment information. fixed.

2 lines of code changed in 1 file:

  • MERGE: MG_species.cxx (+2)
westram 2021-10-07 19:18 Rev.: 18754


* define {{{ItemSelector}}} for SAIs (lacks changekey functionality, i.e. does not fit into a search&query).
* mark places where species-selector is misused for SAIs.

2 lines of code changed in 1 file:

  • MERGE: MG_extendeds.cxx (+2 -2)
westram 2021-09-15 13:52 Rev.: 18730


* remove trailing whitespace from c source.

13 lines of code changed in 3 files:

  • MERGE: MG_main.cxx (+1 -1), MG_preserves.cxx (+3 -3), MG_trees.cxx (+9 -9)
westram 2021-09-15 13:39 Rev.: 18725


* rename {{{CPP_OBJECTS}}} -> {{{OBJECTS}}}.

5 lines of code changed in 1 file:

  • MERGE: Makefile (+5 -5)
westram 2021-05-08 15:19 Rev.: 18647


* reduced optimisation for TEST_remapping() and TEST_shaded_values().

10 lines of code changed in 1 file:

  • MERGE: MG_adapt_ali.cxx (+10 -10)
westram 2020-10-05 16:24 Rev.: 18599


* fix parameters of {{{GBT_rename_alignment}}} + {{{gbt_rename_alignment_of_item}}}
- rename.
- change to bool.
- callers use bool.

1 lines of code changed in 1 file:

  • MERGE: MG_species.cxx (+1 -1)
westram 2020-03-04 11:08 Rev.: 18359


* add new FTS transfer mode to merge-tool (implements #825)
- allows to skip transport of sequence alignment data (i.e. allows plain metadata updates)
* update+fix documentation

41 lines of code changed in 1 file:

  • MERGE: MG_species.cxx (+41 -20)
westram 2019-10-08 17:51 Rev.: 18159


* full update from child 'fix' into 'trunk'
- fix item name accessors ({{{GBT_get_name}}} + {{{GBT_get_name_or_description}}})
- add {{{null2empty}}}
* adds: log:branches/fix@18140:18158

41 lines of code changed in 5 files:

  • MERGE: MG_adapt_ali.cxx (+1 -1), MG_checkfield.cxx (+1 -1), MG_gene_species.cxx (+2 -2), MG_preserves.cxx (+2 -2), MG_species.cxx (+35 -26)
westram 2019-09-17 15:46 Rev.: 18092


* full update from child 'fts' into 'trunk'
- implements #562
* adds:
- [18091/branches/fts]
- log:branches/gui@17754:17924,17926:18090

600 lines of code changed in 5 files:

  • MERGE: MG_adapt_ali.cxx (+46 -42), MG_adapt_ali.hxx (+13 -2), MG_alignment.cxx (+1 -1), MG_species.cxx (+537 -250), Makefile (+3)
westram 2019-09-17 15:13 Rev.: 18088


* reintegrates 'fts' into 'trunk'
* adds:
- log:branches/fts@17653,17655:17717,17724:18087
- [17925/branches/gui]

1 lines of code changed in 1 file:

  • MERGE: needs_libs (+1)
westram 2019-07-17 16:27 Rev.: 17982


* reduced use of GB_change_my_security:
- use GB_securityLevel instead of manually fiddling around with GB_change_my_security.
- inspected and accepted leftover uses (see comments).

1 lines of code changed in 1 file:

  • MERGE: MG_main.cxx (+1 -1)
westram 2019-07-17 16:22 Rev.: 17980


* use security objects instead of manually calling GB_push/pop_my_security.
* eliminate GB_push/pop_my_security.
* fix scoping using a TA object.

8 lines of code changed in 1 file:

  • MERGE: MG_species.cxx (+8 -10)
westram 2019-05-10 13:57 Rev.: 17877


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

1 lines of code changed in 1 file:

  • MERGE: MG_checkfield.cxx (+1 -1)
westram 2019-04-29 14:44 Rev.: 17836


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

10 lines of code changed in 5 files:

  • MERGE: MG_alignment.cxx (+1 -1), MG_configs.cxx (+1 -1), MG_extendeds.cxx (+1 -1), MG_species.cxx (+6 -6), MG_trees.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:

  • MERGE: MG_species.cxx (+1 -1)
westram 2019-04-01 17:41 Rev.: 17724


* partial merge from 'fts' into 'trunk'
- {{{ConfigMapping}}}:
* cleanup
* add missing tests
* fix config bug: trailing backslash at end of values did cause wrong read of data
* adds: log:branches/fts@17718:17723

2 lines of code changed in 1 file:

  • MERGE: Makefile (+2)
westram 2018-10-24 15:58 Rev.: 17534


* partial merge from 'fix' into 'trunk'
- globally define what are "gaps"
- kept behavioral changes to a minimum:
* defaults for (user-defined) gap-definition in EDIT4 changed
* EDIT sequence search also uses user-defined gaps
* adds: log:branches/fix@17529:17533

5 lines of code changed in 3 files:

  • MERGE: MG_adapt_ali.cxx (+3 -1), MG_preserves.cxx (+1 -1), Makefile (+1)
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

3 lines of code changed in 2 files:

  • MERGE: MG_checkfield.cxx (+2 -2), merge.hxx (+1 -1)
westram 2018-07-10 16:48 Rev.: 17178


* reintegrates 'gcc' into 'trunk'
- complete arb port to gcc 8.1
- fixes NDEBUG-related issues (not handled by [16986])
* adds: log:branches/gcc@17164:17177

1 lines of code changed in 1 file:

  • MERGE: MG_checkfield.cxx (+1 -1)
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

118 lines of code changed in 10 files:

  • MERGE: MG_adapt_ali.cxx (+24 -24), MG_alignment.cxx (+2 -2), MG_checkfield.cxx (+10 -10), MG_configs.cxx (+1 -1), MG_extendeds.cxx (+2 -2), MG_gene_species.cxx (+18 -18), MG_main.cxx (+11 -11), MG_names.cxx (+6 -6), MG_species.cxx (+38 -38), MG_trees.cxx (+6 -6)
westram 2017-11-17 13:54 Rev.: 16668


* full update from child 'gcc' into 'trunk'
- fix/suppress (new) compiler warnings
- skip vectorizer notes
* adds: log:branches/gcc@16656:16667

2 lines of code changed in 2 files:

  • MERGE: MG_species.cxx (+1), MG_trees.cxx (+1 -1)
westram 2017-11-14 15:36 Rev.: 16653


* reintegrates 'gcc' into 'trunk' (fixes defect part of #752)
- allow compilation with gcc 7.x series (accepting 2 clang-test-results for gcc 7.x)
- vectorization:
* in {{{SL/CONSENSUS/chartable.cxx}}} works again with gcc 7.x (broken for 6.x series)
- checker: added syntax to exclude a range of versions
* check new 7.x vectorizations + fix vectorization-counts
* adds: log:branches/gcc@16578:16635,16649:16652

1 lines of code changed in 1 file:

  • MERGE: MG_preserves.cxx (+1 -1)
westram 2017-11-06 14:54 Rev.: 16628


* reintegrates 'vectorize' into 'trunk'
- fixes #700
* documented vectorization-checks
* fine-grained check based on gcc-version
- drops old gcc-versions (<4.4.3)
- new attribute {{{__ATTR__DONT_VECTORIZE}}}
* disabled vectorization of {{{POS_TREE2::init_static()}}} for newer gcc-versions (generated code fails tests)
- added a bunch of new vectorization-checks (probably irrelevant to overall performance)
* adds: log:branches/vectorize@15531:16585,16595:16627

5 lines of code changed in 3 files:

  • MERGE: MG_adapt_ali.cxx (+3 -3), MG_checkfield.cxx (+1 -1), MG_preserves.cxx (+1 -1)
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

99 lines of code changed in 6 files:

  • MERGE: MG_alignment.cxx (+9 -14), MG_configs.cxx (+40 -71), MG_extendeds.cxx (+32 -63), MG_species.cxx (+6 -6), Makefile (+2), merge.hxx (+10 -8)
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

8 lines of code changed in 2 files:

  • MERGE: MG_gene_species.cxx (+7 -2), Makefile (+1)
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

9 lines of code changed in 2 files:

  • MERGE: MG_extendeds.cxx (+3 -4), MG_species.cxx (+6 -3)
westram 2016-08-11 11:05 Rev.: 15176


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

26 lines of code changed in 5 files:

  • MERGE: MG_adapt_ali.cxx (+4 -4), MG_checkfield.cxx (+2 -2), MG_species.cxx (+7 -8), MG_trees.cxx (+2 -2), Makefile (+11)
westram 2016-07-27 11:30 Rev.: 15094


* reintegrates 'fix' into 'trunk'
* adds: log:branches/fix@15066,15073:15076,15082,15086:15093

2 lines of code changed in 1 file:

  • MERGE: MG_main.cxx (+2 -1)
westram 2016-07-14 14:45 Rev.: 15053


* merge most WINDOW patches from 'color' into 'trunk'
- color-ranges (completes implementation of #682)
* new types (cyclic, planar and spatial)
* can display as canvas-overlay
* setup in separate window
* allow external access via ID (query, activate)
* adds: log:branches/color@14984,14986:14987,14989,14993,15000,15005:15006,15008,15011,15036

1 lines of code changed in 1 file:

  • MERGE: Makefile (+1)
westram 2016-04-29 18:02 Rev.: 14786


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

212 lines of code changed in 6 files:

  • MERGE: MG_checkfield.cxx (+130 -103), MG_extendeds.cxx (+2 -2), MG_gene_species.cxx (+2 -2), MG_names.cxx (+4 -10), MG_species.cxx (+72 -64), Makefile (+2)
westram 2016-04-18 11:51 Rev.: 14741


* mark more unwanted widget-callbacks (#559)

1 lines of code changed in 1 file:

  • MERGE: MG_names.cxx (+1 -1)
westram 2016-01-23 07:20 Rev.: 14674


* rename {{{GB_write_as_string}}} -> {{{GB_write_autoconv_string}}}

1 lines of code changed in 1 file:

  • MERGE: MG_checkfield.cxx (+1 -1)

(316 more)

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