Directory NALIGNER/

Directory Created:
2000-11-23 11:41
Total Files:
26
Deleted Files:
10
Lines of Code:
7913

[root]/NALIGNER

Lines of Code

NALIGNER/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 393 (100.0%) 19326 (100.0%) 49.1
oldcode 34 (8.7%) 9792 (50.7%) 288.0
westram 353 (89.8%) 9226 (47.7%) 26.1
meierh 1 (0.3%) 295 (1.5%) 295.0
boehnel 1 (0.3%) 9 (0.0%) 9.0
epruesse 1 (0.3%) 2 (0.0%) 2.0
baderk 2 (0.5%) 2 (0.0%) 1.0
artemov 1 (0.3%) 0 (0.0%) 0.0

Most Recent Commits

westram 2019-07-17 16:27 Rev.: 17982


* reduced use of GB_change_my_security:
- use GB_securityLevel instead of manually fiddling around with GB_change_my_security.
- inspected and accepted leftover uses (see comments).

7 lines of code changed in 1 file:

  • NALIGNER: ali_arbdb.cxx (+7 -7)
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:

  • NALIGNER: ali_main.cxx (+1 -1)
westram 2017-11-28 19:22 Rev.: 16766


* reintegrates 'gcc' into 'trunk'
- mostly cosmetics changes
* adds: log:branches/gcc@16655,16741:16743,16752:16765

203 lines of code changed in 18 files:

  • NALIGNER: ali_aligner.cxx (+22 -31), ali_aligner.hxx (+8 -9), ali_arbdb.cxx (+6 -14), ali_global.cxx (+1 -2), ali_main.cxx (+1 -2), ali_misc.hxx (+54 -82), ali_pathmap.cxx (+11 -22), ali_pathmap.hxx (+2 -4), ali_prealigner.cxx (+7 -10), ali_prealigner.hxx (+4 -5), ali_profile.cxx (+10 -18), ali_profile.hxx (+2 -3), ali_pt.cxx (+19 -35), ali_sequence.cxx (+8 -18), ali_sequence.hxx (+2 -2), ali_solution.cxx (+29 -50), ali_tarray.hxx (+4 -6), ali_tlist.hxx (+13 -21)
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

120 lines of code changed in 18 files:

  • NALIGNER: ali_aligner.cxx (+6 -6), ali_aligner.hxx (+3 -3), ali_arbdb.cxx (+7 -7), ali_arbdb.hxx (+3 -3), ali_global.cxx (+3 -3), ali_main.cxx (+4 -4), ali_pathmap.cxx (+11 -11), ali_pathmap.hxx (+1 -1), ali_prealigner.cxx (+6 -6), ali_prealigner.hxx (+6 -6), ali_profile.cxx (+7 -7), ali_profile.hxx (+1 -1), ali_pt.cxx (+27 -27), ali_sequence.cxx (+3 -3), ali_sequence.hxx (+2 -2), ali_solution.cxx (+7 -7), ali_tarray.hxx (+1 -1), ali_tlist.hxx (+22 -22)
westram 2016-08-11 11:05 Rev.: 15176


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

21 lines of code changed in 5 files:

  • NALIGNER: Makefile (+14), ali_arbdb.cxx (+1 -1), ali_global.cxx (+1 -1), ali_pt.cxx (+1 -1), ali_sequence.cxx (+4 -2)
westram 2015-11-17 14:54 Rev.: 14498


* globally add explicit casts (either long or double) for all numeric ellipse arguments of aisc_put, aisc_nput and aisc_create
- errors caused by just changing the type of a passed variable are far too subtle

1 lines of code changed in 1 file:

  • NALIGNER: ali_pt.cxx (+1 -1)
westram 2015-01-23 15:19 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:

  • NALIGNER: Makefile (+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

7 lines of code changed in 1 file:

  • NALIGNER: ali_pt.cxx (+7 -1)
westram 2013-10-31 16:40 Rev.: 11002


* 'class { public' -> struct

2 lines of code changed in 2 files:

  • NALIGNER: ali_profile.hxx (+1 -2), ali_pt.hxx (+1 -2)
westram 2013-10-31 15:10 Rev.: 10996


* use cflags before cxxflags

1 lines of code changed in 1 file:

  • NALIGNER: Makefile (+1 -1)
westram 2013-10-31 14:48 Rev.: 10994


* directly use cflags

1 lines of code changed in 1 file:

  • NALIGNER: Makefile (+1 -5)
westram 2013-10-30 16:58 Rev.: 10974


* renamed include variables

1 lines of code changed in 1 file:

  • NALIGNER: 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:

  • NALIGNER: 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:

  • NALIGNER: Makefile (+1 -1)
westram 2013-10-29 12:43 Rev.: 10954


- document mechanism used by ARB to export variables to submakefiles
- document most important variables

1 lines of code changed in 1 file:

  • NALIGNER: Makefile (+1 -1)
westram 2013-09-09 16:36 Rev.: 10563


- include downcast.h from arbdbt.h
(this break C++11 compilation, i.e. gcc4.8 or newer)[[BR]]
amendment:
* also broke compilation on ubuntu 13.04 and with gcc 4.7.3 (due to nameclash with boost)

16 lines of code changed in 1 file:

  • NALIGNER: Makefile (+16)
epruesse 2013-04-13 19:23 Rev.: 9899

pass down argc/argv to AW_root::AW_root (for GTK)
GTK will pick its parameters (e.g. --g-fatal-warnings) from argv and
remove them, hence argv must not be const and AW_root() should
be called before command line parsing (if possible).

2 lines of code changed in 1 file:

  • NALIGNER: ali_main.cxx (+2 -2)
westram 2013-02-13 13:24 Rev.: 9575


- effect of [9574] (comments only)

1 lines of code changed in 1 file:

  • NALIGNER: Makefile (+1 -1)
westram 2013-02-09 13:52 Rev.: 9521


- updated depends for [9520]

10 lines of code changed in 1 file:

  • NALIGNER: Makefile (+10)
westram 2013-02-09 12:16 Rev.: 9516


- reintegrated branch 'cxx11'

10 lines of code changed in 1 file:

  • NALIGNER: Makefile (+10)
westram 2012-09-15 18:20 Rev.: 8894


* fixed cppcheck warnings

16 lines of code changed in 3 files:

  • NALIGNER: ali_pathmap.cxx (+4 -5), ali_tarray.hxx (+1 -1), ali_tlist.hxx (+11 -18)
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

25 lines of code changed in 2 files:

  • NALIGNER: Makefile (+2), ali_pt.cxx (+23 -17)
westram 2012-04-19 18:39 Rev.: 8616


merge from e4fix [8190] [8196] [8198] [8197] [8199] [8221] [8226]

* callallcallbacks
- allow repeated calls for all orders
- avoid infinite descent into recursive filters
- avoid config managers
* fixes via callallcallbacks
- some un-/over-handled errors
- missing transaction
* make
- optionally keep preprocesser output
* tests
- only explain broken/wanted expectations if warning was shown
- added TEST_EXPECT!__BROKENIF
* spelling
- intervall -> interval

16 lines of code changed in 4 files:

  • NALIGNER: ali_global.cxx (+6 -6), ali_main.cxx (+5 -5), ali_prealigner.cxx (+3 -3), ali_prealigner.hxx (+2 -2)
westram 2012-03-21 16:28 Rev.: 8511


* use GBT_get_species_data instead of inlined code
- replaced all occurrances where
* either code was identical
* or search mode was GB_FIND instead of GB_CREATE_CONTAINER, but following code assumed that the container was found

4 lines of code changed in 1 file:

  • NALIGNER: ali_arbdb.cxx (+4 -4)
westram 2011-12-20 16:11 Rev.: 8313


* removed dead code

(partly reverted by [8316])

0 lines of code changed in 1 file:

  • NALIGNER: ali_prealigner.cxx (-2)
westram 2011-12-20 13:29 Rev.: 8309


* moved much code into static scope

(partly reverted by [8310])

10 lines of code changed in 3 files:

  • NALIGNER: ali_global.cxx (+2 -2), ali_main.cxx (+7 -7), ali_prealigner.cxx (+1 -1)
westram 2011-11-29 18:42 Rev.: 8257


* removed unused(-but-set) variables/params

2 lines of code changed in 1 file:

  • NALIGNER: ali_prealigner.cxx (+2 -4)
westram 2011-11-29 10:33 Rev.: 8249


* wrap main for untested (but testable) units
- still untestable
* ptpan (wont change in this branch)
* GENOM (cyclic dependency with GENOM_IMPORT due to Location)
* fix missing lib dependencies
- DIST -> SL/NDS
- STAT -> SL/ITEMS
- AW_NAME -> libAWT (instead of libWINDOW)

1 lines of code changed in 1 file:

  • NALIGNER: ali_main.cxx (+1 -2)
westram 2011-11-28 22:26 Rev.: 8246


* eliminated several main()'s from lib/obj-code
- replaced by ARB_main
- link executable with wrapper-object (main->ARB_main)
* unit-tests now use their own main()
- this ensures that all static data is initialized when the unit-test starts (previous behavior was working, but undefined)
- all tests pass (versus [8243])

9 lines of code changed in 3 files:

  • NALIGNER: ali_global.cxx (+2 -2), ali_global.hxx (+6 -6), ali_main.cxx (+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

11 lines of code changed in 1 file:

  • NALIGNER: ali_other_stuff.hxx (+11 -2)
westram 2011-10-17 14:17 Rev.: 8100


merge from ptpan_back [8016] [8017] [8021] [8051] [8067]
* added method to get status of GB_shell object
* removed possibility to execute command via DB-server - always use GB_system instead
* valgrinded external tools called by arb_test

4 lines of code changed in 2 files:

  • NALIGNER: ali_pt.cxx (+3 -3), ali_pt.hxx (+1 -1)
westram 2011-08-08 01:06 Rev.: 7812


merge from dev [7751] [7752]
* updated many old-style typedefs (typedef struct/enum)

5 lines of code changed in 2 files:

  • NALIGNER: ali_profile.hxx (+2 -3), ali_pt.hxx (+3 -3)
westram 2011-08-08 01:01 Rev.: 7811


merge from dev [7748] [7749] [7750]
* comments (C->C++ style)
* fixed umlauts in TREEGEN

41 lines of code changed in 5 files:

  • NALIGNER: ali_global.cxx (+13 -13), ali_global.hxx (+6 -6), ali_profile.hxx (+8 -8), ali_pt.cxx (+3 -3), ali_tlist.hxx (+11 -11)
westram 2011-06-10 15:50 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

26 lines of code changed in 13 files:

  • NALIGNER: Makefile (+2), ali_aligner.hxx (+5 -5), ali_arbdb.hxx (+1 -1), ali_misc.hxx (+3), ali_pathmap.hxx (+1 -1), ali_prealigner.hxx (+4 -4), ali_profile.hxx (+1 -1), ali_pt.hxx (+2 -2), ali_sequence.hxx (+2 -2), ali_solution.hxx (+2 -2), ali_tarray.hxx (+1 -1), ali_tlist.hxx (+1 -1), ali_tstack.hxx (+1 -1)
westram 2011-04-14 10:54 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)


1 lines of code changed in 1 file:

  • NALIGNER: ali_pt.cxx (+1 -1)
westram 2011-04-14 10:40 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

12 lines of code changed in 1 file:

  • NALIGNER: ali_pt.cxx (+12 -6)
westram 2011-02-23 14:37 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)

16 lines of code changed in 1 file:

  • NALIGNER: Makefile (+16 -8)
westram 2010-10-25 18:10 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

3 lines of code changed in 2 files:

  • NALIGNER: ali_misc.hxx (+2 -2), ali_sequence.hxx (+1 -1)
westram 2010-09-18 17:20 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)

1 lines of code changed in 1 file:

  • NALIGNER: Makefile (+1 -1)
westram 2010-09-18 17:03 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

1 lines of code changed in 1 file:

  • NALIGNER: needs_libs (+1 -1)

(76 more)

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