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westram 2011-12-01 12:41 Rev.: 8273

- removed dead ALIV3

0 lines of code changed in 30 files:

• ALIV3: BI_helix.cxx (del), BI_helix.hxx (del), Makefile (del), README (del), a3.cxx (del), a3_ali.cxx (del), a3_ali.hxx (del), a3_arbdb.cxx (del), a3_arbdb.hxx (del), a3_basen.c (del), a3_basen.h (del), a3_bihelix.cxx (del), a3_bihelix.hxx (del), a3_darray.cxx (del), a3_darray.hxx (del), a3_helix.cxx (del), a3_helix.hxx (del), a3_matrix.cxx (del), a3_matrix.hxx (del), a3_ptree.hxx (del), a3_ptree1.cxx (del), a3_ptree2.cxx (del), a3_seq.cxx (del), a3_seq.hxx (del), a3_test_ptree.cxx (del), a3_types.h (del), ali_arbdb.cxx (del), ali_arbdb.hxx (del), needs_libs (del), postree.cxx (del)

westram 2011-11-29 10:33 Rev.: 8249

* wrap main for untested (but testable) units
- still untestable
* ptpan (wont change in this branch)
* GENOM (cyclic dependency with GENOM_IMPORT due to Location)
* fix missing lib dependencies
- DIST -> SL/NDS
- STAT -> SL/ITEMS
- AW_NAME -> libAWT (instead of libWINDOW)

4 lines of code changed in 3 files:

• ALIV3: a3.cxx (+2 -2), a3_arbdb.cxx (+1 -1), a3_arbdb.hxx (+1 -1)

westram 2011-08-08 01:06 Rev.: 7812

merge from dev [7751] [7752]
* updated many old-style typedefs (typedef struct/enum)

8 lines of code changed in 3 files:

• ALIV3: a3_basen.c (+1 -1), a3_basen.h (+5 -7), a3_ptree.hxx (+2 -4)

westram 2011-08-08 01:01 Rev.: 7811

merge from dev [7748] [7749] [7750]
* comments (C->C++ style)
* fixed umlauts in TREEGEN

45 lines of code changed in 1 file:

• ALIV3: a3_basen.c (+45 -45)

westram 2011-06-10 15:50 Rev.: 7623

- merge from dev [7450] [7452] [7456] [7457] [7458] [7459] [7460] [7461] [7464] [7465] [7466] [7467] [7468] [7469] [7482]
* tweaked compiler options
- activated -Weffc++
* postfilter warnings where Scott Meyers' advices are too general.
- base classes should not always have virtual destructors, since that renders tiny classes useless and
- members should not always be initialized via initialization list, since that often violates the DRY principle
* fix gcc's inability to detect that Noncopyable implements a private copy-ctor and op=
* this slows down complete ARB recompilation by ~5%
- added -Wold-style-cast (inactive)
- removed -Wno-non-template-friend added in [7447]
* postcompile.pl
- added option --original to show unmodified compiler output
* declared op= for classes which had a copy-ctor
* moved op= macros to arbtools.h
* derived classes containing pointers from Noncopyable (use Noncopyable virtually) or
* made them copyable if needed (awt_mask_item, KnownDB, Code, AWT_registered_itemtype, GEN_gene, !PosGene, !PartialSequence, !PlugIn, Range, Convaln_exception)
* other related changes
- user mask destruction working now

49 lines of code changed in 13 files:

• ALIV3: Makefile (+6), a3_arbdb.hxx (+5 -3), a3_darray.cxx (+1 -1), a3_darray.hxx (+6 -1), a3_helix.hxx (+1 -4), a3_matrix.cxx (+1 -1), a3_matrix.hxx (+4 -3), a3_ptree.hxx (+10 -11), a3_ptree1.cxx (+3 -3), a3_ptree2.cxx (+1 -1), a3_seq.cxx (+1 -1), a3_seq.hxx (+6 -7), a3_types.h (+4)

westram 2011-04-16 11:33 Rev.: 7423

merged from dev [7320] [7418] [7419] [7420]
* !BasePosition
- uses int instead of size_t
- allow empty sequences (gap-only)
- allow to index just a part of a sequence
- use new class !CharPredicate to initialize custom gaps
* moved safeCharIndex() to dupstr.h
* unit tests
- collectIntFunResults (allowed range)
- slow test

4 lines of code changed in 4 files:

• ALIV3: Makefile (+2 -3), a3_ptree1.cxx (+1 -1), a3_ptree2.cxx (+1 -1), a3_seq.cxx (-1)

westram 2011-02-23 14:37 Rev.: 7183

merges [7084] [7086] [7087] [7088] from refactor
* added CORE lib
- added arb_progress (unused yet)
- moved some code from ARBDB to CORE
* added tests to CORE lib
* generate_all_links.sh
- now tests link targets
- able to replace links (if link stays the same, but target changes)
* fixed perl interface
- link with libCORE
- DRYed LINUX.PL and DARWIN.PL
- added wrapper functionality (ARBDB->CORE). Functions starting with GBC_ are wrappers for code that moved into libCORE (which is NOT xsub'd)

6 lines of code changed in 1 file:

• ALIV3: Makefile (+6 -3)

westram 2010-10-25 18:10 Rev.: 7044

* fixed include wrappers (merges [7006] [7007])
- use gcc-style include-wrappers
- use same convention for local wrappers in TREEGEN as rest of ARB

1 lines of code changed in 1 file:

• ALIV3: a3_seq.hxx (+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)

2 lines of code changed in 1 file:

• ALIV3: Makefile (+2 -2)

westram 2010-09-09 22:49 Rev.: 6817

- depends for [6816]

3 lines of code changed in 1 file:

• ALIV3: Makefile (+3)

westram 2010-09-09 20:25 Rev.: 6814

* depends updated for [6812] + [6813]

6 lines of code changed in 1 file:

• ALIV3: Makefile (+6 -3)

westram 2010-09-09 20:23 Rev.: 6813

* merged from refactor [6796] [6804] [6806] [6808]
* added header for planned library ARB_CORE
* renamed inline.h into arb_str.h
* header for global general purpose defines/inlines (arb_defs.h)
- use ARRAY_ELEMS where applicable
* removed duplicate of ARB_strscmp (GBS_strscmp). No longer needed cause ARBDB is now C++

3 lines of code changed in 3 files:

• ALIV3: a3_ptree1.cxx (+1 -1), a3_ptree2.cxx (+1 -1), a3_seq.cxx (+1 -1)

westram 2010-05-14 13:58 Rev.: 6659

* free()
- removed unneeded casts of argument
- removed unneeded if-clauses

2 lines of code changed in 1 file:

• ALIV3: a3_arbdb.cxx (+2 -2)

westram 2010-05-07 20:42 Rev.: 6639

* GB_change_my_security
- removed constant result
- removed unused parameter 'passwd'

1 lines of code changed in 1 file:

• ALIV3: a3_arbdb.cxx (+1 -1)

westram 2010-02-28 17:21 Rev.: 6488

- fixed includes
- added MBI-headers and wrappers

282 lines of code changed in 20 files:

• ALIV3: a3.cxx (+14 -10), a3_ali.cxx (+11 -6), a3_ali.hxx (+20 -24), a3_arbdb.cxx (+11 -8), a3_arbdb.hxx (+16 -17), a3_basen.c (+9 -3), a3_basen.h (+14 -20), a3_darray.cxx (+11 -5), a3_darray.hxx (+17 -22), a3_helix.cxx (+12 -8), a3_helix.hxx (+21 -27), a3_matrix.cxx (+11 -5), a3_matrix.hxx (+16 -16), a3_ptree.hxx (+16 -16), a3_ptree1.cxx (+12 -6), a3_ptree2.cxx (+13 -7), a3_seq.cxx (+14 -10), a3_seq.hxx (+19 -18), a3_test_ptree.cxx (+11 -5), a3_types.h (+14 -12)

westram 2010-02-17 10:30 Rev.: 6448

- added library dependency declarations

4 lines of code changed in 1 file:

• ALIV3: needs_libs (new 4)

westram 2010-01-27 09:05 Rev.: 6381

- fixed includes
- added MBI headers
- removed unused files

6 lines of code changed in 2 files:

• ALIV3: a3_arbdb.cxx (+4 -5), a3_test_ptree.cxx (+2 -2)

westram 2010-01-13 15:41 Rev.: 6347

Moved a lot of dead code to where it belongs: into the depths of SVN.
I didn't care much: If there was no obvious reason (e.g. some coment explaining why it's still there), it has been deleted

34 lines of code changed in 3 files:

• ALIV3: a3.cxx (+34 -51), a3_helix.cxx (-1), a3_seq.cxx (-2)

westram 2010-01-07 15:07 Rev.: 6331

* removed GB_strdup
* moved freeset, nulldup, etc to own header (dupstr.h)
* added freenull
- replacement for freeset(var,NULL)
- freeset is a template now and does no longer work with NULL/0
- replaced all occurrances

4 lines of code changed in 2 files:

• ALIV3: Makefile (+3), a3_arbdb.cxx (+1 -1)

westram 2009-12-30 20:56 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

11 lines of code changed in 2 files:

• ALIV3: Makefile (+9), a3_arbdb.cxx (+2 -2)

westram 2009-05-07 19:24 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()

4 lines of code changed in 1 file:

• ALIV3: a3_arbdb.cxx (+4 -4)

westram 2009-04-19 19:35 Rev.: 5828

* changed ulong->ULONG and uint->UINT (ulong/uint are missing under OSX)

17 lines of code changed in 5 files:

• ALIV3: a3_ptree.hxx (+2 -2), a3_ptree2.cxx (+2 -2), a3_seq.cxx (+6 -6), a3_seq.hxx (+6 -6), a3_types.h (+1 -2)

westram 2009-01-10 00:34 Rev.: 5725

* removed useless macros:
- GB_STRDUP (easily taken for GB_strdup)
- GB_MEMCPY + GB_MEMSET + GB_FREE
- GB_DELETE (replaced by freeset(xx,NULL))
* added macros:
- freeset (= free + assign)
- freedup (= free + assign strdup'ed)
- reassign (= free + assign + clear source var)
- nulldup (=strdup accepting NULL; replacement for GB_strdup in C++ code)
* use these macros where applicable

1 lines of code changed in 1 file:

• ALIV3: a3_arbdb.cxx (+1 -3)

westram 2008-12-31 13:27 Rev.: 5709

- made depends for [5708]

6 lines of code changed in 1 file:

• ALIV3: Makefile (+6)

westram 2008-07-10 13:15 Rev.: 5444

- depends updated

3 lines of code changed in 1 file:

• ALIV3: Makefile (+3)

westram 2008-07-10 13:10 Rev.: 5438

- char array indices
- ambiguous elses

16 lines of code changed in 1 file:

• ALIV3: a3_ptree1.cxx (+16 -14)

westram 2008-07-10 13:07 Rev.: 5436

- fixed signed chars used as array index

8 lines of code changed in 2 files:

• ALIV3: a3_ptree2.cxx (+3 -1), a3_seq.cxx (+5 -3)

westram 2008-07-03 11:29 Rev.: 5411

- depends updated

4 lines of code changed in 1 file:

• ALIV3: Makefile (+4)

westram 2008-06-18 11:42 Rev.: 5405

- use GB_random / GB_frandom instead of rand
- removed calls to srand() - done by GB_[f]random

8 lines of code changed in 1 file:

• ALIV3: a3_seq.cxx (+8 -14)

westram 2008-05-23 16:25 Rev.: 5340

- use GB_CASE parameter
- changed GBS_string_[s]cmp

2 lines of code changed in 1 file:

• ALIV3: a3_arbdb.cxx (+2 -2)

westram 2008-05-19 12:48 Rev.: 5309

- replaced calls to GB_find with new find-functions

6 lines of code changed in 1 file:

• ALIV3: a3_arbdb.cxx (+6 -10)

westram 2008-03-11 20:07 Rev.: 5225

- changed names of linker commands

1 lines of code changed in 1 file:

• ALIV3: Makefile (+1 -1)

westram 2008-02-28 12:18 Rev.: 5129

- depends updated

2 lines of code changed in 1 file:

• ALIV3: Makefile (+2)

baderk 2008-01-03 12:45 Rev.: 5016

64bit conversion fix (int -> long).

1 lines of code changed in 1 file:

• ALIV3: a3_matrix.cxx (+1 -1)

boehnel 2007-12-17 19:10 Rev.: 4992

"int -> long" to get 64bit work

5 lines of code changed in 1 file:

• ALIV3: a3_helix.cxx (+5 -5)

westram 2007-11-06 12:56 Rev.: 4918

- removed unused default-param 'info' from put_sequence_string()

1 lines of code changed in 1 file:

• ALIV3: a3_arbdb.hxx (+1 -2)

westram 2007-11-06 12:56 Rev.: 4917

- removed code creating unused 'mark' entries

7 lines of code changed in 1 file:

• ALIV3: a3_arbdb.cxx (+7 -30)

westram 2007-09-19 15:37 Rev.: 4784

- fixed changed BI_helix access

4 lines of code changed in 1 file:

• ALIV3: a3.cxx (+4 -4)

westram 2007-05-30 15:34 Rev.: 4634

- proper clean (avoid errors if already cleaned)

1 lines of code changed in 1 file:

• ALIV3: Makefile (+1 -2)

westram 2007-05-16 13:28 Rev.: 4578

- fixed warnings

3 lines of code changed in 1 file:

• ALIV3: a3.cxx (+3 -3)

(21 more)