Directory ptpan/

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westram 2020-04-01 16:21 Rev.: 18426

* reintegrates 'unittest' into 'trunk'
* adds: log:branches/unittest@18363:18425

0 lines of code changed in 38 files:

• ptpan: Makefile (del), Makefile.old (del), PTP_buildtree.cxx (del), PTP_etc.cxx (del), PTP_family.cxx (del), PTP_findEx.cxx (del), PTP_io.cxx (del), PTP_main.cxx (del), PTP_match.cxx (del), PTP_new_design.cxx (del), PT_buildtree.cxx (del), PT_cachehandler.cxx (del), PT_etc.cxx (del), PT_family.cxx (del), PT_findEx.cxx (del), PT_hashing.cxx (del), PT_huffman.cxx (del), PT_io.cxx (del), PT_lowlevel.cxx (del), PT_main.cxx (del), PT_match.cxx (del), PT_new_design.cxx (del), PT_treepack.cxx (del), dlist.cxx (del), dlist.h (del), globalprefs.h (del), hooks.cxx (del), hooks.h (del), needs_libs.PROBE_a (del), pd.makefile (del), probe.h (del), probe_debug.cxx (del), pt_manualprotos.h (del), pt_prototypes.h (del), ptp_probe_debug.cxx (del), ptpan.h (del), ptpan_info.txt (del), types.h (del)

westram 2015-01-23 14:19 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:

• ptpan: Makefile (+1 -1)

westram 2013-11-03 14:42 Rev.: 11060

* reintegrates 'ptsfix' into 'trunk':
* adds:
- log:branches/ptsdump@8966:9000
- log:branches/ptsfix@8965:9012,9014:9017,9019:9023,9025:9046,9048:9089,9091:9114,9116:9132,9134:9139,9141:9145,9147:9151,9153:9158,9160:9379,9381:11059
- log:branches/ptsstartup@9160:9235,9237:9278,9280:9336,9339:9361,9363:9446
- log:branches/ptsundef@9061:9358

1 lines of code changed in 1 file:

• ptpan: Makefile (+1 -1)

westram 2013-10-31 14:10 Rev.: 10996

* use cflags before cxxflags

1 lines of code changed in 1 file:

• ptpan: Makefile (+1 -1)

westram 2013-10-30 15:58 Rev.: 10974

* renamed include variables

1 lines of code changed in 1 file:

• ptpan: Makefile (+1 -1)

westram 2013-10-29 12:55 Rev.: 10956

* made A_CC and A_CXX consistent
- A_CXX previously contained cxxflags
- cxxflags are now passed down and used separately

1 lines of code changed in 1 file:

• ptpan: Makefile (+1 -1)

westram 2013-10-29 12:23 Rev.: 10955

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

1 lines of code changed in 1 file:

• ptpan: Makefile (+1 -1)

westram 2011-09-12 08:53 Rev.: 7935

- removed outdated ptpan

17 lines of code changed in 4 files:

• ptpan: Makefile (+6 -372), PTP_main.cxx (+3 -543), needs_libs.PROBE_a (+2 -2), ptpan_info.txt (new 6)

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:

• ptpan: Makefile (+1 -1)

westram 2011-04-14 09:54 Rev.: 7415

merged from dev [7395] [7396] [7397] [7398] [7399] [7400] [7401] [7402] [7403] [7404] [7405]

* server/client interface
- changed invalid casts (now casts are done between classes derived from dll<XXX>)
- re-activated 'unused' warnings (deactivated since [566])
- removed unused functions/variables
- removed 'extern "C"'-voodoo
- when creating two objects containing a DESTROY callback (like PT_local), AISC servers now warn and automatically destroy the 1st created object (which leaked) and then create the 2nd
* fixed multiple creation of PT_local from PT_FamilyFinder
* print ioerror when saving nameserver db fails
* AISC interpreter
- fixed array overflow in command table
- detect "endless" recursive evaluation
- fixed RUIs occurred while scanning backwards
- fixed leak
- GOSUB/CALL (change function argument parsing and evaluation)

177 lines of code changed in 6 files:

• ptpan: Makefile (+1 -14), PTP_findEx.cxx (+1 -9), PTP_main.cxx (+2 -3), pt_prototypes.h (+172 -184), ptp_probe_debug.cxx (+1 -1), ptpan.h (-1)

westram 2011-04-14 09:40 Rev.: 7414

merged from dev [7373] [7375] [7376] [7377] [7378] [7379] [7380] [7381] [7382] [7383] [7384] [7385] [7386] [7387] [7388] [7389] [7390] [7391] [7392] [7393] [7394]
* AISC interpreter
- no longer print TABs (use spaces instead)
- new command INDENT +-<num> (old tab positions act relative to current indentation)
- each stream does formatting independently
- switching between output streams does no longer interfere indentation
- added smart tabulator '$|'
- new command '--' prints empty line
- new command 'PM' prints only if further output occurs (has to be used inside PMSTART/PMEND). Used to avoid empty loops etc.
- removed command 'P\t'
- added new conditional operator '<'
- error messages dump current data-cursor position
- added new command 'CONST' (write-protects variables)
* AISC scripts (.pa)
- removed definition of TABs (use default 4)
- indented
- use smart tabs and INDENT
- better error messages when MAX_OBJECT/MAX_KEY is too small
- use operator '<' for argc-check
* code generated by AISC scripts
- removed unneeded C compatibility
- load/save code only generated when needed (i.e. in nameserver)
- fixed indentation
- fixed constness
- removed many useless return values
- made most callbacks static; replaced the one (get_XXX_CNT) used by server-code by method get_count()
- server dll-objects derived from base-class-template; commented the undefined(but working) hack there
* AISC interface (.aisc)
- fixed plenking
- translated german comments
- reorganized interface IDs to reduce max. amount of attributes. MAX_KEY 100->42
- moved relative search into own ptserver object (PT_family). MAX_KEY 42->33
- changed MAGIC numbers to make communication between client/server before and after this patch impossible
- dont save dll-header to nameserver db (does nothing but generate unused code)
* client/server code
- no longer use old fashioned typenames (struct struct_blablabla)
- fixed constness
- moved invariable code from generator to server.c
* updated description of .aisc format (eliminated duplicated files)
* possibility to pass information from Makefile into AISC scripts

5 lines of code changed in 4 files:

• ptpan: PTP_etc.cxx (+1 -1), PTP_match.cxx (+1 -1), PTP_new_design.cxx (+2 -2), pt_prototypes.h (+1 -1)

westram 2011-03-24 18:20 Rev.: 7314

merged from dev [7300] [7301] [7309] [7310]

* move to CORE
- GBS_strstruct + old interface functions
- GB_strpartdup + GB_strndup
* templates to generate handy test-results
* removed dead code (constructSequence)

2 lines of code changed in 2 files:

• ptpan: Makefile (+1 -2), PTP_match.cxx (+1 -1)

westram 2011-03-16 12:04 Rev.: 7272

merged from dev [7244] [7250] [7251] [7252] [7253] [7254] [7255] [7257] [7258] [7259] [7260] [7261] [7271]
* extracted conversion logic of absolute <-> relative position into !BasePosition
- refactored BI_ecoli_ref and ED4_base_position (using !BasePosition)
- corrected input range of abs_2_rel ([0..N-1] -> [0..N])
* clean up chaos caused by different semantics of positions (biological[1..N] vs informational[0..N-1])
- commented (hopefully) all AWARs and variables which use biological positions
- made semantic changes explicit by using bio2info() and info2bio()
* positions passed to/reported by PTserver are now biological positions. Affects
- probe design (absolute position, ecoli range restriction)
- probe match (absolute position, ecoli position (bugfix see below)).
- !ProbeMatchParser does not change semantics
* fix several bugs
- ED4_jump_to_cursor_position limited position to screen before converting from relative to absolute position
- SEC_root::paintEcoliPositions added 1 to relative pos (instead of including position at cursor)
- ecoli position in probe match/PTserver (did not include ecoli-base at match position)
- ecoli range restriction in probe design/PTserver (check was broken, see [7261])
- base position for consensus terminals

1 lines of code changed in 1 file:

• ptpan: PTP_new_design.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)

26 lines of code changed in 1 file:

• ptpan: Makefile (+26 -13)

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)

22 lines of code changed in 1 file:

• ptpan: Makefile (+22 -3)

westram 2010-09-18 16:03 Rev.: 6865

* loosened dependencies between libraries (merges [6820] [6828] [6830] [6831] [6832] [6833] [6834] [6835] [6836] [6837] [6839] [6840] from refactor)
* needed_libs.pl
- fixed infinite recursion (appeared when defining cyclic lib-dependencies)
- print different error when using wrong directory
* create dependencies for AISC_MKPTPS
* iupac code
- moved interface into namespace iupac
- renamed functions
- defined iupac-groups for aminos
- added 'C' to its own group (was missing)
- added tests for nuc/amino groups data
- adapted client code
- moved iupac code to SL/PRONUC (which no longer depends on libAWT)
* redefined SERVERCNTRL/client dependencies
- SERVERCNTRL.a depends on client.a (apparently it does not matter whether PROBE_COM/client.a or NAMES_COM/client.a is used)
- all clients depend on SERVERCNTRL.a (instead of client.a)
- removed fake aisc-functions from arb_db_server (instead link client.a, as others do)
- replaced PROBE_COM/client.test by SERVERCNTRL/SERVERCNTRL.test
* removed cyclic dependency edit4->(secedit|RNA3D)->edit4
- created EDIT4 plugin interface (ED4_plugin_host)
- plugged in RNA3D and SECEDIT
* fixes:
- add menu-entries for SECEDIT and RNA3D only for RNA-alignments (like buttons)
- added help to these menu-entries

2 lines of code changed in 2 files:

• ptpan: needs_libs.PROBE_a (+1), pt_prototypes.h (+1)

westram 2010-09-15 13:24 Rev.: 6842

* link fixture for ptpan (get_match_overlay not implemented there)

6 lines of code changed in 1 file:

• ptpan: PTP_match.cxx (+6)

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

- depends for [6816]

13 lines of code changed in 1 file:

• ptpan: Makefile (+13)

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

* depends updated for [6812] + [6813]

13 lines of code changed in 1 file:

• ptpan: Makefile (+13)

westram 2010-09-03 19:17 Rev.: 6750

- sync with refactor branch (branching sux)

26 lines of code changed in 1 file:

• ptpan: Makefile (+26)

westram 2010-08-21 11:04 Rev.: 6703

* generate client.h without 'extern "C" {}'-wrapper, instead only use 'extern "C"'-function prefixes
- needed to include 'client_types.h' outside of 'extern "C"'-wrapper

1 lines of code changed in 1 file:

• ptpan: Makefile (+1)

westram 2010-05-14 12:32 Rev.: 6657

- undo part of [6656]

2 lines of code changed in 1 file:

• ptpan: ptpan.h (+2 -2)

westram 2010-05-14 12:08 Rev.: 6656

- removed unneeded 'struct' keyword
- renamed several structs (especially things like 'blabla_struct')

2 lines of code changed in 1 file:

• ptpan: ptpan.h (+2 -2)

westram 2010-05-13 16:43 Rev.: 6655

* struct GBS_strstruct -> GBS_strstruct

5 lines of code changed in 1 file:

• ptpan: PTP_match.cxx (+5 -5)

westram 2010-03-19 13:46 Rev.: 6544

- error handling fixed

29 lines of code changed in 1 file:

• ptpan: PTP_buildtree.cxx (+29 -17)

westram 2010-02-19 09:13 Rev.: 6463

* Changed hash-size passed to GBS_create_hash etc.
- pass number of estimated elements (instead of real size)
* hashes now use size_t for size/count
* extremely slow hashes warn in release code

7 lines of code changed in 1 file:

• ptpan: PTP_io.cxx (+7 -6)

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

- added library dependency declarations

4 lines of code changed in 1 file:

• ptpan: needs_libs.PROBE_a (new 4)

westram 2010-02-10 18:03 Rev.: 6418

- fix #223

2 lines of code changed in 1 file:

• ptpan: PTP_main.cxx (+2 -1)

westram 2010-01-13 19:15 Rev.: 6352

- condensed several comments

1 lines of code changed in 1 file:

• ptpan: pt_prototypes.h (+1 -3)

westram 2010-01-12 19:00 Rev.: 6345

- fixed hard readable '} else {'

2 lines of code changed in 1 file:

• ptpan: PTP_match.cxx (+2 -1)

westram 2010-01-07 14:07 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

33 lines of code changed in 6 files:

• ptpan: Makefile (+13), PTP_buildtree.cxx (+9 -9), PTP_findEx.cxx (+1 -1), PTP_io.cxx (+6 -6), PT_hashing.cxx (+1 -1), PT_treepack.cxx (+3 -3)

westram 2010-01-06 14:03 Rev.: 6325

* ARBDB
- hide internal structures (GBDATA etc.) inside ARBDB. Fixed all layer violations
- splitted up big header files into many. Did not reduce much internal dependencies, but at least there's some kind of semantic separation now.
- moved many decls right into the .cxx file (if only used in one)
- removed several duplicated type-names like
{{{
typedef struct gb_main_type {
...
} GB_MAIN_TYPE;
}}}
- GB_HASHI -> GB_NUMHASH + functions renamed
- gb_assert no longer globally visible. replaced
- fixed includes
- local (ARBDB internal) headers all start with prefix 'gb_'

39 lines of code changed in 1 file:

• ptpan: Makefile (+39)

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

5 lines of code changed in 1 file:

• ptpan: PTP_io.cxx (+5 -5)

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

* spellchecked all (phew)

2 lines of code changed in 2 files:

• ptpan: PTP_main.cxx (+1 -1), ptpan.h (+1 -1)

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

8 lines of code changed in 2 files:

• ptpan: Makefile (+1 -1), pt_prototypes.h (+7)

westram 2009-05-14 18:30 Rev.: 5908

* source files with identical names are really a pain when using valgrind

7946 lines of code changed in 17 files:

• ptpan: Makefile (+163 -163), PTP_buildtree.cxx (new 3290), PTP_etc.cxx (new 101), PTP_family.cxx (new 27), PTP_findEx.cxx (new 153), PTP_io.cxx (new 1287), PTP_main.cxx (new 547), PTP_match.cxx (new 871), PTP_new_design.cxx (new 906), PT_cachehandler.cxx (+1 -1), PT_hashing.cxx (+1 -1), PT_huffman.cxx (+1 -1), PT_lowlevel.cxx (+1 -1), PT_treepack.cxx (+1 -1), pt_prototypes.h (+8 -8), ptp_probe_debug.cxx (new 24), ptpan.h (new 564)

boehnel 2009-02-09 15:54 Rev.: 5744

* bugfixes for Probe Design
* adding Epsilon for floating point comparision

5 lines of code changed in 1 file:

• ptpan: PT_new_design.cxx (+5 -6)

boehnel 2009-02-09 13:57 Rev.: 5743

* changed debug output
* fixed indentation

15 lines of code changed in 1 file:

• ptpan: PT_new_design.cxx (+15 -11)

boehnel 2009-02-02 00:03 Rev.: 5742

* Bugfix to get probe design work

4 lines of code changed in 1 file:

• ptpan: PT_new_design.cxx (+4 -1)

boehnel 2009-02-02 00:03 Rev.: 5741

* adding GB_init_gb() (needed for PT_new_design)

2 lines of code changed in 1 file:

• ptpan: PT_main.cxx (+2)

(53 more)