Lines of Code
[root]/NAMES_COM
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 78 (100.0%) | 612 (100.0%) | 7.8 |
| westram | 72 (92.3%) | 460 (75.2%) | 6.3 |
| oldcode | 4 (5.1%) | 152 (24.8%) | 38.0 |
| epruesse | 1 (1.3%) | 0 (0.0%) | 0.0 |
| baderk | 1 (1.3%) | 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:
* eliminate trailing whitespace from Makefiles.
2 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:
* reintegrates 'fix' into 'trunk'
* adds: log:branches/fix@15066,15073:15076,15082,15086:15093
0 lines of code changed in 1 file:
- update depends for [12591]
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:
* 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
11 lines of code changed in 1 file:
* 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:
* 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 [8376] [8377] [8378] [8379] [8380] [8386] [8387] [8388] [8389]
* do not save AWARs which have default values
- motivation: edit4-props saved after [8362] did not load with older versions
- pros:
* if the user did not change the default, changing the default in code will propagate to the user
- cons:
* AWARs used by multiple applications will trigger in non-saving application, when the database containing the awar is saved
- only happens once if AWAR was previously stored with default-value
- the most obvious ones were those edit4-search-strings linked to ntree (primer, probe, gene). disarmed them by setting the default to NULL
* always generate definitions of SAI color translation tables (since default no longer saved)
- drawback: when user deletes a default color translation table, it will re-appear after restart
* allow experts to save fast-aligner protection to properties
* deliver errors exported by awar callbacks (when triggered by widget change)
* sequence color mapping
- translate stored old default ('=0') to new default (!'') on awar creation
- removed code talking to AWARs via ARBDB interface - just use AWARs straightforward
* ignore request_refresh_for_sequence_terminals when there is no hierarchy yet (now triggered by seq colors)
* lib/arb_default/edit4.arb
- removed default values (where code defaulted to same value)
- changed some defaults
* aligner (explicit, but empty ref)
* helix setting (stolen from WL)
* lib/arb_default/ntree.arb
- removed all values
* equal to default value
* obsolete entries (former awar names)
* entries that are now stored in main DB
* removed unused AWARS (AWTC_create_rename_awars)
* default for AWAR_TREE now "" everywhere
* removed unused AISC variable
* renamed edit direction related variables/awars
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:
- 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
1 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)
6 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:
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)
9 lines of code changed in 1 file:
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
55 lines of code changed in 2 files:
merged from dev [7358] [7359] [7360] [7363] [7364] [7365] [7367]
* tweaked build process
- get rid of '.depends: No such file or directory'
- make clean now is much more scrupulous! removal '''notably''' includes lib/pts, lib/nas and lib/arb_tcp.dat (when they are no symlinks)
- suppress some output
- added several unreached targets (to test random failures)
- fine-grained tools-dependencies
- automatically generate target directories (GENC ...)
- removed duplicated target 'mbin' (same as 'comtools')
- added target 'setup_after_clean' (use after 'clean' when doing a partial build)
1 lines of code changed in 1 file:
- calling 'make clean ; make depends' failed
1 lines of code changed in 1 file:
- added library dependency declarations
9 lines of code changed in 2 files:
- removed trailing whitespace
1 lines of code changed in 1 file:
- removed void
2 lines of code changed in 1 file:
- fixed includes
- added MBI headers
- removed unused files
2 lines of code changed in 1 file:
* fixed whitespace (scripted)
1 lines of code changed in 1 file:
* AISC memory tester
- replaced unportable usage of SUN signal internas by a simple flag (as always, KISS)
- added longjmp to recover from possible SEGV (caused by client sending illegal address)
- rewrote client memory tester in ARBDB in the same way (gbcm_test_address). Moved to GBK_install_SIGSEGV_handler and implemented signal suppression there
* made several functions in AISC server static
* made several functions in ARBDB static
- relocated some functions in adcomm.cxx
* globally removed leftover SUN-specific code
* increased available memory (default fallback) from 512 Mb to 1 Gb
* ARBDB no longer overwrites already installed SIGSEGV handlers
- prints a warning in DEBUG mode
* signal handlers
- renamed type (SIG_PF -> SigHandler)
- removed casts and corrected wrong function types (signal handlers do not return any values - they either return or not)
- added assertions to all signal-handler installations (assert that no handler has been installed before)
* AISC clients now store/restore previously installed SIGPIPE handlers
- ARB_NTREE for example, disabled it's own handler (used by DB server to detect disconnected clients) by connecting to any AISC server (pt_server, nameserver)
* make depends did not update depends in PROBE_COM and NAMES_COM
4 lines of code changed in 1 file:
- added dependency on aisc_include.header
3 lines of code changed in 2 files:
* autogenerated AISC interface depends on prototyper (and so does AISC generation in general)
* AISC prototypes no longer generate empty argument tables for 'func(void)' (because AISC prototyper will warn about that in near future)
2 lines of code changed in 1 file:
* name servers with add.field have to be started with '-fFIELD=DEFAULT' instead of '-fFIELD' only.
* convert existing nameserver-DBs on the fly
* increased namesDB version to 5
* added a version check (too late - as always)
* nameserver sends fatal errors to running ARB (using arb_message)
* fixed nameserver definitions in arb_tcp_org.dat (arb_tcp.dat needs to be updated manually by users)
15 lines of code changed in 1 file:
* tweaked errors/warnings printed by AISC code generator
* AISC expression 'IF $(KEY)'. When variable KEY is empty or undefined, AISC regards the expression always as TRUE.
- On OSX this resulted in a bus error, cause the test for operator '!' accessed the byte b4 the empty expression. Fixed.
* made many functions static / commented out unused code
* deleted unused files
* added dependencies (AISC/*pa) to com makefiles -> recompile if any .pa changes
5 lines of code changed in 1 file:
* com interface build depends on date of generator
3 lines of code changed in 1 file:
(31 more)