February 2011 Commit Log

Number of Commits:
61
Number of Active Developers:
3
westram 2011-02-26 10:40 Rev.: 7201


- test-result for arb_gene_probe no longer depends on ARBDB memory layout

15 lines of code changed in 3 files:

westram 2011-02-25 17:06 Rev.: 7200


- fixed compile conditionals for UNIT_TESTS

52 lines of code changed in 36 files:

westram 2011-02-24 21:20 Rev.: 7198


* fixed wrong probe position (see [7197])

47 lines of code changed in 4 files:

westram 2011-02-24 19:05 Rev.: 7197


- reproduce report of wrong position for designed probe in unittest.
- see http://tech.groups.yahoo.com/group/arb_users/message/3178 for motivation

21 lines of code changed in 5 files:

westram 2011-02-24 15:04 Rev.: 7196


- exception was thrown by std::string when ARB_WORKDIR was undefined

8 lines of code changed in 1 file:

westram 2011-02-24 11:32 Rev.: 7195


- removed leaks

16 lines of code changed in 2 files:

westram 2011-02-24 11:08 Rev.: 7194


- fixed buffer overflow

7 lines of code changed in 1 file:

westram 2011-02-23 16:24 Rev.: 7190


merges [7164] [7165] [7166] [7167] [7168] [7169] [7170] from refactor
* replaced last call to atexit() in ARBDB by GB_atexit()
* introduce GB_shell() - you need an instance for DB access
- handles ARBDB internal memory
- handles GB_atexit calls
* added tests for GB_shell and GB_remove_on_exit
* use GB_shell where needed
* fixed pending callbacks in PGT

251 lines of code changed in 36 files:

westram 2011-02-23 16:17 Rev.: 7189


merges [7108] [7146] [7147] [7148] [7150] [7151] [7152] [7153] [7155] [7156] [7161] [7162] [7163] from refactor
* arb_dnarates
- may read from file (instead of STDIN)
- if dbname is given on command line, expect dbsavename as following argument and save db with that name.
- removed old debug code
- adds a SAI counter to DB
- no longer uses PID for SAI name, instead uses counter
- no longer overwrites existing SAIs
* arb_swap_rnastr (unused, uncommented -> unlinked)
* arb_read_tree
- command line options may appear anywhere / in any order
- new option -db to specify db (load/save).
* arb_export_rates
- new option -d to specify db.
- handle more errors
* arb_export_tree
- optional CLI-argument 'DBNAME' (to specify a DB for unittests)
* arb_gene_probe
- error handling fixes
- do not write debugging-data to gene-ptserver-db (+fixed expected result-db)
* arb_primer
- optional CLI-argument 'dbname'
- replaced scattered exit()-calls by proper error-handling
* arb_probe
- forward errors to top level, to enable error check in unit-test
- allow usage of TEST_SERVER_ID if compiled with UNIT_TESTS==1
* added unit tests for mosts tools in TOOLS. Tests do not try to test complete functionality - they only check that one or a few calls to the tools do not fail.
* fixed sourcefile list

1122 lines of code changed in 20 files:

westram 2011-02-23 16:02 Rev.: 7188


merges [7149] [7154] [7160] from refactor
* added TEST_ASSERT_TEXTFILES_EQUAL()
* forward flag UNIT_TESTS to submakefiles
* other small fixes

13 lines of code changed in 4 files:

westram 2011-02-23 15:55 Rev.: 7187


merges [7099] [7106] [7107] from refactor
* name+type -> !FormattedFile
* simplyfied command line parsing and interactive mode
* renamed output-format 'phylip2' to 'fastdnaml'
* fixed broken calls to arb_convert_aln
- raxml and puzzle expect PHYLIP format
- arb_dnarates and arb_fastdnaml expect FASTDNAML format

168 lines of code changed in 17 files:

westram 2011-02-23 15:47 Rev.: 7186


merges [7097] [7098] [7100] [7101] [7102] [7103] [7105] from refactor
* use arb_progress instead of aw_openstatus, aw_closestatus and aw_status
- allows nested progress bars
- avoids repeatedly popping up progress bars
- avoids passing down info about progress to callees or bookkeeping it in method-objects and similar
- removed many useless status messages (e.g. those that were only visible for ms)
- corrected incrementation / limit for many progress bars (esp. matrix-calculations, parsimony)
* hide aw_open/close/status inside libAW
* hide rests of GB_status inside libCORE
* replaced ARB_null_status by arb_suppress_progress
- suppress progress display in unit-tests
* added GBT_count_alignments
* stuffed a few memleaks on the way
* disabled some deprecation warnings
* use arb_progress in ptserver
* avoid zero progress in GDE export

2498 lines of code changed in 133 files:

westram 2011-02-23 14:48 Rev.: 7185


merges [7096] from refactor
- removed default parameters from nni_rek()

14 lines of code changed in 4 files:

westram 2011-02-23 13:54 Rev.: 7184


merges [7071] [7072] [7073] [7075] [7078] [7079] [7082] [7092] [7094] [7095] from refactor
* moved TOOLS/arb_count_chars.cxx directly into caller (NTREE)
* created helpfile for count chars
* added NTREE to tested units
* added unit test for NT_count_different_chars
* added two test-DBs containing some sequence data (NUC and AA)
* refactored NT_count_different_chars
* added flag to NT_count_different_chars to control status display
* added alias target 'savetest'

2624 lines of code changed in 13 files:

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)

848 lines of code changed in 96 files:

westram 2011-02-23 13:18 Rev.: 7182


merges [7080] [7081] [7083] [7090] [7091] from refactor
* !PersistantFlag can act volatile (i.e. detect that another process changed the flag on disk)
* added volatile !PersistantFlag "any_setup" used by !UnitTester and test_environment
- when a test calls test_environment, it's deadlockguard adds some tolerance before terminating the test
* fixed format-specifiers for hex-printing unsigned and unsigned long
* moved test_create_DB() to new global header arb_unit_test.h
* gb_set_compression_mask -> GB_allow_compression
- allow to change DB-compression from outside ARBDB (e.g. from unit tests)
- returns previous state of compression (for easy restore)
* after temporarily disabling compression, always restore previous state (instead of always allowing all)
* TEST_CREATE_DB: added parameter allowing to specify use of DB compression

221 lines of code changed in 12 files:

westram 2011-02-23 13:07 Rev.: 7181


merges [7074] from refactor
- typo

4 lines of code changed in 3 files:

westram 2011-02-23 13:04 Rev.: 7180


merges [7070] from refactor
* renamed several functions to NT_... (=> they automatically propagate to generated headers)
* cleaned up ad_spec.hxx (only defines prototypes needed by genome-libs). Named them NTX_..

29 lines of code changed in 6 files:

westram 2011-02-23 13:00 Rev.: 7179


merges [7068] from refactor
* demangle backtraces using c++filt
- fallback on failure (e.g. if c++filt is missing)
- suppress creating backtraces from GBK_raises_SIGSEGV (assertion failures are expected there)
* BackTraceInfo::dump()
- fixed a bug (flush out, before printing via fileno(out))
- returns true on successfull write

54 lines of code changed in 3 files:

westram 2011-02-23 12:56 Rev.: 7178


merges [7066] from refactor
* separated target 'touch' from 'modified'

5 lines of code changed in 1 file:

westram 2011-02-23 12:44 Rev.: 7177


merges [7054] [7055] [7057] [7058] [7059] [7062] from refactor
* added GB_unfold_path()
* added GB_install_getenv_hook(). May override expansion of environment variables.
* added unit tests for AW_unfold_path
* rewrote AW_unfold_path() using GB_unfold_path() + hook to expand symbolic directories (PWD and PT_SERVER_HOME)
* replaced duplicate of AW_unfold_path() with different behavior in SL/SEQIO by calling GB_unfold_path()
* removed default argument "PWD" from AW_unfold_path
* swapped argument order of GB_unfold_path and AW_unfold_path to "(dir,file)"
* Tests for path functions
* GB_path_in_ARBLIB/ARBHOME
- versions with one argument
- using GB_unfold_path
* replaced AW_unfold_path / GB_unfold_path ("ARBHOME") with GB_path_in_ARBHOME
* replaced GB_path_in_ARBHOME("lib/") by GB_path_in_ARBLIB
* GB_canonical_path (former GB_get_full_path)
- old version had undefined behavior (which was working in many cases)
- now "never" return NULL, instead it may return a non-canonical path (in case of non-existing directories)
* assert that param 'pwd_envar' to GB_unfold_path() really is the name of an envar (to avoid passing a path by mistake)

256 lines of code changed in 21 files:

westram 2011-02-23 12:32 Rev.: 7176


merges [7067] from refactor
* reduced direct usage of test_assert
* test_assert now takes a 2nd parameter to request a backtrace
* when compiling with unit-tests, normal (non-test) assertions (i.e. arb_assert) is redefined to dump a backtrace

30 lines of code changed in 6 files:

westram 2011-02-23 11:40 Rev.: 7175


merges [7056] from refactor

* macro UNCOVERED()
- may stay in code
- doesn't fail outside of tests

13 lines of code changed in 3 files:

westram 2011-02-23 11:18 Rev.: 7174


merges [6763] from refactor

* quicksave test
- put into its own TEST
- refactored
- uses minimal (=empty) DB

141 lines of code changed in 4 files:

westram 2011-02-23 10:55 Rev.: 7173


- depends

6 lines of code changed in 1 file:

westram 2011-02-23 10:48 Rev.: 7172


merged [6787] [6803] [6941] [6944] [6947] [7064] [7065]
* ptserver tests implemented via test_environment stubbed in [6810]
- handles different environments
- setup of environments may be requested by client-TEST_functions
- different tests using the ptserver use the same instance
- rebuilding ptserver is possible now (before concurrent tests often terminated each others ptserver)
- always rebuild ptserver database and compare resulting file
- really kill running ptservers
- cleanup is done automatically after running all unit-tests
* again run slow tests not more often than every 15 minutes

278 lines of code changed in 12 files:

westram 2011-02-23 09:54 Rev.: 7171


* merged [6754] [6756] [6756] [7069] from refactor
- aisc_server_shutdown_and_exit marked deprecated
- added aisc_server_shutdown
- ptserver (eliminate multiple exit-points):
- ensure proper cleanup
- delete half-written pt-server-file on error
- two calls to PT_exit() remain: from main() and from server_shutdown().
- removed obsolete file probe_debug.cxx
* fixed conflicts with [7158] [7159]

580 lines of code changed in 11 files:

baderk 2011-02-19 14:01 Rev.: 7159

Two fixed memory leaks (using Ralfs !SmartMallocPtr smart pointer).

23 lines of code changed in 3 files:

baderk 2011-02-18 17:51 Rev.: 7158

Various fixes to free most of the memory when terminating / having built a PT-Server.
Removes lots of warnings from valgrind...

(This is a backport from CaSSiS.)

98 lines of code changed in 7 files:

westram 2011-02-16 13:05 Rev.: 7144


- save marked items in ASCII format

16 lines of code changed in 4 files:

baderk 2011-02-16 11:32 Rev.: 7143

Fixed two memory leaks in the pt-server.

7 lines of code changed in 2 files:

westram 2011-02-11 15:33 Rev.: 7141


* DRYed partof InsertDatainGDE()

41 lines of code changed in 1 file:

westram 2011-02-11 13:51 Rev.: 7140


* replaced magic buffersizes by defines
- fixed one potential buffer overflow (for 'short_name')

29 lines of code changed in 5 files:

westram 2011-02-11 12:14 Rev.: 7139


* fixed non-terminated buffers in GDE exporter
- caused arb_convert_aln to fail (e.g. when length of author was longer than 79 byte)
- bug existed since [2], most likely popped up now due to arb_convert_aln being more picky.

25 lines of code changed in 6 files:

westram 2011-02-10 14:25 Rev.: 7138


- do not try to bind callbacks to missing secondary structure

2 lines of code changed in 1 file:

westram 2011-02-10 11:49 Rev.: 7137


- fixed consensus calculation (if no seq-data is loaded, e.g. when configuration is not found)

5 lines of code changed in 1 file:

westram 2011-02-10 11:47 Rev.: 7136


- do not show skip-message if nothing has been skipped

5 lines of code changed in 1 file:

westram 2011-02-10 09:37 Rev.: 7135


- csv export: quote fields containing separator

53 lines of code changed in 1 file:

westram 2011-02-09 16:18 Rev.: 7134


- test whether arb_tcp.dat is a link and then dont overwrite contents
(on some systems 'test -e' returns false for links)

2 lines of code changed in 1 file:

westram 2011-02-09 11:03 Rev.: 7133


* added parameter 'expose' to NT_reload_tree_event
- arb_pars crashes when exposing tree with zombies
* remove_leafs() returns number of removed leafs
- arb_pars now shows message about removed leafs

20 lines of code changed in 6 files:

westram 2011-02-09 09:23 Rev.: 7131


- removed leftover doc-refs to xview

0 lines of code changed in 2 files:

westram 2011-02-09 09:04 Rev.: 7130


- fixed buffer overflow

6 lines of code changed in 1 file:

westram 2011-02-09 08:50 Rev.: 7129


- failed to report error if input file was missing

8 lines of code changed in 2 files:

epruesse 2011-02-06 20:47 Rev.: 7128

have make clean remove PERL2ARB/Makefile
it's a generated file and its contents depend on the compile host

1 lines of code changed in 1 file:

baderk 2011-02-05 13:58 Rev.: 7127

Added gcc v4.4.5 to the Makefile.

1 lines of code changed in 1 file:

westram 2011-02-04 16:30 Rev.: 7126


- added GDE entry to import fields from calc-sheets
- importer
- can now handle CSV with quoted entries
- report and forward error to ARB (if using ':')
- renamed NDS exporter

127 lines of code changed in 4 files:

westram 2011-02-04 13:24 Rev.: 7125


- use label from parent window as title in file-browser

16 lines of code changed in 1 file:

westram 2011-02-04 12:45 Rev.: 7124


- drop alignment error

3 lines of code changed in 1 file:

westram 2011-02-04 12:45 Rev.: 7123


- attached elements in file browser to window-bottom

18 lines of code changed in 1 file:

westram 2011-02-04 12:27 Rev.: 7122


- use file browser in existing GDE menus

3 lines of code changed in 2 files:

westram 2011-02-04 12:01 Rev.: 7121


* added new GDE argument type 'filename' (textfield+browse button)
* fixed "alignment not found" error

183 lines of code changed in 8 files:

westram 2011-02-04 11:54 Rev.: 7120


- assertion crashed for seqtype:-

3 lines of code changed in 1 file:

westram 2011-02-02 20:35 Rev.: 7119


* import_from_table
- save DB (if loaded)
- implemented '--marked-only' + '--as-integer'
- added '--mark' (marks species where field has been imported)
- check more errors
- list unmatched entries sorted by calc-sheet-row-number
- print summary for unmatched/unhandled

57 lines of code changed in 1 file:

epruesse 2011-02-02 17:36 Rev.: 7118

fix typo in help msg

1 lines of code changed in 1 file:

westram 2011-02-02 12:23 Rev.: 7117

dav test commit

0 lines of code changed in 1 file:

westram 2011-02-02 12:14 Rev.: 7116

depends

0 lines of code changed in 1 file:

westram 2011-02-02 10:02 Rev.: 7115


- set executable flag

1 lines of code changed in 1 file:

westram 2011-02-02 10:00 Rev.: 7114


- merged [7112] to trunk

8 lines of code changed in 1 file:

westram 2011-02-01 17:38 Rev.: 7111


* added export as comma-separated-values (NDS export)
* renamed enum NDS_Type-members

37 lines of code changed in 8 files:

westram 2011-02-01 17:27 Rev.: 7110


- fixed include path

1 lines of code changed in 1 file:

westram 2011-02-01 17:27 Rev.: 7109


- basic implementation of calc-sheet import

231 lines of code changed in 1 file:

January 2011 »

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