Directory TEMPLATES/

Directory Created:
2001-08-16 08:52
Total Files:
44
Deleted Files:
6
Lines of Code:
8070

[root]/TEMPLATES

Lines of Code

TEMPLATES/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 299 (100.0%) 9185 (100.0%) 30.7
westram 297 (99.3%) 9184 (100.0%) 30.9
epruesse 1 (0.3%) 1 (0.0%) 1.0
baderk 1 (0.3%) 0 (0.0%) 0.0

Most Recent Commits

westram 2019-05-10 13:57 Rev.: 17877


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

56 lines of code changed in 1 file:

  • TEMPLATES: cxxforward.h (+56 -8)
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:

  • TEMPLATES: arb_unit_test.h (+1 -1)
westram 2019-04-02 19:10 Rev.: 17730


* introduce "hybrid" result-type {{{ErrorOr<TYPE>}}}
- is either an error xor a value

65 lines of code changed in 1 file:

  • TEMPLATES: ErrorOrType.h (new 65)
westram 2019-04-02 18:15 Rev.: 17729


* fix test condition "contains":
- checking for empty part
* always returned 'true'
* now fails assertion and returns 'false' (it is unwanted to test that)
- fix callers

8 lines of code changed in 2 files:

  • TEMPLATES: command_output.h (+7 -7), ut_valgrinded.h (+1 -1)
westram 2019-03-04 15:22 Rev.: 17634


* reintegrates 'mix' into 'trunk'
* prepare arb for hybrid svn/git use (central svn + local git)
* adds: log:branches/mix@17631:17633

2 lines of code changed in 1 file:

  • TEMPLATES: .gitignore (new 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

6 lines of code changed in 1 file:

  • TEMPLATES: arb_global_defs.h (+6)
westram 2018-05-04 18:06 Rev.: 16986


* reintegrates 'gcc' into 'trunk'
- ports arb to gcc 8.1 (fixing warnings)
* adds: log:branches/gcc@16965:16985

Update: continued by [17178]

4 lines of code changed in 1 file:

  • TEMPLATES: arbtools.h (+4)
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

53 lines of code changed in 1 file:

  • TEMPLATES: sized_cstr.h (new 53)
westram 2018-04-25 11:08 Rev.: 16919


* reintegrates 'pvp' into 'trunk'
- adds {{{arb_calc_pvp}}} (CLI tool to calculate posvar)
* adds: log:branches/pvp@16906:16918

16 lines of code changed in 1 file:

  • TEMPLATES: command_output.h (+16 -10)
westram 2018-04-11 16:48 Rev.: 16880


* 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

8 lines of code changed in 1 file:

  • TEMPLATES: cxxforward.h (+8 -5)
westram 2017-12-05 10:48 Rev.: 16787


* perform some checks after reading import format (report error instead of crash)
- {{{NEW_FORMAT}}} and {{{SYSTEM}}} have to be used together
- {{{SEQUENCESTART}}}/{{{SEQUENCEAFTER}}} required if not using {{{NEW_FORMAT}}}, forbidden otherwise
* fix {{{update_format_description}}} when selecting "no filter"

2 lines of code changed in 1 file:

  • TEMPLATES: FileWatch.h (+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

2 lines of code changed in 1 file:

  • TEMPLATES: cache.h (+2 -4)
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

83 lines of code changed in 16 files:

  • TEMPLATES: ChecksumCollector.h (+1 -1), SuppressOutput.h (+4 -4), arb_error.h (+8 -8), arb_simple_assert.h (+4), arb_sleep.h (+2 -2), arb_str.h (+2 -2), attributes.h (+1 -1), cache.h (+5 -5), command_output.h (+11 -8), config_parser.h (+6 -6), cxxforward.h (+8 -2), downcast.h (+1 -1), dupstr.h (+7 -7), output.h (+7 -7), perf_timer.h (+4 -4), smartptr.h (+12 -12)
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

10 lines of code changed in 1 file:

  • TEMPLATES: cxxforward.h (+10)
westram 2017-11-12 15:53 Rev.: 16649


* partial merge from 'gcc' into 'trunk'
- handles #770 by reducing optimizations of several bleeding test functions
* adds: log:branches/gcc@16636:16648

3 lines of code changed in 1 file:

  • TEMPLATES: attributes.h (+3 -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

7 lines of code changed in 2 files:

  • TEMPLATES: attributes.h (+5), gccver.h (+2 -2)
westram 2017-10-31 14:13 Rev.: 16592


* partial merge from 'vectorize' into 'trunk'
- eliminates {{{usleep}}} (using {{{nanosleep}}} via {{{ARB_sleep}}})
* adds: log:branches/vectorize@16587:16591

63 lines of code changed in 1 file:

  • TEMPLATES: arb_sleep.h (+63 -9)
westram 2017-10-21 13:40 Rev.: 16564


* reintegrates 'io' into 'trunk'
- implements #691
* adds: log:branches/io@16436:16510,16513:16514,16517,16533:16535,16537:16563

112 lines of code changed in 1 file:

  • TEMPLATES: FileWatch.h (new 112)
westram 2017-10-03 18:26 Rev.: 16469


* reintegrates 'textedit' into 'trunk'
- fixes #586
* editor now always started asynchronously
* uses inotify to track file changes
- ~~also use inotify to track directory updates (in order to update file selections when needed)~~\\(./) by [16515] ff.; merged by [16551]
* adds: log:branches/textedit@16448:16468

1 lines of code changed in 1 file:

  • TEMPLATES: command_output.h (+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

6 lines of code changed in 2 files:

  • TEMPLATES: arbtools.h (+5 -1), command_output.h (+1 -1)
westram 2017-09-03 17:51 Rev.: 16261


* add new sort-criteria to 'search&query' (sort numerically; fixes #203)

14 lines of code changed in 1 file:

  • TEMPLATES: arbtools.h (+14)
westram 2017-07-19 13:25 Rev.: 16164


* reintegrates 'group' into 'trunk'
- implements #653
* adds: log:branches/group@16147:16163

77 lines of code changed in 1 file:

  • TEMPLATES: lazy.h (new 77)
westram 2017-07-10 12:29 Rev.: 16119


* reintegrates 'saiexport' into 'trunk'
- implements #743
* adds: log:branches/saiexport@16023:16118

35 lines of code changed in 1 file:

  • TEMPLATES: command_output.h (+35 -21)
westram 2017-06-29 15:18 Rev.: 16043


* 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

15 lines of code changed in 1 file:

  • TEMPLATES: ut_valgrinded.h (+15 -11)
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 1 file:

  • TEMPLATES: arbtools.h (+2)
westram 2017-04-29 13:28 Rev.: 15852


* reintegrates 'refactor' into 'trunk'
- separates query logic (as used in search&query) from actual data retrieval
* adds: log:branches/refactor@15820:15851

Note: introduces bug in merge-tool (fixed by [15996])

3 lines of code changed in 1 file:

  • TEMPLATES: downcast.h (+3)
westram 2017-04-05 11:06 Rev.: 15738


* rename only

2 lines of code changed in 1 file:

  • TEMPLATES: smartptr.h (+2 -2)
westram 2017-01-09 16:10 Rev.: 15529


* 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

50 lines of code changed in 6 files:

  • TEMPLATES: arb_algo.h (+1 -1), arb_defs.h (+2 -2), arbtools.h (+11 -9), cxxforward.h (+31 -5), dupstr.h (+4 -1), mode_text.h (+1 -1)
westram 2017-01-04 18:06 Rev.: 15513


* 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 2 files:

  • TEMPLATES: attributes.h (+2), cxxforward.h (+34)
westram 2016-08-22 15:34 Rev.: 15223


* 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

8 lines of code changed in 1 file:

  • TEMPLATES: downcast.h (+8 -1)
westram 2016-08-11 11:05 Rev.: 15176


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

32 lines of code changed in 5 files:

  • TEMPLATES: ChecksumCollector.h (+1 -1), arb_backtrace.h (+27 -9), config_parser.h (+2 -2), dupstr.h (+1 -9), smartptr.h (+1 -1)
westram 2016-07-21 17:53 Rev.: 15082


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

26 lines of code changed in 2 files:

  • TEMPLATES: arbtools.h (+21), config_parser.h (+5 -11)
westram 2016-07-14 15:15 Rev.: 15054


* reintegrates 'color' into 'trunk'
- implements #443 (+parts of #444)
* adds: log:branches/color@14920:14921,14923:14928,14930:14939,14941:14951,14954:14956,14958:14959,14961:14964,14968,14970:14981,14985,14988,14990:14992,14994:14999,15001:15004,15007,15009,15012:15026,15028:15035,15037:15039,15041:15053

1 lines of code changed in 1 file:

  • TEMPLATES: downcast.h (+1 -1)
westram 2016-05-04 13:36 Rev.: 14807


* fix compilation with gcc 6.1.0
- fix shift-overflow in mafft
- fix return type in {{{eigen}}} (using patch)
- let Cxx14 compilers use all Cxx11 features

6 lines of code changed in 1 file:

  • TEMPLATES: cxxforward.h (+6 -2)
westram 2015-12-19 16:14 Rev.: 14641


* reintegrates 'remote' into 'trunk'
- implements #52 and #362
* adds: log:branches/remote@14624:14640

34 lines of code changed in 1 file:

  • TEMPLATES: arb_sleep.h (+34)
westram 2015-11-03 16:09 Rev.: 14451


* use typed callbacks (partial binding)
- move untyped code into namespace UNTYPED
- added template wrappers (doing the type checks)
- added template-helper-struct {{{disallow_type}}}
* revealed wrong enum-types used in {{{awt_create_collect_buttons}}}

12 lines of code changed in 1 file:

  • TEMPLATES: arbtools.h (+12)
westram 2015-10-28 11:58 Rev.: 14425


* reintegrates 'consensus' into 'trunk'
- fixes #663 (consistent consensus calculation)
- allow to load SAI into existing EDIT4 config
- tweaked "View differences"
- minor fixes for SAI MAX_FREQUENCY
* adds:
- log:branches/addtest@14319:14326
- log:branches/consensus@14276:14424

0 lines of code changed in 1 file:

  • TEMPLATES: consensus_config.h (del)
westram 2015-09-02 17:31 Rev.: 14256


* reintegrates 'config' into 'trunk' (implements #607)
* adds: log:branches/config@14199:14255

1 lines of code changed in 1 file:

  • TEMPLATES: arbtools.h (+1 -1)
epruesse 2015-08-27 02:13 Rev.: 14217

fix warning

1 lines of code changed in 1 file:

  • TEMPLATES: static_assert.h (+1 -1)
westram 2015-08-26 13:06 Rev.: 14206


* use templates to avoid (compiler version dep.) type errors

4 lines of code changed in 1 file:

  • TEMPLATES: arbtools.h (+4 -2)

(165 more)

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