Lines of Code
[root]/PARSIMONY
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 780 (100.0%) | 26647 (100.0%) | 34.1 |
| westram | 752 (96.4%) | 19035 (71.4%) | 25.3 |
| oldcode | 21 (2.7%) | 7371 (27.7%) | 351.0 |
| meierh | 1 (0.1%) | 233 (0.9%) | 233.0 |
| yadhu | 1 (0.1%) | 4 (0.0%) | 4.0 |
| epruesse | 2 (0.3%) | 2 (0.0%) | 1.0 |
| boehnel | 1 (0.1%) | 1 (0.0%) | 1.0 |
| baderk | 2 (0.3%) | 1 (0.0%) | 0.5 |
* rename {{{GBT_add_new_changekey}}} -> {{{GBT_add_new_species_changekey}}}.
1 lines of code changed in 1 file:
* reintegrates 'ali' into 'trunk'
* adds: log:branches/ali@19183:19205
17 lines of code changed in 2 files:
* 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.
1 lines of code changed in 1 file:
* reintegrates 'progress' into 'trunk'
- implements #789
* adds: log:branches/progress@18885:18958
14 lines of code changed in 3 files:
* reintegrates 'nds' into 'trunk'
- fixes #841
* adds: log:branches/nds@18843:18882
1 lines of code changed in 1 file:
* reintegrates 'help' into 'trunk'
- relocate help sources
* adds: log:branches/help@18763:18780
2 lines of code changed in 1 file:
* remove trailing whitespace from c source.
2 lines of code changed in 2 files:
* rename {{{CPP_OBJECTS}}} -> {{{OBJECTS}}}.
5 lines of code changed in 1 file:
* reintegrates 'tree' into 'trunk'
* adds: log:branches/tree@18666:18703
3 lines of code changed in 2 files:
* change many WARN_TODO triggered warnings into todo markers.
1 lines of code changed in 1 file:
* fixes #824
- define stacksize required for tree-display in {{{TreeDisplay.hxx}}} (currently 20Mb)
- use that stacksize NTREE and PARSIMONY.
4 lines of code changed in 2 files:
* full update from child 'fix' into 'trunk'
* adds: log:branches/fix@18339:18351
1 lines of code changed in 1 file:
* reintegrates 'saicalc' into 'trunk'
- implements #730
* adds: log:branches/saicalc@18141:18310
2 lines of code changed in 1 file:
* 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
5 lines of code changed in 1 file:
* use security objects instead of manually calling GB_push/pop_my_security.
* eliminate GB_push/pop_my_security.
* fix scoping using a TA object.
2 lines of code changed in 1 file:
* 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 1 file:
* reintegrates 'gcc' into 'trunk'
* adds: log:branches/gcc@17850:17876
1 lines of code changed in 1 file:
* reintegrates 'clone' into 'trunk'
* adds: log:branches/clone@17813:17835
1 lines of code changed in 1 file:
* 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:
* 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
10 lines of code changed in 2 files:
* reintegrates 'svalues' into 'trunk'
- implements #614
* adds: log:branches/svalues@17357:17419,17428:17464,17469,17471:17477
4 lines of code changed in 3 files:
* partial merge from 'svalues' into 'trunk'
- root branches always need to have identical remarks (associated with the root-edge)
* condition previously implicit, now hardened by tests/assertions/...
* fixed several bugs that violated this condition
* adds: log:branches/svalues@17420:17427
33 lines of code changed in 4 files:
* reintegrates 'fix' into 'trunk'
- elim dead code
- use const hash loop
* adds: log:branches/fix@17380,17388:17395
4 lines of code changed in 1 file:
* typos
- some had ''two'' good language skills ;-)
- fix some plural forms
1 lines of code changed in 1 file:
* refer to ticket
4 lines of code changed in 2 files:
* 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
61 lines of code changed in 2 files:
* reintegrates 'tree' into 'trunk'
- implements #735
* adds:
- log:branches/addtest@17040:17044
- log:branches/tree@16921:17109
68 lines of code changed in 8 files:
* 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
6 lines of code changed in 1 file:
* reintegrates 'cleanup' into 'trunk'
- performs #762 (shrink 3.7 k)
* adds: log:branches/cleanup@16924:16935
0 lines of code changed in 1 file:
* reintegrates 'multicore' into 'trunk'
- derive sequence classes able to be combined from new class {{{AP_combinableSeq}}}
* elim dummy functions from rest of hierarchy
- implements non-writing combine for add-species (speedup: 25-35%)
- introduce type {{{Mutations}}} => uses long everywhere (before mostly, but not always used float)
- allows use of {{{future}}}s
* nucleotide combine is able to calculate async (disabled via define atm -> {{{NEVER_COMBINE_ASYNC}}}; needs more work on calling algorithm)
* adds: log:branches/multicore@16769:16879
146 lines of code changed in 10 files:
* reintegrates 'unittest' into 'trunk'
- fixed non-deterministic behavior of add-species:
* 2 sequences in test-DB were identical (changed 1 bp)
* {{{AP_tree_edge}}} cannot be used to store insert-positions (uses pair of {{{AP_tree_nlen}}} instead)
* corrected some undefined behavior (results did depend on compiler version+flags):
- general order of inserts was undefined
- order of initial-insert was undefined (used by complete tree reconstruction)
- bugs fixed:
* not all possible insert-positions were tested
* sometimes species were added at wrong positions
* if multiple species were inserted at the same position, the following optimization
- did modify topology
- now optimizes all multi-inserts globally
- at leaf-positions: includes the leaf (Note: this does not modify the original topology)
* insert order now is "longest sequence first" (was "shortest sequence first")
- fixed unwanted behavior when testing for content of generated files
* adds: log:branches/unittest@16807:16860
366 lines of code changed in 3 files:
* reintegrates 'gcc' into 'trunk'
- mostly cosmetics changes
* adds: log:branches/gcc@16655,16741:16743,16752:16765
27 lines of code changed in 5 files:
* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751
173 lines of code changed in 12 files:
* full update from child 'gcc' into 'trunk'
- fix/suppress (new) compiler warnings
- skip vectorizer notes
* adds: log:branches/gcc@16656:16667
1 lines of code changed in 1 file:
* 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
18 lines of code changed in 2 files:
* reintegrates 'fix' into 'trunk'
- valgrind fixes
* generally repaired valgrinding (external tools)
* {{{group_scaling}}} was not initialized correct (RUI)
- DRYed code to run external tools from unittests
* adds: log:branches/fix@16037:16042
10 lines of code changed in 3 files:
* reintegrates 'group' into 'trunk'
- implements #709
* adds: log:branches/group@15693:15702
6 lines of code changed in 1 file:
* reintegrates 'keys' into 'trunk'
- implements part of #687 (species traversal via keys)
- adds temp. unfolding of selected species
- several fixes to [15665] (PARSIMONY)
* adds: log:branches/keys@15591:15690
67 lines of code changed in 3 files:
* 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
16 lines of code changed in 5 files:
* reintegrates 'unittest' into 'trunk'
- activates unittests under OSX (performs #740)
* disabled a few tests + accepted a few modified results (see #741)
* {{{RegExpr}}} no longer uses exception
* fix quoting of {{{char*}}} (in reported test result)
- fixes several compiler flags unknown under OSX/clang
- fix usability of compile log (make now prints directory)
* adds: log:branches/unittest@15534:15578
* removes: [15520/branches/warnings]
21 lines of code changed in 1 file:
(344 more)