January 2009 Commit Log

Number of Commits:
25
Number of Active Developers:
4
arb_build 2009-01-15 15:48 Rev.: 5736

Auto version upgrade to 4.22 by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2009-01-15 13:17 Rev.: 5735


* In SAI group assignment user can select from existing SAI-groups now (fixing #107)
* replaced simple rename windows by single callbacks using aw_input (SAI: copy, copy->species, rename). Target is auto-selected now.
* aw_input/aw_string_selection
- '<<' and '>>' buttons are working as history now (fixing #121 and #99)
- Temporary input awars now located in properties database, to ensure that no transaction is open in aw_input (needed cause awar refresh isn't working in that case and so history won't work either).
- separated awar-using versions from those with normal default value (aw_input2awar, aw_string_selection2awar)
- made all default parameters explicit

518 lines of code changed in 19 files:

westram 2009-01-15 11:54 Rev.: 5734


* added GBT_get_SAI_data
* GBT_first/next_marked_extended -> GBT_first/next_marked_SAI
* GBT_first/find_SAI_rel_exdata -> GBT_first/find_SAI_rel_SAI_data
* variables renamed: (gb_ex[tended[_data]] -> gb_sai[_data])

170 lines of code changed in 22 files:

westram 2009-01-15 10:59 Rev.: 5733


* added GBT_join_names and GBT_split_string

72 lines of code changed in 2 files:

westram 2009-01-15 09:36 Rev.: 5732


- rtfm

7 lines of code changed in 1 file:

westram 2009-01-15 00:04 Rev.: 5731


* added GB_get_transaction_level()

7 lines of code changed in 2 files:

baderk 2009-01-14 12:21 Rev.: 5730

Fixed missing dependency on Ubuntu 8.10 (AMD64)

1 lines of code changed in 1 file:

westram 2009-01-13 14:26 Rev.: 5729


* 64 bit version crashed with bus error on ACI command 'count'

3 lines of code changed in 1 file:

westram 2009-01-13 09:26 Rev.: 5728


* removed duplicated link

1 lines of code changed in 1 file:

westram 2009-01-13 09:26 Rev.: 5727


* warn if helpfiles contain 'TODO' or '@@@' (DEBUG version only)

21 lines of code changed in 1 file:

westram 2009-01-13 09:25 Rev.: 5726


* ACI commands 'filter', 'diff' and 'change' can now use either the first or every 2nd stream as filter (or compare) sequence (previously only a explicitely named species or SAI was possible)
- if 'SAI' or 'species' is used, the alignment still defaults to the current alignment. Using the 'align=' param any other alignment can be selected.
* added new ACI param type 'CHAR'
* added and using some macros in adlang1.c (STREAM_OUT, STREAM_DUPOUT, STREAM_INOUT)
* params can be declared "into" an existing struct using GBL_STRUCT_PARAM_..
* BIT params previously had to be specified like 'fun(bitx=)', now 'fun(bitx)' or 'fun(bitx=1)' work as well
* CHAR param can be empty (e.g. 'fun(charx=)'). The param value is set to char(0) then, deleting a possibly existing default value
* Inserted some linefeeds into command interpreter error messages to make them more readable

568 lines of code changed in 3 files:

westram 2009-01-09 23:34 Rev.: 5725

* removed useless macros:
- GB_STRDUP (easily taken for GB_strdup)
- GB_MEMCPY + GB_MEMSET + GB_FREE
- GB_DELETE (replaced by freeset(xx,NULL))
* added macros:
- freeset (= free + assign)
- freedup (= free + assign strdup'ed)
- reassign (= free + assign + clear source var)
- nulldup (=strdup accepting NULL; replacement for GB_strdup in C++ code)
* use these macros where applicable

720 lines of code changed in 124 files:

arb_build 2009-01-08 11:14 Rev.: 5724

Auto version upgrade to 4.21 by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2009-01-08 11:13 Rev.: 5723

* do not apply insertDots to ACGTU only, instead apply to all upper case chars

5 lines of code changed in 2 files:

boehnel 2009-01-08 04:37 Rev.: 5722

* Fixed indentation

20 lines of code changed in 1 file:

boehnel 2009-01-08 04:30 Rev.: 5721

* adding EPSILON define and change comparison of floats from "a == b" to "fabs(a - b) < EPSILON"

7 lines of code changed in 2 files:

boehnel 2009-01-08 03:46 Rev.: 5720

* Added comment for ALLOWDOTSINMATCH and MAXDOTSINMATCH

5 lines of code changed in 1 file:

boehnel 2009-01-08 03:35

Bugfixes for ALLOWDOTSINMATCH

82 lines of code changed in 3 files:

boehnel 2009-01-08 03:35 Rev.: 5717

ULLONG should be unsigned long long

1 lines of code changed in 1 file:

boehnel 2009-01-08 03:34 Rev.: 5716

Bugfixes for ALLOWDOTSINMATCH

2 lines of code changed in 1 file:

westram 2009-01-07 09:18 Rev.: 5715

fix TAB and indentation

14 lines of code changed in 1 file:

westram 2009-01-07 09:07 Rev.: 5714

* Removed MAUS

2 lines of code changed in 10 files:

arb_build 2009-01-05 20:41 Rev.: 5713

Auto version upgrade to 4.20 by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2009-01-05 20:25 Rev.: 5712


* New feature: insert dots where bases are potentially missing in alignment
* ED4_create_consensus_definition_window usable from multiple callbacks
* general ED4_create_SAI_selection_button function
* made SAI awar definitions local
* wrote general description for consensus calculation (hopefully replacing contents of consensus.ps, which is useless for more than 10 years now)
* added missing e4_consensus.hlp

640 lines of code changed in 16 files:

westram 2009-01-05 19:56 Rev.: 5711


* can show *.pdf from ARB help (done same way as *ps)
* arb.ps -> arb.pdf
* help history
- wrap around
- dont add pages twice
- get_full_qualified_help_file_name now returns "" if helpfilename is "" (previously return help directory, which was added to help history then)
- do not delete help-history when a 'HELP' button is pressed


2617 lines of code changed in 16 files:

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