Directory GDE/CLUSTAL/

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westram 2023-08-11 13:40 Rev.: 19480

* reintegrates 'gde' into 'trunk'
* adds: log:branches/gde@19460:19479

93 lines of code changed in 8 files:

• GDE/CLUSTAL: amenu.c (+48 -51), clustalv.c (+1 -1), myers.c (+3 -3), sequence.c (+17 -17), showpair.c (+3 -3), trees.c (+8 -11), upgma.c (+1 -1), util.c (+12 -12)

westram 2023-08-05 13:40 Rev.: 19446

* introduce {{{onlyC_flags}}}
- flags used for C compilation only.
- similar to {{{cxxflags}}} (references added).
- pass down onlyC_flags into AxML, CLUSTAL, CLUSTALW, FASTDNAML, FASTTREE, GL, MrBAYES, PHYLIP, PHYML*, RAxML, SINA(unused), SOURCE_TOOLS, SUPPORT, TOOLS, TREEGEN + TREEPUZZLE.
- set flags to {{{-Werror-implicit-function-declaration}}}
* error is only effective in a small part of these modules.
* TODO: need to activate warnings -> will activate the error as well.

2 lines of code changed in 1 file:

• GDE/CLUSTAL: Makefile (+2 -2)

westram 2023-08-05 13:27 Rev.: 19443

* fix use of {{{gets()}}} (globally):
- provide a drop-in replacement for {{{gets()}}}
* only requires to specify buffersize.
- use {{{gets_noOverflow()}}} in READSEQ, SUPPORT, CLUSTAL + CLUSTALW.
* adapt {{{getstr()}}}

30 lines of code changed in 4 files:

• GDE/CLUSTAL: Makefile (+2), amenu.c (+19 -18), sequence.c (+2 -2), util.c (+7 -5)

westram 2015-05-30 14:37 Rev.: 13845

- remove executable flag

0 lines of code changed in 11 files:

• GDE/CLUSTAL: amenu.c (-1), clustalv.h (-1), gcgcheck.c (-1), general.h (-1), matrices.h (-1), myers.c (-1), sequence.c (-1), showpair.c (-1), trees.c (-1), upgma.c (-1), util.c (-1)

westram 2015-01-23 15:19 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:

• GDE/CLUSTAL: Makefile (+1 -1)

epruesse 2014-09-02 17:51 Rev.: 12815

fix common typos reported by lintian
- splitted -> split (irregular verb)
- ressources -> resources
- explicitely -> explicitly

3 lines of code changed in 1 file:

• GDE/CLUSTAL: amenu.c (+3 -3)

westram 2013-10-30 16:58 Rev.: 10974

* renamed include variables

1 lines of code changed in 1 file:

• GDE/CLUSTAL: Makefile (+1 -1)

westram 2013-10-29 13:23 Rev.: 10955

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

2 lines of code changed in 1 file:

• GDE/CLUSTAL: Makefile (+2 -2)

westram 2013-02-13 13:24 Rev.: 9575

- effect of [9574] (comments only)

1 lines of code changed in 1 file:

• GDE/CLUSTAL: Makefile (+1 -1)

westram 2010-09-18 17:20 Rev.: 6866

* compiler-messages (merges [6848] [6849] [6850] [6851] [6853] [6855] [6856] [6860] from refactor)
- errors get listed before warnings
- pipe all compilations through postcompile filter
- optionally filter warnings and/or stop at 1st error (controllable by POST_COMPILE in ARB Makefile)
- no warnings for ptpan (too many; version in trunk is outdated)

1 lines of code changed in 1 file:

• GDE/CLUSTAL: Makefile (+1 -1)

westram 2009-04-01 17:58 Rev.: 5782

* fixed spelling of 'occurrence'

1 lines of code changed in 1 file:

• GDE/CLUSTAL: trees.c (+1 -1)

boehnel 2008-03-01 23:12 Rev.: 5172

removing some format warnings

2 lines of code changed in 2 files:

• GDE/CLUSTAL: amenu.c (+1 -1), clustalv.c (+1 -1)

westram 2007-05-30 15:39 Rev.: 4635

- added 'clean'

5 lines of code changed in 1 file:

• GDE/CLUSTAL: Makefile (+5 -1)

westram 2004-01-23 19:08 Rev.: 2338

fixed and reformatted dependencies (using fix_depends.pl)

20 lines of code changed in 1 file:

• GDE/CLUSTAL: Makefile (+20 -8)

westram 2003-08-09 14:00 Rev.: 1617

- updated dependencies for all Makefiles
- rewrote dependency generation code. Only real changes
propagate into Makefiles - so it does no longer hurt to
call 'make depends' in ARB directory!

24 lines of code changed in 1 file:

• GDE/CLUSTAL: Makefile (+24 -12)

westram 2002-05-29 17:46 Rev.: 597

*** empty log message ***

9 lines of code changed in 1 file:

• GDE/CLUSTAL: Makefile (+9 -13)

yadhu 2002-05-29 11:53 Rev.: 593

makefile dependency generation fixed for GDE

13 lines of code changed in 1 file:

• GDE/CLUSTAL: Makefile (+13 -87)

westram 2002-05-23 09:29 Rev.: 566

Most changes are made due to activating more warnings for the c++ compiler (linux)

25 lines of code changed in 1 file:

• GDE/CLUSTAL: Makefile (+25 -23)

westram 2001-01-11 16:58 Rev.: 83

*** empty log message ***

33 lines of code changed in 1 file:

• GDE/CLUSTAL: Makefile (+33 -68)

meierh 2001-01-11 16:24 Rev.: 80

haralds checkin

68 lines of code changed in 1 file:

• GDE/CLUSTAL: Makefile (+68 -33)

westram 2001-01-04 16:36 Rev.: 68

Updated dependencies

61 lines of code changed in 1 file:

• GDE/CLUSTAL: Makefile (+61 -8)

oldcode 2000-11-23 11:41 Rev.: 2

Initial revision

4960 lines of code changed in 13 files:

• GDE/CLUSTAL: Makefile (new 50), amenu.c (new 2054), clustalv.c (new 160), clustalv.h (new 40), gcgcheck.c (new 17), general.h (new 43), matrices.h (new 68), myers.c (new 539), sequence.c (new 336), showpair.c (new 476), trees.c (new 679), upgma.c (new 241), util.c (new 257)