Directory CONVERTALN/

Directory Created:
2000-11-23 10:41
Total Files:
36
Deleted Files:
23
Lines of Code:
6584

[root]/CONVERTALN

Lines of Code

CONVERTALN/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 481 (100.0%) 38318 (100.0%) 79.6
westram 453 (94.2%) 29066 (75.9%) 64.1
oldcode 21 (4.4%) 9140 (23.9%) 435.2
meierh 1 (0.2%) 102 (0.3%) 102.0
jobb 1 (0.2%) 7 (0.0%) 7.0
epruesse 2 (0.4%) 2 (0.0%) 1.0
baderk 2 (0.4%) 1 (0.0%) 0.5
boehnel 1 (0.2%) 0 (0.0%) 0.0

Most Recent Commits

westram 2018-10-24 14:58 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

21 lines of code changed in 2 files:

  • CONVERTALN: Makefile (+17), global.h (+4 -1)
westram 2018-05-04 17:06 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 3 files:

  • CONVERTALN: date.cxx (+1 -1), macke.cxx (+2 -2), mg.cxx (+1 -1)
westram 2018-02-15 11:51 Rev.: 16861


* 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

1 lines of code changed in 1 file:

  • CONVERTALN: fconv.cxx (+1 -1)
westram 2017-11-28 18:22 Rev.: 16766


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

26 lines of code changed in 8 files:

  • CONVERTALN: date.cxx (+2 -2), embl.cxx (+8 -9), genbank.cxx (+1 -1), global.h (+1 -3), mg.cxx (+5 -5), rdp_info.h (+7 -6), seq.h (+1 -2), util.cxx (+1 -1)
westram 2017-11-28 17:09 Rev.: 16763


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

48 lines of code changed in 21 files:

  • CONVERTALN: convert.cxx (+1 -1), date.cxx (+1 -1), embl.cxx (+2 -2), fconv.cxx (+6 -6), fun.h (+1 -1), gcg.cxx (+1 -1), genbank.cxx (+4 -4), global.h (+3 -3), input_format.h (+1 -1), macke.cxx (+6 -6), macke.h (+1 -1), main.cxx (+2 -2), mg.cxx (+1 -1), rdp_info.h (+1 -1), reader.cxx (+6 -6), reader.h (+4 -4), refs.h (+1 -1), seq.h (+1 -1), util.cxx (+3 -3), wrap.cxx (+1 -1), wrap.h (+1 -1)
westram 2017-11-19 15:19 Rev.: 16683


* full update from child 'gcc' into 'trunk'
- more warning fixes
- fix bug in prettyprint
* adds: log:branches/gcc@16668:16682

1 lines of code changed in 1 file:

  • CONVERTALN: embl.cxx (+1 -1)
westram 2017-11-12 14:53 Rev.: 16649


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

1 lines of code changed in 1 file:

  • CONVERTALN: date.cxx (+1 -1)
westram 2017-01-09 15:10 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

15 lines of code changed in 3 files:

  • CONVERTALN: fun.h (+1 -1), global.h (+10 -10), macke.h (+4 -4)
westram 2017-01-04 17:06 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

18 lines of code changed in 6 files:

  • CONVERTALN: date.cxx (+2 -2), embl.h (+1 -1), genbank.h (+1 -1), macke.h (+1 -1), reader.cxx (-10), reader.h (+13 -2)
westram 2016-08-17 19:39 Rev.: 15198


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

5 lines of code changed in 4 files:

  • CONVERTALN: embl.h (+1 -1), genbank.h (+1 -1), input_format.h (+2 -2), macke.h (+1 -1)
westram 2016-08-11 10:05 Rev.: 15176


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

103 lines of code changed in 15 files:

  • CONVERTALN: Makefile (+33), date.cxx (+1 -1), embl.cxx (+5 -5), embl.h (+12 -9), genbank.cxx (+3 -3), genbank.h (+10 -7), global.h (+7 -5), macke.cxx (+2 -2), macke.h (+6 -3), paup.cxx (+1 -1), prototypes.h (-1), reader.cxx (+1 -1), seq.h (+16 -14), util.cxx (+5 -22), wrap.h (+1 -1)
westram 2015-12-23 16:13 Rev.: 14655


* spelling

2 lines of code changed in 1 file:

  • CONVERTALN: date.cxx (+2 -2)
westram 2015-12-03 17:50 Rev.: 14587


* fix error-forwarding (from external tools -> ARB GUI)
- {{{GBK_singlequote}}} error message (replaces various wrong ways to do that)
- always call {{{arb_message}}} asynchronously

6 lines of code changed in 2 files:

  • CONVERTALN: Makefile (+1), main.cxx (+5 -8)
westram 2015-12-03 17:48 Rev.: 14586


* fix truncated error-messages

6 lines of code changed in 1 file:

  • CONVERTALN: util.cxx (+6 -3)
westram 2015-01-23 14:19 Rev.: 13443


* reintegrates 'vectorize' into 'trunk'
- adds vectorization check for gcc 4.9.x / NDEBUG compile
* adds:
- log:branches/vectorize@13428:13442

1 lines of code changed in 1 file:

  • CONVERTALN: Makefile (+1 -1)
westram 2014-10-17 15:43 Rev.: 13077


* reintegrates 'sanitize' into 'trunk'
* adds:
- log:branches/sanitize@13023:13076

28 lines of code changed in 1 file:

  • CONVERTALN: printable.cxx (+28 -23)
westram 2014-10-09 17:48 Rev.: 13018


* merge a bunch of fixes from 'gcc' into 'trunk'
- detected using !AddressSanitizer
- fixing #613, #580 and other (undetected) bugs
* adds:
- log:branches/gcc@12996,13001:13003,13005:13006,13010:13014,13016

35 lines of code changed in 3 files:

  • CONVERTALN: embl.h (+16 -16), genbank.h (+19 -19), global.h (-7)
westram 2014-10-06 16:02 Rev.: 12992


* ~~valgrind was reporting 'invalid reads' in CONVERTALN when compiled with gcc-4.8.2 + NDEBUG~~
- ~~added (weird) workaround for broken optimizer~~
- ~~added some comments about broken gcc version; afaik problems are similar to those of gcc 4.9.0 (see [12988])~~

(reverted by [12996])

7 lines of code changed in 1 file:

  • CONVERTALN: global.h (+7)
westram 2014-06-09 05:16 Rev.: 12411


- CONVERTALN.a was relinked unconditionally (fixed)

10 lines of code changed in 1 file:

  • CONVERTALN: Makefile (+10 -6)
westram 2014-04-04 17:22 Rev.: 11947


* merge misc changes from 'customize' into 'trunk'
* adds:
- log:branches/customize@11920,11943:11944

1 lines of code changed in 1 file:

  • CONVERTALN: fconv.cxx (+1 -1)
westram 2014-03-22 09:34 Rev.: 11844


* merge [11840:11843] from 'customize' into 'trunk'
* adds:
- log:branches/customize@11841:11843
* skipped changes in ARB_GDE
- log:branches/customize/ARB_GDE@11841:11843 ~~(might fail to reintegrate)~~

28 lines of code changed in 5 files:

  • CONVERTALN: Makefile (+17 -17), fun.h (+2 -2), reader.cxx (+1 -1), reader.h (+7 -7), util.cxx (+1 -1)
westram 2014-02-21 12:52 Rev.: 11651


- warn only once about incomplete LOCUS data

7 lines of code changed in 1 file:

  • CONVERTALN: genbank.cxx (+7 -2)
westram 2014-02-15 15:51 Rev.: 11626


* reintegrates 'fix' into 'trunk'
- implements: #158
- fixes: #386, #463, #459
* adds:
- log:branches/fix@11579:11625

24 lines of code changed in 1 file:

  • CONVERTALN: main.cxx (+24 -3)
westram 2013-10-31 15:40 Rev.: 11002


* 'class { public' -> struct

2 lines of code changed in 2 files:

  • CONVERTALN: input_format.h (+1 -2), reader.h (+1 -2)
westram 2013-10-31 14:10 Rev.: 10996


* use cflags before cxxflags

1 lines of code changed in 1 file:

  • CONVERTALN: Makefile (+1 -1)
westram 2013-10-30 16:04 Rev.: 10975


* fixed wrong include variables (CC-CXX-mix). Harmless since includes do not differ atm

1 lines of code changed in 1 file:

  • CONVERTALN: Makefile (+1 -1)
westram 2013-10-30 15:58 Rev.: 10974


* renamed include variables

1 lines of code changed in 1 file:

  • CONVERTALN: Makefile (+1 -1)
westram 2013-10-29 12:55 Rev.: 10956


* made A_CC and A_CXX consistent
- A_CXX previously contained cxxflags
- cxxflags are now passed down and used separately

1 lines of code changed in 1 file:

  • CONVERTALN: Makefile (+1 -1)
westram 2013-10-29 12:23 Rev.: 10955


- renamed
* ACC -> A_CC
* CPP -> A_CXX (misleading atm, since it contains c++flags)

1 lines of code changed in 1 file:

  • CONVERTALN: Makefile (+1 -1)
westram 2013-10-09 10:07 Rev.: 10764


* renamed file- and mem-cmp-functions
* added parameter 'blockStartAddress' to ARB_test_mem_equal
- use it to show correct file-offset when called from ARB_files_are_equal
* removed unused function files_are_equal()

1 lines of code changed in 1 file:

  • CONVERTALN: fconv.cxx (+1 -1)
westram 2013-10-03 12:11 Rev.: 10704


- reintegrated branch 'helptest'

2 lines of code changed in 2 files:

  • CONVERTALN: Makefile (+1), fconv.cxx (+1)
westram 2013-09-09 15:36 Rev.: 10563


- include downcast.h from arbdbt.h
(this break C++11 compilation, i.e. gcc4.8 or newer)[[BR]]
amendment:
* also broke compilation on ubuntu 13.04 and with gcc 4.7.3 (due to nameclash with boost)

1 lines of code changed in 1 file:

  • CONVERTALN: Makefile (+1)
westram 2013-09-09 11:55 Rev.: 10557


- rename

3 lines of code changed in 1 file:

  • CONVERTALN: fconv.cxx (+3 -3)
westram 2013-08-25 14:09 Rev.: 10482


* Tree IO (patch reintegrates branch 'tree')
- added unit test (!TreeReader, export/import consistency for most export-parameters combinations)
- refactorings: moved more behavior into !TreeReader; deny access to class internals
- improved error messages/warnings
* show error-position in input data when bailing out
* warn about unused data behind tree
* trees < 2 species produce error now
- behavior
* fixed export/import of bootstrap values (expect ':' as separator; avoiding misinterpretation of group names starting with digits)
* auto-name unnamed nodes
* supports bootstrap values specified as percent (e.g. '12.5%')
* no longer interpret {{{''}}} as escape sequence for a single {{{'}}}
* no longer remove leading '_' from leaf-/groupnames (no idea why this was done)
- fixes:
* export+import of tree using double quotes often resulted in leaf-/groupnames enclosed in double-quotes (or more often failed to load completely)
* name of root-node was lost after import.
* better support for single-node subtrees, e.g. '(leafname)'. Nodes were skipped.
* deadlock occurring when tree file was truncated somewhere in the middle.
* leaks stuffed

1 lines of code changed in 1 file:

  • CONVERTALN: fconv.cxx (+1)
epruesse 2013-04-13 18:23 Rev.: 9899

pass down argc/argv to AW_root::AW_root (for GTK)
GTK will pick its parameters (e.g. --g-fatal-warnings) from argv and
remove them, hence argv must not be const and AW_root() should
be called before command line parsing (if possible).

2 lines of code changed in 2 files:

  • CONVERTALN: main.cxx (+1 -1), prototypes.h (+1 -1)
westram 2013-02-27 19:30 Rev.: 9620


- effects of [9619]; only shifts some spaces

30 lines of code changed in 1 file:

  • CONVERTALN: prototypes.h (+30 -30)
westram 2013-02-26 11:32 Rev.: 9600


* aisc_mkpt
- default is to generate ANSI headers now (options -A and -z are invalid now)
- added options to force K&R (not used)
- reordered help options
* fixed all calls using -A and/or -z
* no longer use K&R prototypes in SL/TREEDISP

1 lines of code changed in 1 file:

  • CONVERTALN: Makefile (+1 -1)
westram 2013-02-13 12:24 Rev.: 9575


- effect of [9574] (comments only)

1 lines of code changed in 1 file:

  • CONVERTALN: Makefile (+1 -1)
westram 2013-02-09 12:52 Rev.: 9521


- updated depends for [9520]

2 lines of code changed in 1 file:

  • CONVERTALN: Makefile (+2)
westram 2013-02-09 12:50 Rev.: 9520


- include cxxforward.h via arbtools.h (which declares Noncopyable)

0 lines of code changed in 3 files:

  • CONVERTALN: embl.h (-3), genbank.h (-3), input_format.h (-3)

(98 more)

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