Lines of Code
[root]/EDIT4
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 2545 (100.0%) | 74888 (100.0%) | 29.4 |
| westram | 2292 (90.1%) | 42459 (56.7%) | 18.5 |
| oldcode | 31 (1.2%) | 22406 (29.9%) | 722.7 |
| yadhu | 158 (6.2%) | 5944 (7.9%) | 37.6 |
| murban | 23 (0.9%) | 2127 (2.8%) | 92.4 |
| urban | 4 (0.2%) | 1160 (1.5%) | 290.0 |
| meierh | 2 (0.1%) | 521 (0.7%) | 260.5 |
| epruesse | 18 (0.7%) | 179 (0.2%) | 9.9 |
| jobb | 3 (0.1%) | 49 (0.1%) | 16.3 |
| baderk | 5 (0.2%) | 22 (0.0%) | 4.4 |
| boehnel | 7 (0.3%) | 20 (0.0%) | 2.8 |
| foerster | 1 (0.0%) | 1 (0.0%) | 1.0 |
| artemov | 1 (0.0%) | 0 (0.0%) | 0.0 |
* 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:
* 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
12 lines of code changed in 1 file:
* reintegrates 'cleanup' into 'trunk'
* adds: log:branches/cleanup@17627:17650
4 lines of code changed in 1 file:
* 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
11 lines of code changed in 2 files:
* 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
11 lines of code changed in 5 files:
* partial merge from 'fix' into 'trunk'
* adds: [17508/branches/fix]
2 lines of code changed in 1 file:
* use {{{SmartPtr::content()}}}
1 lines of code changed in 1 file:
* reintegrates 'fix' into 'trunk'
- elim dead code
- use const hash loop
* adds: log:branches/fix@17380,17388:17395
7 lines of code changed in 2 files:
* fix {{{GB_xcmd}}} for OSX with SIP
1 lines of code changed in 1 file:
* 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:
* 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
68 lines of code changed in 6 files:
* reintegrates 'cleanup' into 'trunk'
- performs #762 (shrink 3.7 k)
* adds: log:branches/cleanup@16924:16935
5 lines of code changed in 3 files:
* reintegrates 'gcc' into 'trunk'
- mostly cosmetics changes
* adds: log:branches/gcc@16655,16741:16743,16752:16765
212 lines of code changed in 20 files:
* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751
585 lines of code changed in 32 files:
* full update from child 'gcc' into 'trunk'
- more warning fixes
- fix bug in prettyprint
* adds: log:branches/gcc@16668:16682
17 lines of code changed in 2 files:
* full update from child 'gcc' into 'trunk'
- fix/suppress (new) compiler warnings
- skip vectorizer notes
* adds: log:branches/gcc@16656:16667
13 lines of code changed in 1 file:
* 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
49 lines of code changed in 2 files:
* 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
2 lines of code changed in 1 file:
* 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
20 lines of code changed in 3 files:
* reintegrates 'fix' into 'trunk'
- fixes #267
- adds new default color translation table 'PVP'
* adds: log:branches/fix@16107:16111
14 lines of code changed in 1 file:
* solve remaining confusion in terminology (concerning "selected species"):
- sequence-range-blocks in EDIT4 are now called "highlighted species" or "highlighted block"
- Note: code still talks about selected species
16 lines of code changed in 1 file:
* rename only
1 lines of code changed in 1 file:
* fix click on species flags
- did not work when display was scrolled vertically
1 lines of code changed in 1 file:
* reintegrates 'warnings' into 'trunk'
- use gnu++14-standard for gcc>=6
- use gnu++0x-standard for gcc<4.7 (bugfix)
- defines many inlines as constexpr
* adds: log:branches/warnings@15515:15522,15525:15528
1 lines of code changed in 1 file:
* reintegrates 'warnings' into 'trunk'
- activate additional warnings (gcc 5.x++)
- Cxx11-forward final (classes+methods)
- fix tag problems caused by using preprocessor
* adds: log:branches/warnings@15486:15489,15491:15501,15506:15512
36 lines of code changed in 4 files:
* partial merge from 'warnings' into 'trunk'
- remove some useless virtuality (mostly functions only usable with ED4_manager)
- other design fixes (get_parent returns ED4_manager, ...)
* adds: log:branches/warnings@15502:15505
44 lines of code changed in 7 files:
* reintegrates 'mladd' into 'trunk'
- improves raxml8 interface
* new functions
- score tree (=calculate likelihood and append to comment)
- calculate branchlengths
- optimize tree
- add to tree (implements #681)
* calculate bootstraps (as separate function or combined with other functions)
- allow to skip bootstrap calculation
* writes comment to generated trees (similar to raxml7-interface)
* fix key-wait on terminate
* time all functions
* fix thread usage
- use 'distinct alignment patterns' (as reported by RAxML) to select maximum threads
- slightly reduce threads in favor of asynchronous bootstrapping
- allow to override (used) cores and used threads separate
- adds {{{arb_write_tree_comment}}}
* adds: log:branches/mladd@15394,15396,15398:15424
1 lines of code changed in 1 file:
* remove outdated link
1 lines of code changed in 1 file:
* add some predefined settings for editor flags
9 lines of code changed in 1 file:
* reintegrates 'flags' into 'trunk'
- implements #261
* adds: log:branches/flags@15225:15230,15232:15238,15240:15241,15243:15246,15248,15250:15287
825 lines of code changed in 17 files:
* reintegrates 'errhandle' into 'trunk'
* adds: log:branches/errhandle@15275:15278
3 lines of code changed in 1 file:
* {{{GB_xcmd}}}
- remove from perl interface
- replace bool-flag-couple by enum
- guard unused case {{{XCMD_SYNC_WAITKEY}}}
1 lines of code changed in 1 file:
* document used references from display-elements to database-entries
12 lines of code changed in 1 file:
* {{{EDB_root_bact::search_sequence_data_rek}}} now always called with alignment-container (or one of its subcontainers)
* rename some variables
26 lines of code changed in 3 files:
* replace redundant data {{{AW_font_limits::height}}} with {{{get_height()}}}
1 lines of code changed in 1 file:
* depends for [15253]
26 lines of code changed in 1 file:
* remove undocumented feature (build IUPAC string from block selected in detailed column stat and write it to probe-match IUPAC input)
- code was unstable
- if multiple detailed column stat terminals were visible/selected, awar was modified multiple times
- more or less just a hack (should be implemented differently, e.g. optionally sync probe-match-target with single selected block)
5 lines of code changed in 4 files:
* reintegrates 'flags' into 'trunk'
- DRYed
* group generation code
* ref-terminal access
- layout done by managers (removed manual coordinate calculation)
- dynamic size calculated by terminals themselves
- fix design issues
* brackets were used where groups should have been used. fixed
* fix many bad/spammy names
- fix broken member-code (only worked with a NULL sentinel present)
- dynamic indentation (according to visible group-nesting)
* adds: log:branches/flags@15098:15222
1803 lines of code changed in 28 files:
* remove {{{virtual}}} if {{{OVERRIDE}}} is present
- OVERRIDE implies 'implicit virtual' (if code compiles as C++11 <- tested on build server!)
79 lines of code changed in 2 files:
* reintegrates 'fixres' into 'trunk'
- fixes #715
* adds: log:branches/fixres@15127:15175
170 lines of code changed in 20 files:
(865 more)