October 2010 Commit Log

Number of Commits:
26
Number of Active Developers:
1
westram 2010-10-31 09:30 Rev.: 7076


* fixed 2 bugs in date-conversion
- did not accept day==31
- did not accept month==12
* check max day for months (i.e. 31.Sep and 30.Feb now fail)

33 lines of code changed in 1 file:

westram 2010-10-27 13:42 Rev.: 7060


* if e.g. decompression of a DB field fails
- search tool now properly reports an error if sth goes wrong during the query
- pt-server prints error and handles the sequence as "missing" (i.e. simply does not index it)
* related with [http://tech.groups.yahoo.com/group/arb_users/message/3095]

40 lines of code changed in 2 files:

westram 2010-10-26 08:51 Rev.: 7053


* updated broken date (1910->2010)

0 lines of code changed in 2 files:

westram 2010-10-26 08:01 Rev.: 7052


- reverted part of merge [7038]

1 lines of code changed in 1 file:

westram 2010-10-25 19:31 Rev.: 7051


- missing depends

5 lines of code changed in 1 file:

westram 2010-10-25 19:11 Rev.: 7049


- completes [7044] (possible lost by merging)

1 lines of code changed in 1 file:

westram 2010-10-25 19:07 Rev.: 7048


* merges [6940] [6942]
- fixed wrong use of ASSERT_RESULT
- to be a bit more intuitive, swapped arguments of ASSERT_RESULT + ASSERT_RESULT_PREDICATE
- removed ASSERT_RESULT_BELOW / ASSERT_RESULT_ABOVE (even less intuitive) and replaced by 'ASSERT_RESULT_PREDICATE(isBelow<int>(MAXIDSIZE)..)'

42 lines of code changed in 8 files:

westram 2010-10-25 19:04 Rev.: 7047


- do not print full paths (merges [6951])

35 lines of code changed in 1 file:

westram 2010-10-25 18:47 Rev.: 7046


* refactored CONVERTALN (merges [6885] [6886] [6888] [6889] [6890] [6891] [6894] [6906] [6907] [6908] [6910] [6911] [6914] [6915] [6916] [6917] [6918] [6922] [6923] [6925] [6927] [6928] [6929] [6930] [6931] [6933] [6934] [6935] [6937] [6945] [6950] [6956] [6961] [6962] [6963] [6964] [6965] [6967] [6968] [6972] [6973] [6974] [6975] [6976] [6977] [6979] [6980] [6981] [6982] [6983] [6985] [6986] [6987] [6988] [6990] [6991] [6992] [6993] [6994] [6995] [6996] [6997] [6998] [6999] [7002] [7003] [7008] [7009] [7010] [7011] [7012] [7025] [7026] [7027] [7029] [7030] [7031] [7032] [7034] [7035] [7036])
- build arb_convert_aln in ARB standard way
- added unit-test
- fixed various date bugs (even Y2K)
- fixed conversion MACKE -> GCG.
- fixed crash in conversions EMBL/GENBANK -> GCG
- fixed SWISSPROT->MACKE conversion
- dropped conversion support for ALMA
- removed completely unused "formats" NBRF and STADEN
- removed 1x1 sequence conversions for interleaved formats
- converter is more picky (fails instead of doing nonsense)
- added self conversions for all input formats
- proper formatting of 3/5 info
- proper line wrapping
- fixed acc broken by genbank reader
- fixed broken IDs (short-names)
- fixed embl reader (added number @ EOL to sequence data)
- errors now refer to the input file + linenumber
- abort with error if sequence data contains invalid characters
- removed C-interface for FileBuffer (CONVERTALN was the only client)

9644 lines of code changed in 82 files:

westram 2010-10-25 17:20 Rev.: 7045


* fix for broken nightly builds (merges [6952])
- UnitTester sets global flag when tests run
- added assertion vs use of aw_message() in unit-tests
- replaced aw_message by GB_warning (which does the same in GUI applications)

13 lines of code changed in 6 files:

westram 2010-10-25 17:10 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

127 lines of code changed in 56 files:

westram 2010-10-25 16:54 Rev.: 7043


* merges [6969]
- GB_test_textfile_difflines did not detect when 2 lines were swapped. bump. fixed.
- added unit tests for GB_test_textfile_difflines

60 lines of code changed in 1 file:

westram 2010-10-25 16:43 Rev.: 7042


* do not fail assertion when uninstalled sighandler is SIG_IGN (merges [6895])
- sighandler may have been changed when the signal occurred (this is implementation-defined)

7 lines of code changed in 1 file:

westram 2010-10-25 16:38 Rev.: 7041


* unit-test improvements (merged from refactor [6873] [6874] [6887] [6896] [6897] [6898] [6899] [6900] [6901] [6926] [6932] [6939] [6943] [6946] [6948] [6949] [6984])
- flush output before triggering assertion
- test_environment failed to link with COVERAGE=1
- showed 'Ok' when tests crashed (but none failed). fixed.
- structed globals
- interrupt tests that DNF, after some time (forks a guard)
- ensure working directory is correct before each single test)
- updated README
- assertions may be annotated in test code
- added default priorities for TEST_BASIC_ and TEST_EARLY_
- print strings with \n etc.
- assertion vs. double instanciation of GlobalTestData

347 lines of code changed in 10 files:

westram 2010-10-25 15:52 Rev.: 7040


* merged from refactor [6875] [6876] [6877] [6878] [6879] [6880] [6881] [6882] [6892] [6893] [6902] [6909] [6919] [6920] [6921] [6924] [6938]
- formatted alignment of test-db
- added TEST_ASSERT_TEXTFILE_DIFFLINES
- added special mode that treats different dates as equal
- moved file compare tests to ARBDB (shall goto ARBCORE later)
- added tests for sequence export
- big test indicator
- skip SLOW warning when running under valgrind
- no ':' in patch names
* fixes included:
- do not export full installation path when exporting sequences as xml
- stuffed a leak in XML-exporter

628 lines of code changed in 34 files:

westram 2010-10-25 15:44 Rev.: 7039


- default now is 64bit

1 lines of code changed in 1 file:

westram 2010-10-25 14:39 Rev.: 7038


* merged from refactor [6883] [6954] [6970]
- updated source.lst

(partly reverted by [7052])

4 lines of code changed in 2 files:

westram 2010-10-25 14:10 Rev.: 7037


* merged from refactor [6936] [7000] [7001] [7004]
- interface to get line-specific error from anonymous FILE_BUFFER
- fixed return of temporary
- fixed memleak

17 lines of code changed in 3 files:

westram 2010-10-22 18:43 Rev.: 7024


- readded helpfiles.lst (merges [7023] from stable)
- removed 2 files from svn ignore list

1 lines of code changed in 1 file:

westram 2010-10-22 18:22 Rev.: 7021


- fixed index name

3 lines of code changed in 2 files:

westram 2010-10-22 17:59 Rev.: 7018


* create a simple index page (to invite google to search all pages)
- link to index page from all pages
* no longer generate unused files 'helpfiles.lst' and '_index.html'
* write backlink into comments of generated xml
* fixed a few helppages which refused to get scanned by generate_index.pl
* updated depends

185 lines of code changed in 10 files:

westram 2010-10-22 16:51 Rev.: 7017


* added unit-test to arb_help2xml
- fixed title whitespace
* added notes about how to add new unit-tests

53 lines of code changed in 6 files:

westram 2010-10-22 15:10 Rev.: 7016


* removed option to convert from Xml only (was and will not be used)

0 lines of code changed in 1 file:

westram 2010-10-22 12:31 Rev.: 7015


- updated help for ARB_PARS branchlength calculation

61 lines of code changed in 1 file:

westram 2010-10-21 15:48 Rev.: 7014


- cluster search no longer crashes when used on protein alignments (no idea whether results make sense)

2 lines of code changed in 1 file:

westram 2010-10-21 14:38 Rev.: 7013


- when field 'codon_start' was missing, but field 'transl_table' was present, ARB wrote a default 'codon_start' as GB_INT, which caused a crash. Introduced in [5768]

1 lines of code changed in 1 file:

September 2010 »

Generated by StatSVN 0.7.0