Directory ARBDBPP/

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westram 2009-12-30 19:56 Rev.: 6318

* ARBDB
- compiles as C++ (no longer compiled as plain C)
- removed ARBDB2 + ARBDBS
- removed rotten C++-wrappers (ARBDBPP)
- generates special header for perl-interface to reduce dependencies (ad_p_prot.h)
* removed (ARBDB)
- gb_search_enum (merged with GB_TYPES)
* renamed (ARBDB)
- gbs_malloc_copy -> GB_memdup
- gb_search_types -> GB_SEARCH_TYPE + renamed enum-members
* tweaked perl interface
- code in ARBDB is now able to 'die' correctly (see GBP_croak_function)
- compiles as C++
- wrote generic functions for enum <-> string conversion (perl uses strings for enum values)
- added needed conversion functions
- removed handcoded xsubs (now all are generated by arb_proto_2_xsub - nevertheless, it's still possible to define xsubs manually)
- ARB::find and ARB::find_string (3rd parameter needs different values, only one file affected: PERL_SCRIPTS/GENOME/GI.pm - fixed)
- removed all functions using GBQUARK from perl interface
* perl interface generator (arb_proto_2_xsub)
- completely rewritten
- does automatic type conversion (expecting that the needed functions are defined in ARBDB/adperl.c)
* prototype generator
- compiles as C++
- switch -F accept's '!^' as beginning-of-name expression
* removed ARB_EDIT
- moved naligner interface code to EDIT4

0 lines of code changed in 12 files:

• ARBDBPP: Makefile (del), adali.cxx (del), adextended.cxx (del), admain.cxx (del), adseq.cxx (del), adspecies.cxx (del), adt_edit.cxx (del), adtali.cxx (del), adtools.hxx (del), adtsequence.cxx (del), arbdb++.hxx (del), liste.cxx (del)

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

* spellchecked all (phew)

13 lines of code changed in 4 files:

• ARBDBPP: admain.cxx (+1 -1), adseq.cxx (+2 -2), adspecies.cxx (+1 -1), arbdb++.hxx (+9 -9)

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

31 lines of code changed in 4 files:

• ARBDBPP: adt_edit.cxx (+1 -2), adtools.hxx (+15 -11), adtsequence.cxx (-1), arbdb++.hxx (+15 -9)

westram 2009-05-07 18:24 Rev.: 5894

* reactivated original GB_close
* removed GB_exit (use GB_close)
* gb_delete_entry now takes and invalidates a GBDATA** (to avoid further undetected usage)
* gb_do_callback_list called with GB_MAIN_TYPE (instead of possibly already deleted gb_main)
* added some missing transactions
* moved declaration of GBDATA into arbdb_base.h (and include where needed)
* GB_MAIN_TYPE is no longer void
* AW_default is no longer void
* replaced the 3 differing ways to exit EDIT4 by ED4_exit()
* added AW_root::unlink_awars_from_DB() and call in arb_ntree, arb_dist, arb_edit4, arb_pars and arb_phylo
* rewrote arb_2_ascii, arb_2_bin, arb_perf_test, arb_read_tree (single exit point, error handling)
* unlinked AWARs now return "" not "?????"
* AW_awar::read_string works only with awars of type AW_STRING. Added assertion + fixed one wrong usage.
* inlined AW_awar::get()
* added AW_awar::remove_all_callbacks() and AW_awar::remove_all_target_vars()

1 lines of code changed in 1 file:

• ARBDBPP: admain.cxx (+1 -1)

westram 2009-04-22 12:13 Rev.: 5839

* followup to [5824] (more to follow)
- GB_get_error() -> GB_await_error() where appropriate (ARBDB mostly)
- fixed error handling in several functions

2 lines of code changed in 2 files:

• ARBDBPP: adseq.cxx (+1 -1), arbdb++.hxx (+1 -1)

westram 2009-04-19 18:36 Rev.: 5829

* included some patches for OSX (thx to Matt Cottrell)
* added global switch LINK_STATIC
* added script which checks for tools needed to compile ARB
* typo CCPLIB->CPPLIB

1 lines of code changed in 1 file:

• ARBDBPP: Makefile (+1 -1)

westram 2009-04-15 13:58 Rev.: 5823

* more uniform function names
- EXP_create_experiment_rel_experiment_data -> EXP_find_or_create_experiment_rel_exp_data
- EXP_find_experiment_rel_experiment_data -> EXP_find_experiment_rel_exp_data
- GBT_create_SAI -> GBT_find_or_create_SAI
- GBT_create_item -> GBT_find_or_create_item_rel_item_data
- GBT_create_species -> GBT_find_or_create_species
- GBT_create_species_rel_species_data -> GBT_find_or_create_species_rel_species_data

2 lines of code changed in 2 files:

• ARBDBPP: adextended.cxx (+1 -1), adspecies.cxx (+1 -1)

westram 2009-01-15 11:54 Rev.: 5734

* added GBT_get_SAI_data
* GBT_first/next_marked_extended -> GBT_first/next_marked_SAI
* GBT_first/find_SAI_rel_exdata -> GBT_first/find_SAI_rel_SAI_data
* variables renamed: (gb_ex[tended[_data]] -> gb_sai[_data])

14 lines of code changed in 3 files:

• ARBDBPP: adextended.cxx (+1 -1), admain.cxx (+5 -5), arbdb++.hxx (+8 -8)

westram 2008-12-31 12:27 Rev.: 5709

- made depends for [5708]

18 lines of code changed in 1 file:

• ARBDBPP: Makefile (+18)

westram 2008-06-06 13:23 Rev.: 5390

- TAB-Ex

361 lines of code changed in 4 files:

• ARBDBPP: adtali.cxx (+102 -102), adtools.hxx (+150 -153), adtsequence.cxx (+58 -60), liste.cxx (+51 -61)

westram 2008-05-21 21:18 Rev.: 5330

- mostly const fixes

2 lines of code changed in 1 file:

• ARBDBPP: adseq.cxx (+2 -2)

westram 2008-05-19 11:48 Rev.: 5309

- replaced calls to GB_find with new find-functions

43 lines of code changed in 4 files:

• ARBDBPP: adali.cxx (+14 -9), admain.cxx (+15 -33), adseq.cxx (+10 -10), adspecies.cxx (+4 -4)

westram 2008-03-11 19:07 Rev.: 5225

- changed names of linker commands

1 lines of code changed in 1 file:

• ARBDBPP: Makefile (+1 -1)

westram 2008-02-29 18:41 Rev.: 5156

- indented

753 lines of code changed in 1 file:

• ARBDBPP: adt_edit.cxx (+753 -753)

westram 2008-02-29 18:18 Rev.: 5155

- removed register keywords

9 lines of code changed in 1 file:

• ARBDBPP: adt_edit.cxx (+9 -12)

westram 2008-02-29 15:51 Rev.: 5144

- again changed variables names (renamed to ugly tmp_... by joerg)

37 lines of code changed in 6 files:

• ARBDBPP: adali.cxx (+2 -2), adextended.cxx (+3 -3), adseq.cxx (+19 -22), adspecies.cxx (+3 -3), adtali.cxx (+7 -8), adtsequence.cxx (+3 -3)

boehnel 2008-02-28 21:39 Rev.: 5141

removing some compiler warnings

(changes to ED4_cursor.cxx reverted by [5146], changes to AWTC_constructSequence.cxx reverted by [5145])

36 lines of code changed in 5 files:

• ARBDBPP: adali.cxx (+2 -2), adextended.cxx (+3 -3), adseq.cxx (+20 -20), adspecies.cxx (+3 -3), adtali.cxx (+8 -8)

boehnel 2008-02-28 18:20 Rev.: 5139

removed some compiler warnings

3 lines of code changed in 1 file:

• ARBDBPP: adtsequence.cxx (+3 -3)

westram 2008-02-28 11:18 Rev.: 5129

- depends updated

9 lines of code changed in 1 file:

• ARBDBPP: Makefile (+9)

baderk 2007-11-08 19:14 Rev.: 4932

Fixed various typos...

2 lines of code changed in 1 file:

• ARBDBPP: admain.cxx (+2 -2)

westram 2007-05-30 14:39 Rev.: 4635

- added 'clean'

3 lines of code changed in 1 file:

• ARBDBPP: Makefile (+3)

westram 2007-05-15 14:54 Rev.: 4536

- renamed AW_KEY_... into AW_KEYMODE_...

2 lines of code changed in 1 file:

• ARBDBPP: adseq.cxx (+2 -2)

westram 2006-06-07 16:28 Rev.: 4030

- gcc 4.1.1 fixes

9 lines of code changed in 1 file:

• ARBDBPP: arbdb++.hxx (+9 -2)

westram 2006-06-07 16:28 Rev.: 4029

- cosmetics

2 lines of code changed in 1 file:

• ARBDBPP: adspecies.cxx (+2 -4)

westram 2005-01-05 12:52 Rev.: 3538

- changed include wrapper
- removed GB_INCLUDED

1 lines of code changed in 1 file:

• ARBDBPP: arbdb++.hxx (+1 -6)

westram 2004-12-17 20:12 Rev.: 3472

- fixed calls to GB_write_bits

4 lines of code changed in 1 file:

• ARBDBPP: adseq.cxx (+4 -2)

westram 2004-12-17 20:11 Rev.: 3468

- beautified

330 lines of code changed in 1 file:

• ARBDBPP: arbdb++.hxx (+330 -327)

westram 2004-10-07 13:08 Rev.: 3233

- fixed includes + indentation

956 lines of code changed in 5 files:

• ARBDBPP: adali.cxx (+123 -124), adextended.cxx (+106 -107), admain.cxx (+140 -137), adseq.cxx (+469 -468), adspecies.cxx (+118 -115)

westram 2004-03-11 13:56 Rev.: 2512

- include fixes

1 lines of code changed in 1 file:

• ARBDBPP: adtsequence.cxx (+1 -2)

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

fixed and reformatted dependencies (using fix_depends.pl)

52 lines of code changed in 1 file:

• ARBDBPP: Makefile (+52 -37)

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!

28 lines of code changed in 1 file:

• ARBDBPP: Makefile (+28 -9)

westram 2002-10-09 12:21 Rev.: 887

make depend

6 lines of code changed in 1 file:

• ARBDBPP: Makefile (+6 -6)

westram 2002-08-23 19:53 Rev.: 866

changed assert macros (see arb_assert.h)

14 lines of code changed in 1 file:

• ARBDBPP: Makefile (+14 -64)

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

Mac OSX patches from Ben Hines

172 lines of code changed in 4 files:

• ARBDBPP: adseq.cxx (+39 -39), adt_edit.cxx (+105 -105), adtali.cxx (+24 -24), adtsequence.cxx (+4 -4)

westram 2001-01-11 15:58 Rev.: 83

*** empty log message ***

96 lines of code changed in 1 file:

• ARBDBPP: Makefile (+96 -141)

meierh 2001-01-11 15:24 Rev.: 80

haralds checkin

141 lines of code changed in 1 file:

• ARBDBPP: Makefile (+141 -96)

westram 2001-01-04 15:36 Rev.: 68

Updated dependencies

25 lines of code changed in 1 file:

• ARBDBPP: Makefile (+25 -18)

oldcode 2000-11-23 10:41 Rev.: 2

Initial revision

4373 lines of code changed in 12 files:

• ARBDBPP: Makefile (new 101), adali.cxx (new 183), adextended.cxx (new 153), admain.cxx (new 387), adseq.cxx (new 1062), adspecies.cxx (new 311), adt_edit.cxx (new 1020), adtali.cxx (new 163), adtools.hxx (new 334), adtsequence.cxx (new 123), arbdb++.hxx (new 456), liste.cxx (new 80)