Directory GDE/MOLPHY/

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westram 2011-11-10 10:30 Rev.: 8205

merge from stable_5.0 [8203]
* removed molphy (protml)

0 lines of code changed in 52 files:

• GDE/MOLPHY: .cvsignore (del), Dpstree.c (del), Makefile (del), Ndistan.c (del), Njdist.c (del), Nmlklhd.c (del), Nseqstat.c (del), Ntranprb.c (del), Nucml.c (del), Nucst.c (del), Nuctpm.c (del), Prottpm.c (del), README.txt (del), abratio.c (del), altree.c (del), distan.c (del), distproc.c (del), dyhfjtt.c (del), getseq.c (del), matrixut.c (del), matrixut.h (del), mlklhd.c (del), mltree.c (del), mo_assert.h (del), molphy.h (del), mtrev22.c (del), mtrev24.c (del), mygetopt.c (del), njmtree.c (del), njproc.c (del), njtree.c (del), nucproc.c (del), optimtpm.c (del), prot_tml.h (del), protml.c (del), protml.h (del), protproc.c (del), protst.c (del), protst.h (del), prtree.c (del), pstree.c (del), qltree.c (del), seqproc.c (del), seqstat.c (del), sltree.c (del), totalml.c (del), totalml.h (del), tranprb.c (del), tridist.c (del), tridist.h (del), triproc.c (del), unused_molphy_sources.tgz (del)

westram 2011-10-17 13:05 Rev.: 8098

merge from ptpan_back [8023] [8030] [8052] [8058] [8062]
* suppress several boost-warnings
* store old SIGSEGV-handler in AISC-servers
* removed chroot (unused and name conflicts with libc)
* fixed abuse of GB_export_errorf
* accept if sighandler is already installed (happens when opening 2 DB-clients from same binary)

0 lines of code changed in 2 files:

• GDE/MOLPHY: mlklhd.c (-56), prot_tml.h (-1)

westram 2011-08-08 08:56 Rev.: 7818

merge from dev [7773] [7776] [7797]
* remove indirection via links in directory MAKEBIN
* ignore json/yml for PERL2ARB
* stopper vs compiling RNA3D w/o ARB_OPENGL

1 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (+1 -1)

westram 2011-04-16 13:35 Rev.: 7428

* 'make clean up' generated wrong dependencies (merged from dev [7427])

260 lines of code changed in 2 files:

• GDE/MOLPHY: Makefile (+8 -5), prot_tml.h (new 252)

westram 2011-04-13 19:21 Rev.: 7409

merged from dev [7358] [7359] [7360] [7363] [7364] [7365] [7367]
* tweaked build process
- get rid of '.depends: No such file or directory'
- make clean now is much more scrupulous! removal '''notably''' includes lib/pts, lib/nas and lib/arb_tcp.dat (when they are no symlinks)
- suppress some output
- added several unreached targets (to test random failures)
- fine-grained tools-dependencies
- automatically generate target directories (GENC ...)
- removed duplicated target 'mbin' (same as 'comtools')
- added target 'setup_after_clean' (use after 'clean' when doing a partial build)

1 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (+1 -1)

westram 2011-02-04 12:01 Rev.: 7121

* added new GDE argument type 'filename' (textfield+browse button)
* fixed "alignment not found" error

2 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (+2)

westram 2011-02-02 12:14 Rev.: 7116

depends

0 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (-2)

westram 2010-09-18 16:20 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/MOLPHY: Makefile (+1 -1)

westram 2010-09-09 21:49 Rev.: 6817

- depends for [6816]

18 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (+18)

westram 2009-12-10 17:20 Rev.: 6299

- depends + prototype

2 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (+2)

westram 2009-12-08 16:37 Rev.: 6293

- fixed "uninitialized" warnings

0 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (-2)

westram 2009-08-14 15:29 Rev.: 6141

* spellchecked all (phew)

1 lines of code changed in 1 file:

• GDE/MOLPHY: mltree.c (+1 -1)

westram 2009-06-06 14:48 Rev.: 6029

* compile error, aisc_mkpt arguments in wrong order

2 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (+2 -2)

westram 2009-05-30 16:13 Rev.: 5968

* new flag -w to aisc_mkpt (add include wrapper)
* uniform style for several include wrappers
* removed duplicated includes
* removed useless nt_concatenate.hxx

1 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (+1 -1)

westram 2008-12-31 12:24 Rev.: 5708

* backtrace gets printed to console from
- GB_internal_error
- SIGSEGV (currently GB_login installs the handler using GBK_install_SIGSEGV_handler. Most likely needs to be called manually for some executables)
- GBK_terminate
* added GBK_dump_backtrace, GBK_terminate and GBK_assert_msg
* Default assertion dumps backtrace now
* added -rdynamic and --export-dynamic compiler/linker flags, leaving symbols in code. This raises size of executables by approx. 8%, but we will get meaningful backtraces from users.
* removed old inactive SIGSEGV code
* replaced GB_CORE either by xx_assert() or GBK_terminate()
* removed GBS_do_core (was used conditionally together with GB_CORE)
* disabled crash provoked via arb_panic (using 'core' as savename)
* Linkage changed:
- The future plan is to try some kind of emergency save on open DBs when GBK_terminate or similar is called.
- Since arb_assert calls GBK_terminate this affects ALL applications.
- The drawback is all executables have to be linked vs ARBDB (done with: arb_help2xml and arb_convert_aln, all others already had ARBDB linked)
- Molphy uses #define SIMPLE_ARB_ASSERT before including arb_assert.h
* renamed define GBL_INCLUDED -> ADLOCAL_H
* added arbdb_base.h (defining some types and including ad_k_prot.h, which contains all GBK_*-functions). Intended as minimal and seldom changed interface to libARBDB as needed by arb_assert(), to keep build dependencies low.
* arb_assert.h now automatically includes arbdb_base.h
* trigger compilation of test functions in parsimony via define

4 lines of code changed in 2 files:

• GDE/MOLPHY: matrixut.c (+3 -1), protml.h (+1)

westram 2008-12-25 13:03 Rev.: 5675

- removed automatic timestamps (the best they were good for, were vc-conflicts)

0 lines of code changed in 1 file:

• GDE/MOLPHY: mo_assert.h (-1)

westram 2008-05-21 21:17 Rev.: 5329

- depends updated

2 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (+2)

westram 2008-05-19 12:04 Rev.: 5312

- depends updated

0 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (-2)

westram 2007-05-30 14:34 Rev.: 4634

- proper clean (avoid errors if already cleaned)

1 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (+1 -1)

westram 2004-06-08 14:28 Rev.: 2867

molphy license

40 lines of code changed in 1 file:

• GDE/MOLPHY: README.txt (new 40)

westram 2004-05-13 12:10 Rev.: 2743

dependencies updated

2 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (+2)

westram 2004-05-06 15:04 Rev.: 2702

- if 'star decomposition' and 'rearrangement' were used together
protml crashed, because of undefined vectors and matrixes

12 lines of code changed in 1 file:

• GDE/MOLPHY: protml.c (+12 -1)

westram 2004-05-06 15:03 Rev.: 2701

- assertion macro

24 lines of code changed in 1 file:

• GDE/MOLPHY: mo_assert.h (new 24)

westram 2004-05-06 15:03 Rev.: 2700

- added assertions (avoiding to create empty ?vector, ?matrix and ?cube)

46 lines of code changed in 1 file:

• GDE/MOLPHY: matrixut.c (+46 -8)

westram 2004-01-23 18:08 Rev.: 2338

fixed and reformatted dependencies (using fix_depends.pl)

75 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (+75 -19)

westram 2003-09-21 13:09 Rev.: 1907

- does no longer generate c files
- only generates dependencies for SOURCES_TML

48 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (+48 -86)

westram 2003-09-19 10:32 Rev.: 1893

*** empty log message ***

0 lines of code changed in 1 file:

• GDE/MOLPHY: .cvsignore (new)

westram 2003-09-19 10:31 Rev.: 1892

- missing parameter type
- one array element wasn't initialized

8 lines of code changed in 1 file:

• GDE/MOLPHY: sltree.c (+8 -9)

westram 2003-09-19 10:30 Rev.: 1891

- minor change

3 lines of code changed in 1 file:

• GDE/MOLPHY: pstree.c (+3 -3)

westram 2003-09-19 10:20 Rev.: 1890

this is a generated files!

0 lines of code changed in 1 file:

• GDE/MOLPHY: prot_tml.h (del)

westram 2003-09-19 10:17 Rev.: 1889

contains removed sources

0 lines of code changed in 1 file:

• GDE/MOLPHY: unused_molphy_sources.tgz (new)

westram 2003-09-19 10:11 Rev.: 1887

- use calloc

3 lines of code changed in 1 file:

• GDE/MOLPHY: protml.c (+3 -3)

westram 2003-09-19 10:11 Rev.: 1886

- added mo_assert

3 lines of code changed in 1 file:

• GDE/MOLPHY: protml.h (+3)

westram 2003-09-19 10:08 Rev.: 1885

missing parameter type

12 lines of code changed in 2 files:

• GDE/MOLPHY: mltree.c (+10 -10), njtree.c (+2 -1)

westram 2003-09-19 10:06 Rev.: 1884

const fix

7 lines of code changed in 3 files:

• GDE/MOLPHY: getseq.c (+4 -4), matrixut.c (+1 -1), matrixut.h (+2 -2)

westram 2003-08-09 13:00 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!

93 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (+93 -641)

westram 2002-06-20 15:08 Rev.: 655

Mac OSX patches from Ben Hines

16 lines of code changed in 8 files:

• GDE/MOLPHY: Nucml.c (+2 -2), Nucst.c (+1 -1), Nuctpm.c (+2 -2), Prottpm.c (+2 -2), prot_tml.h (+1 -1), protml.c (+2 -2), protst.c (+1 -1), seqproc.c (+5 -6)

westram 2002-05-29 16:46 Rev.: 597

*** empty log message ***

637 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (+637 -39)

yadhu 2002-05-29 10:53 Rev.: 593

makefile dependency generation fixed for GDE

39 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (+39 -637)

westram 2002-05-23 08:29 Rev.: 566

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

241 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (+241 -225)

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