[root]/PROBE_COM
Author | Changes | Lines of Code | Lines per Change |
---|---|---|---|
Totals | 107 (100.0%) | 1296 (100.0%) | 12.1 |
westram | 99 (92.5%) | 913 (70.4%) | 9.2 |
oldcode | 5 (4.7%) | 383 (29.6%) | 76.6 |
epruesse | 2 (1.9%) | 0 (0.0%) | 0.0 |
baderk | 1 (0.9%) | 0 (0.0%) | 0.0 |
* reintegrates 'progress' into 'trunk'
- implements #789
* adds: log:branches/progress@18885:18958
1 lines of code changed in 1 file:
* change names of related variables in ptserver.
2 lines of code changed in 1 file:
* rename ptserver flags
- MATCH_COMPLEMENT -> COMPLEMENT_FIRST
- MATCH_REVERSED -> MATCH_ALSO_REVCOMP
* comments and TODOs.
9 lines of code changed in 1 file:
* 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:
* 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:
* 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:
* reintegrates 'fixres' into 'trunk'
- fixes #715
* adds: log:branches/fixres@15127:15175
4 lines of code changed in 1 file:
- remove unused dependency
0 lines of code changed in 1 file:
* 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:
* reintegrates 'slv' into 'trunk'
* performs #624
* adds:
- log:branches/slv@13152:13190
17 lines of code changed in 1 file:
- update depends for [12591]
0 lines of code changed in 1 file:
remove more traces of common.a
0 lines of code changed in 1 file:
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:
pass down CXX_INCLUDES
1 lines of code changed in 1 file:
* 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:
* 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:
* use cflags before cxxflags
1 lines of code changed in 1 file:
* 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:
- renamed
* ACC -> A_CC
* CPP -> A_CXX (misleading atm, since it contains c++flags)
1 lines of code changed in 1 file:
* fix AISC dependency problems
- see [9678] for an example
- added some test-targets (dependstest[1..])
1 lines of code changed in 1 file:
- effect of [9574] (comments only)
1 lines of code changed in 1 file:
- updated depends for [9520]
5 lines of code changed in 1 file:
- reintegrated branch 'cxx11'
7 lines of code changed in 1 file:
* fixed missing depends for code in NAMES_COM and PROBE_COM
91 lines of code changed in 1 file:
* allow to define whether 'T' or 'U' is used in iterated probes
1 lines of code changed in 1 file:
* 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:
* 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 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:
* 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:
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:
* next neighbour search can report errors to client
- reports error if oligo len < 1
2 lines of code changed in 1 file:
* 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:
* 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:
* 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:
* 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:
- clang-fix: explicitely pass language type to compiler when .c is compiled as c++
1 lines of code changed in 1 file:
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:
* 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:
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:
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:
(54 more)