Directory SL/FILE_BUFFER/

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westram 2012-04-15 18:18 Rev.: 8588

- moved SL/FILE_BUFFER into CORE

0 lines of code changed in 4 files:

• SL/FILE_BUFFER: FileBuffer.cxx (del), FileBuffer.h (del), Makefile (del), needs_libs (del)

westram 2012-04-11 12:19 Rev.: 8574

* [8567] failed on WCs where shared libs were up-to-date, but not yet present in $ARBHOME/lib
- link libs directly in $ARBHOME/lib
* no longer create 'SHARED.a' in shared-library-dirs
* unit tests caused build of 'SHARED.so' (instead of 'libSHARED.so'). Every library existed twice.
- changed test-target-names for shared libaries (e.g. ARBDB/ARBDB.test -> ARBDB/libARBDB.test)
- added failing stopper targets to main-Makefile and shared-lib-Makefiles
* changed all dependencies to shared libs
* fixed dependency scripts to perform correct translations from lib/libUNIT.so <-> UNIT/UNIT.(dummy|a). omg :/
* updated predefined RESTRICT_LIB entries in UNIT_TESTER/Makefile.setup.template
- check whether RESTRICT_LIB uses obsolete test-names (e.g. ARBDB instead of libARBDB) and fail if.

1 lines of code changed in 1 file:

• SL/FILE_BUFFER: needs_libs (+1 -1)

westram 2011-06-10 14:50 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

1 lines of code changed in 1 file:

• SL/FILE_BUFFER: FileBuffer.h (+1 -1)

westram 2011-03-11 11:31 Rev.: 7246

merged from dev [7227] [7228]

* extended !SmartPtr
* compile fix for coverage

1 lines of code changed in 1 file:

• SL/FILE_BUFFER: FileBuffer.cxx (+1 -1)

westram 2011-02-23 13:37 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)

0 lines of code changed in 1 file:

• SL/FILE_BUFFER: Makefile (-3)

westram 2010-10-25 18:47 Rev.: 7046

* refactored CONVERTALN (merges [6885] [6886] [6888] [6889] [6890] [6891] [6894] [6906] [6907] [6908] [6910] [6911] [6914] [6915] [6916] [6917] [6918] [6922] [6923] [6925] [6927] [6928] [6929] [6930] [6931] [6933] [6934] [6935] [6937] [6945] [6950] [6956] [6961] [6962] [6963] [6964] [6965] [6967] [6968] [6972] [6973] [6974] [6975] [6976] [6977] [6979] [6980] [6981] [6982] [6983] [6985] [6986] [6987] [6988] [6990] [6991] [6992] [6993] [6994] [6995] [6996] [6997] [6998] [6999] [7002] [7003] [7008] [7009] [7010] [7011] [7012] [7025] [7026] [7027] [7029] [7030] [7031] [7032] [7034] [7035] [7036])
- build arb_convert_aln in ARB standard way
- added unit-test
- fixed various date bugs (even Y2K)
- fixed conversion MACKE -> GCG.
- fixed crash in conversions EMBL/GENBANK -> GCG
- fixed SWISSPROT->MACKE conversion
- dropped conversion support for ALMA
- removed completely unused "formats" NBRF and STADEN
- removed 1x1 sequence conversions for interleaved formats
- converter is more picky (fails instead of doing nonsense)
- added self conversions for all input formats
- proper formatting of 3/5 info
- proper line wrapping
- fixed acc broken by genbank reader
- fixed broken IDs (short-names)
- fixed embl reader (added number @ EOL to sequence data)
- errors now refer to the input file + linenumber
- abort with error if sequence data contains invalid characters
- removed C-interface for FileBuffer (CONVERTALN was the only client)

0 lines of code changed in 2 files:

• SL/FILE_BUFFER: FileBuffer.cxx (-48), FileBuffer.h (-13)

westram 2010-10-25 17:10 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

2 lines of code changed in 1 file:

• SL/FILE_BUFFER: FileBuffer.h (+2 -2)

westram 2010-10-25 14:10 Rev.: 7037

* merged from refactor [6936] [7000] [7001] [7004]
- interface to get line-specific error from anonymous FILE_BUFFER
- fixed return of temporary
- fixed memleak

17 lines of code changed in 3 files:

• SL/FILE_BUFFER: FileBuffer.cxx (+15 -5), FileBuffer.h (+1), Makefile (+1)

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)

2 lines of code changed in 1 file:

• SL/FILE_BUFFER: Makefile (+2 -2)

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

- depends for [6816]

1 lines of code changed in 1 file:

• SL/FILE_BUFFER: Makefile (+1)

westram 2010-09-09 19:25 Rev.: 6814

* depends updated for [6812] + [6813]

7 lines of code changed in 1 file:

• SL/FILE_BUFFER: Makefile (+7)

westram 2010-03-17 14:24 Rev.: 6528

- compile fix (NDEBUG+UNIT_TESTS)

4 lines of code changed in 1 file:

• SL/FILE_BUFFER: FileBuffer.cxx (+4 -4)

westram 2010-02-17 09:30 Rev.: 6448

- added library dependency declarations

4 lines of code changed in 1 file:

• SL/FILE_BUFFER: needs_libs (new 4)

westram 2010-01-27 09:48 Rev.: 6385

- removed trailing whitespace

2 lines of code changed in 1 file:

• SL/FILE_BUFFER: FileBuffer.cxx (+2 -2)

westram 2010-01-27 08:05 Rev.: 6381

- fixed includes
- added MBI headers
- removed unused files

15 lines of code changed in 2 files:

• SL/FILE_BUFFER: FileBuffer.cxx (+13 -12), FileBuffer.h (+2 -2)

westram 2010-01-24 16:05 Rev.: 6374

* fixed doxygen-alike comments
- either use explicit qt-style triggers (/*! and //!)
- or made them simple comments
* converted several "normal" comments into doxygen-comments
* moved many comments inside the function/struct to which they (seemed) to belong (otherwise function and comments tend to get separated over the years)
* deleted several comments
- obvious things like paraphrases of the function name
- spammy things like repeating the function prototype
* reduced comments for vertical seperation

2 lines of code changed in 1 file:

• SL/FILE_BUFFER: FileBuffer.h (+2 -4)

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

33 lines of code changed in 2 files:

• SL/FILE_BUFFER: FileBuffer.cxx (+10 -10), FileBuffer.h (+23 -18)

baderk 2009-11-30 12:15 Rev.: 6285

Karmic Koala (gcc 4.4.1) patch.

1 lines of code changed in 1 file:

• SL/FILE_BUFFER: FileBuffer.cxx (+1)

westram 2009-05-29 09:53 Rev.: 5958

* assertion if rewind fails

5 lines of code changed in 1 file:

• SL/FILE_BUFFER: FileBuffer.cxx (+5 -1)

westram 2009-04-13 11:37 Rev.: 5811

* fixed undefined behavior at EOF (when testing for DOS linefeed)

5 lines of code changed in 1 file:

• SL/FILE_BUFFER: FileBuffer.cxx (+5 -3)

westram 2009-04-11 14:47 Rev.: 5802

* FileBuffer: added toggle to suppress output of filename

26 lines of code changed in 2 files:

• SL/FILE_BUFFER: FileBuffer.cxx (+21 -6), FileBuffer.h (+5 -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 2 files:

• SL/FILE_BUFFER: FileBuffer.cxx (-1), FileBuffer.h (-1)

westram 2008-07-30 09:57 Rev.: 5489

private Noncopyable

2 lines of code changed in 1 file:

• SL/FILE_BUFFER: FileBuffer.h (+2 -2)

westram 2008-07-09 12:50 Rev.: 5428

- fixed includes for gcc 4.3.1

4 lines of code changed in 1 file:

• SL/FILE_BUFFER: FileBuffer.cxx (+4 -2)

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

- changed names of linker commands

1 lines of code changed in 1 file:

• SL/FILE_BUFFER: Makefile (+1 -1)

westram 2008-03-03 13:08 Rev.: 5189

- removed gcc 2.95 compat-code

1 lines of code changed in 1 file:

• SL/FILE_BUFFER: FileBuffer.cxx (+1 -6)

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

- proper clean (avoid errors if already cleaned)

1 lines of code changed in 1 file:

• SL/FILE_BUFFER: Makefile (+1 -2)

westram 2007-03-21 01:02 Rev.: 4413

- added missing swap template for gcc 2.95.3 or below

5 lines of code changed in 1 file:

• SL/FILE_BUFFER: FileBuffer.cxx (+5 -1)

westram 2007-02-01 11:08 Rev.: 4308

- debug-only variable

5 lines of code changed in 1 file:

• SL/FILE_BUFFER: FileBuffer.cxx (+5 -2)

westram 2007-01-27 12:49 Rev.: 4290

- removed virtual destructor
- added rewind
- removed is_EOL (no longer used)
- FILE_BUFFER_read() returns length of read line

11 lines of code changed in 1 file:

• SL/FILE_BUFFER: FileBuffer.h (+11 -9)

westram 2007-01-27 12:49 Rev.: 4289

- use memchr to search for EOL in input buffer.
- added method rewind()
- cleaned up C->C++ interface functions

65 lines of code changed in 1 file:

• SL/FILE_BUFFER: FileBuffer.cxx (+65 -19)

westram 2006-12-13 19:19 Rev.: 4254

- an ascii-file reader

272 lines of code changed in 3 files:

• SL/FILE_BUFFER: FileBuffer.cxx (new 102), FileBuffer.h (new 129), Makefile (new 41)