September 2012 Commit Log

Number of Commits:
87
Number of Active Developers:
2
westram 2012-09-27 14:44 Rev.: 8964


* leave(s) -> leaf(s)

45 lines of code changed in 12 files:

westram 2012-09-27 13:14 Rev.: 8963


* default for ptserver-related tests

1 lines of code changed in 1 file:

westram 2012-09-27 13:02 Rev.: 8962


* added auto-update-code for normal ptserver
* inserted '...' behind 'GUUUGAUCAAGUCGAGCGGU' in ptserver-test-source-DB
- probe has exactly two occurrances in the middle of the sequence data
- updated test-results for changed data
* ran TEST_SLOW_find_unmatched_probes to check for further index-errors
- no additional errors caused
- i.e. index-errors seem to occur only on 3'-end

25 lines of code changed in 7 files:

westram 2012-09-27 11:06 Rev.: 8961


* inlined code
* added expectation that full-probe hits (to detect outdated tests)

14 lines of code changed in 1 file:

westram 2012-09-27 10:04 Rev.: 8960


* examined and commented index-errors (according to location in source-sequence)

12 lines of code changed in 1 file:

westram 2012-09-27 09:46 Rev.: 8959


* added (disabled) test-code to detect errors in ptserver index
- for all 20mers it checks whether any subprobe doesn't hit any species hit by the 20mer
- prints test-code for each index-error
* document found index-errors in normal test

150 lines of code changed in 2 files:

westram 2012-09-26 16:11 Rev.: 8958


* resolve name conflict with <iterator>

11 lines of code changed in 2 files:

westram 2012-09-26 12:45 Rev.: 8955


* allow to define whether 'T' or 'U' is used in iterated probes

17 lines of code changed in 5 files:

westram 2012-09-26 10:30 Rev.: 8952


* remove extra-dot at end of each probe in readable-mode

14 lines of code changed in 2 files:

westram 2012-09-26 10:29 Rev.: 8951


* DRY

12 lines of code changed in 2 files:

westram 2012-09-26 10:17 Rev.: 8950


* test one result in "unreadable" format

8 lines of code changed in 1 file:

westram 2012-09-26 09:54 Rev.: 8948


* arb_probe unittest: stuffed leak

10 lines of code changed in 1 file:

westram 2012-09-25 17:54 Rev.: 8947


* 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)

53 lines of code changed in 3 files:

westram 2012-09-25 16:04 Rev.: 8946


* added parameter -r to arb_2_ascii
- only run in recovery mode when -r is specified
* changed recovery-mode-messages in ARBDB
* parse and name parameters in arb_repair

61 lines of code changed in 3 files:

westram 2012-09-25 14:33 Rev.: 8945


* 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.

163 lines of code changed in 5 files:

westram 2012-09-25 12:52 Rev.: 8944


* added class PTserverConnection to remove duplicated code
* fixed locals and error handling in AP_probe_design_event + AP_probe_match_event

140 lines of code changed in 1 file:

westram 2012-09-25 11:53 Rev.: 8943


* added a test demonstrating a case where ptserver reports more matches for a 20-mer than for a 10-mer which is a substring of the 20-mer
- i.e. the ptserver index is incomplete
- this happens at the 3'-end of the alignment, if several species end in the SAME 20-mer

80 lines of code changed in 1 file:

westram 2012-09-25 07:38 Rev.: 8942


* fixed cppcheck warnings

18 lines of code changed in 3 files:

westram 2012-09-24 18:49 Rev.: 8941


* fixed cppcheck warnings

582 lines of code changed in 3 files:

westram 2012-09-24 15:53 Rev.: 8940


* added MBI copyright
* fixed include wrappers
* fixed cppcheck warning

49 lines of code changed in 6 files:

westram 2012-09-24 15:48 Rev.: 8939


* fix cppcheck warnings

49 lines of code changed in 6 files:

westram 2012-09-24 14:47 Rev.: 8937


* AP_matrix (made members private)

27 lines of code changed in 3 files:

westram 2012-09-24 14:27 Rev.: 8936


* fixed cppcheck warnings

58 lines of code changed in 9 files:

westram 2012-09-23 13:50 Rev.: 8933


* fixed cppcheck warnings

7 lines of code changed in 1 file:

westram 2012-09-23 13:43 Rev.: 8932


* !CompactedSubSequence
- use generic assignment-operator
- use !SmartPtr instead of homegrown ref-counting
* !CompactedSequence
- removed friend
- made class public (no longer dangerous)
* !FastSearchSequence derived from Noncopyable (private cctor/assop removed)

49 lines of code changed in 2 files:

westram 2012-09-23 13:10 Rev.: 8931


* variable rename (unique)

28 lines of code changed in 1 file:

westram 2012-09-23 12:47 Rev.: 8930


* pass result parameters to ClustalV_align by reference (using const for result buffers)

31 lines of code changed in 3 files:

westram 2012-09-23 12:29 Rev.: 8929


* avoid error in target 'savetest' when SVN-file is missing (unclear why it happens)

9 lines of code changed in 1 file:

westram 2012-09-23 12:19 Rev.: 8928


* terminate clustalV result buffer
- tests failed randomly in NDEBUG mode

3 lines of code changed in 1 file:

westram 2012-09-23 12:11 Rev.: 8927


* fixed valgrind warnings for clustalv-tests
- gaps-array has to be (size of seq1) + 1

7 lines of code changed in 1 file:

westram 2012-09-22 19:18 Rev.: 8926


* fixed rest of locals

47 lines of code changed in 1 file:

westram 2012-09-22 19:05 Rev.: 8925


* more brace fixes

20 lines of code changed in 2 files:

westram 2012-09-22 18:49 Rev.: 8924


* inlines are static by default

28 lines of code changed in 3 files:

westram 2012-09-22 18:46 Rev.: 8923


* braces fixed

140 lines of code changed in 4 files:

westram 2012-09-22 18:25 Rev.: 8922


* MAXN dependent code removed (only MAXN==2 possible now)

2 lines of code changed in 1 file:

westram 2012-09-22 18:21 Rev.: 8921


* fixed cppcheck warnings

54 lines of code changed in 1 file:

westram 2012-09-22 17:54 Rev.: 8920


* use 'svn status' instead of 'svn list' introduced in [8913]
- status works offline and is much faster (<1s vs >6s)

32 lines of code changed in 1 file:

westram 2012-09-22 17:37 Rev.: 8919


* unit-test for clustalv

93 lines of code changed in 2 files:

westram 2012-09-22 15:05 Rev.: 8918


* script 'arb' now detects ARBHOME using its own location
- no need to set ARBHOME, but no harm if it is set
* 'arb help' shows script and ntree usage

40 lines of code changed in 1 file:

westram 2012-09-22 15:00 Rev.: 8917


* 'arb_ntree --help' no longer starts up GUI

85 lines of code changed in 2 files:

westram 2012-09-22 14:08 Rev.: 8916


* fixed cppcheck warnings

5 lines of code changed in 2 files:

westram 2012-09-22 14:07 Rev.: 8915


* dont dump font lookup

2 lines of code changed in 1 file:

westram 2012-09-22 10:36 Rev.: 8914


* avoid useless warnings when ARBHOME is not defined

1 lines of code changed in 1 file:

westram 2012-09-21 16:38 Rev.: 8913


* it's no longer possible to read .svn/entries, since svn-client format changed with v1.7
* instead use 'svn list'

41 lines of code changed in 1 file:

westram 2012-09-21 11:11 Rev.: 8912


* check gcc-version using perl-script (some gccs report patchlevels on -dumpversion, others dont e.g. SuSE gccs)
* removed versions w/o patchlevel from list of allowed versions

32 lines of code changed in 2 files:

westram 2012-09-21 09:58 Rev.: 8911


* fixed bug in GBT_check_arb_file (only tried to check remote DB). Introduced in [8642]
* removed an annoying message popup

1 lines of code changed in 1 file:

westram 2012-09-20 08:31 Rev.: 8910


* 32bit fix for [8909]

2 lines of code changed in 1 file:

westram 2012-09-19 14:39 Rev.: 8909


* fixed cppcheck warnings

103 lines of code changed in 4 files:

westram 2012-09-19 13:56 Rev.: 8908


* init_Advisor in AWT_create_root instead of AW_insert_common_property_menu_entries (crashed when an early advice got triggered)

3 lines of code changed in 3 files:

westram 2012-09-19 13:32 Rev.: 8907


* fixed cppcheck warnings

102 lines of code changed in 6 files:

westram 2012-09-19 12:30 Rev.: 8906


* fixed cppcheck warnings

275 lines of code changed in 1 file:

westram 2012-09-19 11:31 Rev.: 8905


* fixed cppcheck warnings

65 lines of code changed in 8 files:

westram 2012-09-19 10:46 Rev.: 8904


* fixed cppcheck warnings

25 lines of code changed in 1 file:

westram 2012-09-19 10:37 Rev.: 8903


* fixed cppcheck warnings

149 lines of code changed in 16 files:

westram 2012-09-19 09:49 Rev.: 8902


* fixed cppcheck warnings

38 lines of code changed in 5 files:

westram 2012-09-19 09:25 Rev.: 8901


* PH_root
- made members private
- added ctor/dtor
- made a singleton
* fixed other cppcheck warnings

56 lines of code changed in 5 files:

westram 2012-09-15 18:46


* fixed cppcheck warnings

36 lines of code changed in 10 files:

westram 2012-09-15 18:29 Rev.: 8895


* fixed cppcheck warnings

113 lines of code changed in 8 files:

westram 2012-09-15 17:20 Rev.: 8894


* fixed cppcheck warnings

16 lines of code changed in 3 files:

westram 2012-09-15 17:11 Rev.: 8893


* fixed cppcheck warnings

54 lines of code changed in 6 files:

westram 2012-09-15 17:00 Rev.: 8892


* eliminated gotos

80 lines of code changed in 1 file:

westram 2012-09-15 16:39 Rev.: 8891


* fixed cppcheck warnings

8 lines of code changed in 3 files:

westram 2012-09-15 16:33 Rev.: 8890


* fixed cppcheck warnings

34 lines of code changed in 7 files:

westram 2012-09-15 16:17 Rev.: 8889


* fixed cppcheck warnings

424 lines of code changed in 11 files:

westram 2012-09-15 13:14 Rev.: 8888


* fixed cppcheck warnings

29 lines of code changed in 3 files:

westram 2012-09-15 13:00 Rev.: 8887


* upcased names of several constants

186 lines of code changed in 4 files:

westram 2012-09-15 12:38 Rev.: 8886


* fixed cppcheck warnings

14 lines of code changed in 3 files:

westram 2012-09-15 12:26 Rev.: 8885


* fixed cppcheck warnings

35 lines of code changed in 6 files:

westram 2012-09-15 10:57 Rev.: 8884


* fixed cppcheck warnings

86 lines of code changed in 4 files:

westram 2012-09-14 17:55 Rev.: 8883


* fixed cppcheck warnings

12 lines of code changed in 1 file:

westram 2012-09-14 17:42 Rev.: 8882


* fixed cppcheck warnings in ARBDB

350 lines of code changed in 27 files:

westram 2012-09-14 17:42 Rev.: 8881


* fixed cppcheck warnings

24 lines of code changed in 4 files:

westram 2012-09-13 18:20 Rev.: 8880


* fix buffer-overflow mentioned in [8879] (+added assertion vs overflow)

2 lines of code changed in 2 files:

westram 2012-09-13 18:04 Rev.: 8879


* g_b_put_number2 / g_b_read_number2
- now also supports int-range {{{[0x10000000 .. 0x7fffffff]}}}
* that range works for 64- and 32-bit
* previously it silently wrote nothing; read fixed (wrong shift)
- assert put/read numbers are in valid range {{{[0x0 .. 0x7fffffff]}}}
- memtest of generated binary data is broken somehow (64bit: valgrind-reports, 32bit: SEGV)
- pass buffer as *&

74 lines of code changed in 2 files:

westram 2012-09-13 15:50 Rev.: 8878


* fix binary representation of g_b_put_number2 (affects DB-content)

(changes to test_unit.h reverted by [9508])

60 lines of code changed in 2 files:

westram 2012-09-13 14:32 Rev.: 8877


* added unit-tests for sequence compression (by master-sequences)
- shows input-restrictions of g_b_put_number2

166 lines of code changed in 3 files:

westram 2012-09-12 10:45 Rev.: 8876


- disabled assertion

1 lines of code changed in 1 file:

westram 2012-09-10 12:44 Rev.: 8875


- removed gotos

33 lines of code changed in 1 file:

westram 2012-09-07 15:06 Rev.: 8872


* restrict number of ARB_NT-windows to 5
- added NT_get_canvas_id() which returns a unique number for each canvas
* separate config-admin window for each canvas (needed to ensure correct tree is used when creating a config)
* store !BranchWindow statically in array

81 lines of code changed in 8 files:

epruesse 2012-09-06 16:28 Rev.: 8871

add "time" to required packages for building ARB

1 lines of code changed in 1 file:

westram 2012-09-06 11:20 Rev.: 8870


* removed dead module
* compile NTREE-modules via wildcard

9 lines of code changed in 2 files:

westram 2012-09-06 09:52 Rev.: 8869


* style-fix

2 lines of code changed in 1 file:

westram 2012-09-06 09:44 Rev.: 8868


* NT_global
- renamed instance (GLOBAL_NT -> GLOBAL)
- swallow GLOBAL_gb_main (-> GLOBAL.gb_main)

437 lines of code changed in 25 files:

westram 2012-09-06 09:18 Rev.: 8867


* removed AWT_graphic_tree from NT_global (this is not a global! every NT-window has it's own treedisp)
- the following functions always used the tree of the 2nd NT-window (once it has been opened; even if it was closed again):
* Species/Sort Species/According to Phylogeny
* anything concerned with species configs (included species were ok, but order depended on wrong tree). Was only notable when EDIT4 was used on configuration.

40 lines of code changed in 7 files:

westram 2012-09-05 15:12 Rev.: 8866


* separate distance analysis for marked species

50 lines of code changed in 3 files:

westram 2012-09-05 14:14 Rev.: 8865


* distance analysis (collect mean, min and max distances between leafs in tree)

159 lines of code changed in 5 files:

westram 2012-09-05 11:55 Rev.: 8863


* new module for branch analysis
- moved code to mark long, deep and degenerated branches into analysis window
* added help
* 'long branch'-detection: new way to calc 'relative length diff'
* functions output more verboose info about topology

634 lines of code changed in 9 files:

August 2012 »

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