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westram 2022-03-04 12:26 Rev.: 18959

* reintegrates 'progress' into 'trunk'
- implements #789
* adds: log:branches/progress@18885:18958

1 lines of code changed in 1 file:

• PROBE_COM: Makefile (+1)

westram 2019-07-24 17:26 Rev.: 17989

* change names of related variables in ptserver.

2 lines of code changed in 1 file:

• PROBE_COM: PT.aisc (+2 -2)

westram 2019-07-24 17:24 Rev.: 17988

* rename ptserver flags
- MATCH_COMPLEMENT -> COMPLEMENT_FIRST
- MATCH_REVERSED -> MATCH_ALSO_REVCOMP
* comments and TODOs.

9 lines of code changed in 1 file:

• PROBE_COM: PT.aisc (+9 -9)

westram 2019-03-04 15:22 Rev.: 17634

* reintegrates 'mix' into 'trunk'
* prepare arb for hybrid svn/git use (central svn + local git)
* adds: log:branches/mix@17631:17633

9 lines of code changed in 1 file:

• PROBE_COM: .gitignore (new 9)

westram 2018-05-04 18:06 Rev.: 16986

* reintegrates 'gcc' into 'trunk'
- ports arb to gcc 8.1 (fixing warnings)
* adds: log:branches/gcc@16965:16985

Update: continued by [17178]

1 lines of code changed in 1 file:

• PROBE_COM: PT_extern.c (+1 -1)

westram 2017-11-28 18:09 Rev.: 16763

* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751

1 lines of code changed in 1 file:

• PROBE_COM: PT_extern.c (+1 -1)

westram 2016-08-11 11:05 Rev.: 15176

* reintegrates 'fixres' into 'trunk'
- fixes #715
* adds: log:branches/fixres@15127:15175

4 lines of code changed in 1 file:

• PROBE_COM: PT_extern.c (+4 -4)

westram 2015-07-24 11:25 Rev.: 14066

- remove unused dependency

0 lines of code changed in 1 file:

• PROBE_COM: needs_libs.common_a (del)

westram 2015-07-17 13:11 Rev.: 14038

* fix #618 (use ar for linking)
- library order does matter now
* {{{PROBE_COM/server.a}}} and {{{PROBE/PROBE.a}}} depend on each other -> hack: unpack lib and directly link objects
- do not export {{{pt_init_bond_matrix}}} "extern C"
- {{{sym2testcode.pl}}}: ignore several additional lines from nm-output

1 lines of code changed in 1 file:

• PROBE_COM: PT_extern.c (+1 -11)

westram 2014-11-17 16:42 Rev.: 13191

* reintegrates 'slv' into 'trunk'
* performs #624
* adds:
- log:branches/slv@13152:13190

17 lines of code changed in 1 file:

• PROBE_COM: PT.aisc (+17 -14)

westram 2014-07-28 10:48 Rev.: 12593

- update depends for [12591]

0 lines of code changed in 1 file:

• PROBE_COM: Makefile (-8)

epruesse 2014-07-28 03:17 Rev.: 12592

remove more traces of common.a

0 lines of code changed in 1 file:

• PROBE_COM: needs_libs.client_a (-1)

epruesse 2014-07-28 02:57 Rev.: 12591

AISC now uses arb_open_socket, arb_socket_write and ..._read.
- SIGPIPE is disabled via setsockopt on mac and via MSG_NOSIGNAL
on Linux.
- No more usleep in write loop.
- arb_socket_write returns -1 on failure
(needed change to client.c as aisc_s_write and aisc_c_write
differed in error handling)
- common.[hc] are gone
- fixes build failure in build 797

0 lines of code changed in 1 file:

• PROBE_COM: Makefile (-3)

westram 2014-05-06 13:00 Rev.: 12151

pass down CXX_INCLUDES

1 lines of code changed in 1 file:

• PROBE_COM: Makefile (+1 -1)

westram 2014-01-23 13:28 Rev.: 11492

* fix several doxygen issues (doxygen 1.6.3)
- force macro expansion for IF_ASSERTION_USED
- fixed changed param names
- named some anonymous (nested) structs
- remove/quote several '#' (triggering unknown commands)

1 lines of code changed in 1 file:

• PROBE_COM: PT.aisc (+1 -1)

westram 2013-11-03 15:42 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

47 lines of code changed in 4 files:

• PROBE_COM: Makefile (+11), PT.aisc (+32 -51), needs_libs.client_a (+1 -1), needs_libs.common_a (new 3)

westram 2013-10-31 15:10 Rev.: 10996

* use cflags before cxxflags

1 lines of code changed in 1 file:

• PROBE_COM: Makefile (+1 -1)

westram 2013-10-29 13:55 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:

• PROBE_COM: Makefile (+1 -1)

westram 2013-10-29 13:23 Rev.: 10955

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

1 lines of code changed in 1 file:

• PROBE_COM: Makefile (+1 -1)

westram 2013-06-13 20:04 Rev.: 10153

* fix AISC dependency problems
- see [9678] for an example
- added some test-targets (dependstest[1..])

1 lines of code changed in 1 file:

• PROBE_COM: Makefile (+1 -1)

westram 2013-02-13 13:24 Rev.: 9575

- effect of [9574] (comments only)

1 lines of code changed in 1 file:

• PROBE_COM: Makefile (+1 -1)

westram 2013-02-09 13:52 Rev.: 9521

- updated depends for [9520]

5 lines of code changed in 1 file:

• PROBE_COM: Makefile (+5)

westram 2013-02-09 12:16 Rev.: 9516

- reintegrated branch 'cxx11'

7 lines of code changed in 1 file:

• PROBE_COM: Makefile (+7)

westram 2013-01-24 12:28 Rev.: 9452

* fixed missing depends for code in NAMES_COM and PROBE_COM

91 lines of code changed in 1 file:

• PROBE_COM: Makefile (+91 -1)

westram 2012-09-26 13:45 Rev.: 8955

* allow to define whether 'T' or 'U' is used in iterated probes

1 lines of code changed in 1 file:

• PROBE_COM: PT.aisc (+1)

westram 2012-09-25 18:54 Rev.: 8947

* probe-iterator (see [8945])
- added parameter to define separator used in result
- removed parameter 'iterate_reset' from 'arb_probe' (always returns first XXX or all indexed probes)
- not optimized for bigger ptservers (result is kept in memory)

2 lines of code changed in 1 file:

• PROBE_COM: PT.aisc (+2 -1)

westram 2012-09-25 15:33 Rev.: 8945

* tweak probe-iterator (iterates through all probes in ptserver)
- added new param 'READABLE' (report readable probes, instead of internal format)
- added new CLI-params to 'arb_probe' to access probe-iterator
- added unit-tests to secure behavior
Note: feature not used inside ARB atm. Was used by probe-library in the past. Left for debugging.

1 lines of code changed in 1 file:

• PROBE_COM: PT.aisc (+1)

westram 2012-05-26 10:17 Rev.: 8757

* probe match no longer calculates different results depending on whether PT_PDC-object was generated or not
- bonds and split are members of PT_LOCS now
* now they always exist, so several conditional calculations concerning weighted mismatches are done unconditionally now
- removed hacks (see [8755], [8741])
* probe match also depended on split-threshold (as specified in probe-design export window)
- made that value as well available in probe-match-expert-window
- renamed awar

39 lines of code changed in 2 files:

• PROBE_COM: PT.aisc (+37 -36), PT_extern.c (+2 -2)

westram 2012-05-22 18:11 Rev.: 8744

* AISC clients
- client-handles for server-side objects are distinguishable types now (esp. can no longer be confounded w/o compiler messages)
- main server object has to be passed to aisc_close

0 lines of code changed in 1 file:

• PROBE_COM: PT_extern.c (-1)

westram 2012-04-19 09:13 Rev.: 8607

merge from e4fix [8135] [8136] [8137] [8138] [8139] [8140] [8141] [8142] [8143] [8144] [8222]
(this revives the reverted patches [8129] [8130] [8131] [8132]; see [8133])

* fixes
- some free/delete mismatches
- wrong definition of ORF objects (Level was no bit value)
- amino consensus (failed for columns only containing 'C')
* rename
- AA_sequence_term -> orf_term
- ED4_sequence_terminal_basic -> ED4_abstract_sequence_terminal
* cleaned up hierarchy dumps
* tweaked is_terminal()/to_terminal()

0 lines of code changed in 1 file:

• PROBE_COM: aisc.README (changed)

westram 2012-03-28 18:02 Rev.: 8536

* next neighbour search can report errors to client
- reports error if oligo len < 1

2 lines of code changed in 1 file:

• PROBE_COM: PT.aisc (+2 -1)

westram 2012-03-28 17:32 Rev.: 8535

* scaling of relative scores in 'Next neighbour search' can be configured now
- scale vs source or target POC (or min/max of both)
- added toggles to 'Search next neighbours of ...'
- added tests
* help (score/scaling)
- describe new options
- fix wrong facts

1 lines of code changed in 1 file:

• PROBE_COM: PT.aisc (+1)

westram 2012-03-27 15:27 Rev.: 8531

* added header with global defines for ptserver and its clients
- moved enum FF_complement there and use it in ptserver

1 lines of code changed in 1 file:

• PROBE_COM: PT.aisc (+1 -1)

westram 2012-03-27 13:02 Rev.: 8530

* ptserver now can filter found relatives by minimum score
- allow to use that feature from 'Next Neighbours of Selected'
- also use from 'Next Neighbours of Listed' (which did client-side filtering)
- added tests
- updated window layout and help
* renamed awars to make clearer which belong to which window and which are shared
* fixed wrong calculation of display width (when there where no hits or hits were limited)
* added @@@-comments to aligner (who could also use filtering by score)

2 lines of code changed in 1 file:

• PROBE_COM: PT.aisc (+2 -1)

westram 2012-03-22 15:04 Rev.: 8518

* allow oligo-length=1 for next-relative-search
- regardless whether this makes sense or not, the restriction was an artifical one (i guess optimization regarding PT-traversal)

1 lines of code changed in 1 file:

• PROBE_COM: PT.aisc (+1 -1)

westram 2011-12-23 13:57 Rev.: 8324

- clang-fix: explicitely pass language type to compiler when .c is compiled as c++

1 lines of code changed in 1 file:

• PROBE_COM: Makefile (+1 -1)

westram 2011-10-17 14:34 Rev.: 8104

merge from ptpan_back [8085] [8088] [8091]
* avoid shadow warnings from some TEST_ASSERTions
* patch name shows whether tests were valgrinded
* added template IGNORE_RESULT(), to ignore results tagged with !__ATTR!__USERESULT

1 lines of code changed in 1 file:

• PROBE_COM: PT_extern.c (+1)

westram 2011-09-29 19:43 Rev.: 7986

* PT-SERVER
- allow to specify amount+limit where N is accept
- moved hardcoded PT_MAX_MATCHES into AISC interface as parameter (with same limit)
* added links to information related to MAGIC_NUMBER
- maintain a list of previously used MAGIC_NUMBERs
* AISC parameters
- removed unused parameter MATCH_MAX_SPECIES
- added new parameters MATCH_MAX_HITS, MATCH_N_ACCEPT, MATCH_N_LIMIT
* defaulted them to previously hardcoded limits
* parametrized set_table_for_PT_N_mis() using MATCH_N_ACCEPT + MATCH_N_LIMIT
* protect vs illegal index into psg.N_mismatches
* arb_probe
- fixed commandline parser (no longer modifies passed argv)
- added new parameters matchacceptN, matchlimitN + matchmaxresults
- added some unit tests
* testing N-matches (in match-string and/or seqdata)
* testing truncation of results

4 lines of code changed in 1 file:

• PROBE_COM: PT.aisc (+4 -2)

westram 2011-08-08 10:22 Rev.: 7819

merge from dev [7774] [7778] [7779] [7780] [7781] [7782] [7783] [7784] [7785] [7786] [7787] [7788] [7789] [7790] [7791] [7792] [7793] [7794] [7795] [7796] [7817]
* fixes/improvements to build ARB on multicores
- made dependencies between targets explicit (let make resolve them)
- fixed several failures caused by async calls ('dep_graph', 'up', tests)
- try to make 'perl' 1st ("big target")
* other changes
- ctags (bug in 5.8; tag-order)
- removed obsolete things from Makefiles
- added SOURCE_TOOLS/remake_after_change.pl (call from ARB subdirs, knows what to do)
- tests use own ARB_PID (no clash with running ARB)

8 lines of code changed in 1 file:

• PROBE_COM: Makefile (+8 -6)

westram 2011-08-08 09:56 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

2 lines of code changed in 1 file:

• PROBE_COM: Makefile (+2 -2)

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