April 2009 Commit Log

Number of Commits:
104
Number of Active Developers:
2
westram 2009-04-30 21:34 Rev.: 5885


* moved fast-aligner to separate library

4107 lines of code changed in 23 files:

westram 2009-04-30 11:05 Rev.: 5884


* EDIT4 depends on $(GL) and 'menus' (for pretty print)
* make 'wetc', 'help' and 'readseq' with 'e4'

4 lines of code changed in 1 file:

westram 2009-04-30 10:17 Rev.: 5883


* ISLAND_HOPPING is not part of NTREE

0 lines of code changed in 1 file:

westram 2009-04-30 10:03 Rev.: 5882


grml

1 lines of code changed in 1 file:

westram 2009-04-30 10:01 Rev.: 5881


* define variables GLLIBS and GL empty if OPENGL=0

6 lines of code changed in 1 file:

westram 2009-04-30 09:55 Rev.: 5880


* revived Makefile deleted in [5875] - make proto in ../Makefile depends on it
* added some info about AISC_COM directory

16 lines of code changed in 1 file:

westram 2009-04-30 09:15 Rev.: 5879


* Nameserver admin functions didn't work
- generally, due to wrong spelling of names file (if not using an add. ID)
- especially awtc_remove_arb_acc(), cause system call was missing (since years)
- removed '_' from replace expression (nameserver does not store the '_')
* changed error messages in GB_rename_file

15 lines of code changed in 2 files:

westram 2009-04-30 09:12 Rev.: 5878


* test perl scripts only if perllib updated since last test

23 lines of code changed in 3 files:

westram 2009-04-29 19:48 Rev.: 5877


* OSX patches (thx again to Matt Cottrell)
* added some notes about using bswap in PT-Server

146 lines of code changed in 5 files:

westram 2009-04-29 17:44 Rev.: 5876


typos

2 lines of code changed in 2 files:

westram 2009-04-29 17:44 Rev.: 5875


* tweaked errors/warnings printed by AISC code generator
* AISC expression 'IF $(KEY)'. When variable KEY is empty or undefined, AISC regards the expression always as TRUE.
- On OSX this resulted in a bus error, cause the test for operator '!' accessed the byte b4 the empty expression. Fixed.
* made many functions static / commented out unused code
* deleted unused files
* added dependencies (AISC/*pa) to com makefiles -> recompile if any .pa changes

201 lines of code changed in 10 files:

westram 2009-04-29 13:46 Rev.: 5874


* changed flavour of variables (addition to [5872])

14 lines of code changed in 1 file:

westram 2009-04-29 13:41 Rev.: 5873


* com interface build depends on date of generator

8 lines of code changed in 3 files:

westram 2009-04-29 12:20 Rev.: 5872


* Changed variable transfer to sub-makefiles
- most variables are now exported via environment (using SOURCE_TOOLS/export2sub or AISC/export2sub)
- only variables that contain different values for different sub-makefile-calls are passed by cl (e.g. cflags, MAIN)
- changed flavour of exported variables (recursively expanded -> simply expanded variables). Please use VAR := VALUE in Makefiles (not VAR = VALUE). See http://www.gnu.org/software/make/manual/html_node/Flavors.html#Flavors for details
* removed/fixed all undefined variables in Makefiles (using 'make --warn-undefined-variables')
* changed names of compile-logs generated in GDE subdir
* added target 'xmlin' (broken, print warning)

128 lines of code changed in 19 files:

westram 2009-04-29 11:50 Rev.: 5871


* automatically remove logfiles from old aborted compilations

12 lines of code changed in 1 file:

westram 2009-04-29 11:49 Rev.: 5870


* fixed warnings in GL/glAW/GLwDrawA.c
* no longer build GLwDrawA.o (not used)

79 lines of code changed in 2 files:

westram 2009-04-28 16:18 Rev.: 5869


* fixed illegal XtEventHandler-casts

14 lines of code changed in 2 files:

westram 2009-04-28 16:11 Rev.: 5868


* separated openGL parts from WINDOW library (it's nonsense to link openGL into all applications when only one application actually uses openGL)
- created GL/glWINDOW library (extending normal WINDOW library) and moved relevant code there
- created an interface header for applications needing access to Motif/X11 internals (aw_window_Xm_interface.hxx)
- RNA3D uses that interface header (instead of hardcoded links into ../WINDOW)
- AW_variable_update_struct went local (AW_button.cxx)
- some functions exported (aw_create_help_entry, aw_create_shell, aw_realize_widget). Needed by libglWINDOW

1778 lines of code changed in 29 files:

westram 2009-04-28 09:38 Rev.: 5867


* Sequence/Distance matrix (renamed and enabled for non-expert-mode)

2 lines of code changed in 1 file:

arb_build 2009-04-27 17:34 Rev.: 5866

Auto version upgrade to 4.32 by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2009-04-27 17:27 Rev.: 5865

* replaced REFRESH button but sort-toggle
- default sort order and display is same as before [5785]
* fixed format of columns in query result
* fixed several bugs (occurring in queries for long data, e.g. 'ali_genome/data')
* process bar for search
* updated help for result sorting
* slight changes to layout of query window
* search next relatives
- warn if not all relatives are in current DB (when moving to hitlist)
- format numbering of relatives (to improve sorting in query results)
* extended struct ad_item_selector
- added name of field containing unique id (aka 'name' for species)
- added function to get parent item
- set item_name_length to -1 (=unknown) -> detect dynamically if needed
* added GB_get_grandfather

692 lines of code changed in 16 files:

westram 2009-04-25 13:10 Rev.: 5864

* added GBS_shorten_repeated_data()
- use in DBbrowser, search+query + GB_dump()

75 lines of code changed in 5 files:

westram 2009-04-24 14:35 Rev.: 5863


* fixed bug introduced in [5839], causing trees to be deleted when they are modified

5 lines of code changed in 1 file:

westram 2009-04-24 13:38 Rev.: 5862


- fix for [5861]

1 lines of code changed in 1 file:

westram 2009-04-24 13:33 Rev.: 5861


- type fixes; mostly format arguments (warnings from 64bit-compile)

24 lines of code changed in 12 files:

westram 2009-04-24 13:31 Rev.: 5860


- added 2 more examples for nameservers with additional field

4 lines of code changed in 1 file:

westram 2009-04-24 12:30 Rev.: 5859


- one warning more

1 lines of code changed in 1 file:

westram 2009-04-24 12:25 Rev.: 5858


* fixed errors and warnings in perl scripts

40 lines of code changed in 8 files:

westram 2009-04-24 12:21 Rev.: 5857


* test-compile perl scripts

135 lines of code changed in 3 files:

westram 2009-04-24 09:47 Rev.: 5856


- fix compile error

10 lines of code changed in 2 files:

westram 2009-04-24 09:41 Rev.: 5855

* final followup to [5854]
- GB_get_error() -> GB_await_error() where appropriate
- fixed error handling in several functions

108 lines of code changed in 20 files:

westram 2009-04-24 09:38 Rev.: 5854

* followup to [5853] (more to follow)
- GB_get_error() -> GB_await_error() where appropriate (EDIT4, SECEDIT)

18 lines of code changed in 5 files:

westram 2009-04-24 09:36 Rev.: 5853

* followup to [5852] (more to follow)
- GB_get_error() -> GB_await_error() where appropriate (GENOM,GENOM_IMPORT)
- fixed error handling in several functions

42 lines of code changed in 8 files:

westram 2009-04-24 09:31 Rev.: 5852

* followup to [5851] (more to follow)
- GB_get_error() -> GB_await_error() where appropriate (MERGE)
- fixed error handling in several functions

81 lines of code changed in 8 files:

westram 2009-04-24 09:28 Rev.: 5851

* followup to [5842] (more to follow)
- GB_get_error() -> GB_await_error() where appropriate (NTREE)
- fixed error handling in several functions

105 lines of code changed in 16 files:

westram 2009-04-24 09:21 Rev.: 5850


* added xutils-dev (xmkmf, makedepend) to build dependencies

2 lines of code changed in 2 files:

westram 2009-04-24 09:06 Rev.: 5849


* added GBT_expect_(item/species/SAI/experiment)-functions. They do the same as their GBT_find_... similars, but export an error if the item is missing.
- use at some locations

87 lines of code changed in 7 files:

westram 2009-04-23 17:29 Rev.: 5848


* since [5827] EDIT4 folded SAIs quite strange and hided Sequences inside SAI-groups [fixed]

1 lines of code changed in 1 file:

westram 2009-04-23 10:31 Rev.: 5847

* added GB_unlink_or_warn + use where possible

41 lines of code changed in 10 files:

westram 2009-04-23 09:52 Rev.: 5846

* final ORS removal (finishes [5221] and [5259])

4 lines of code changed in 17 files:

westram 2009-04-23 08:47 Rev.: 5845


* AISC_COM/AISC/Makefile: new target 'pregenerate' creates all code that might be linked into $(ARBHOME)/INCLUDE
* NAMES_COM/Makefile + PROBE_COM/Makefile: previously empty target 'depends' now makes 'AISC/Makefile pregenerate'
* Makefile: target 'depends' no longer compiles complete com interfaces

39 lines of code changed in 4 files:

westram 2009-04-23 08:38 Rev.: 5844


* AISC code generator refuses to work with empty input files
* put a comment into the two existing empty input files

51 lines of code changed in 4 files:

westram 2009-04-23 06:49 Rev.: 5843


- undo [4680]

2 lines of code changed in 1 file:

westram 2009-04-22 14:09 Rev.: 5842


* like [5839], but AWT, AWTC, AWTI and WINDOW

151 lines of code changed in 23 files:

westram 2009-04-22 12:40 Rev.: 5841

* removed PH_ prefix

34 lines of code changed in 1 file:

westram 2009-04-22 12:40 Rev.: 5840

- depends updated

5 lines of code changed in 1 file:

westram 2009-04-22 12:13 Rev.: 5839


* followup to [5824] (more to follow)
- GB_get_error() -> GB_await_error() where appropriate (ARBDB mostly)
- fixed error handling in several functions

577 lines of code changed in 24 files:

westram 2009-04-22 11:39 Rev.: 5838


- warning fixed

8 lines of code changed in 1 file:

westram 2009-04-22 11:34 Rev.: 5837


* fixed error handling in classes AP_tree + AP_tree_root
- many functions returned GB_ERROR, but NEVER failed
- some functions now crash instead of reporting error (AP_tree::moveTo, AP_tree::swap_assymetric) when they are used in an illegal way.
* when using the current tree, sequence quality calculation removed that tree, if no species was marked and 'marked species only' was checked
- fixed that problem in sequence quality (using GBT_remove_leafs)
- column statistic is completely based on AP_tree(_root), can't fix there.
* Instead fixed behavior of AP_tree/AP_tree_root
- when tree gets emptied by tree operations, AP_tree_root only remembers to delete the tree from DB
- saveTree() finally deletes previously remembered tree

643 lines of code changed in 15 files:

arb_build 2009-04-22 10:11 Rev.: 5836

Auto version upgrade to 4.31 by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2009-04-22 10:09 Rev.: 5835


- when no DB selected in intro-window + 'open selected' was pressed -> arb crashed

2 lines of code changed in 1 file:

westram 2009-04-22 09:46 Rev.: 5834


* novice mode -> expert mode (thx to Elmar Pruesse)
- expert mode automatically propagates to clients
- reassigned which items are visible in non-expert-mode

225 lines of code changed in 20 files:

westram 2009-04-22 07:29 Rev.: 5833


- moved cleanup-subtarget of 'relocated' to 'reloc_clean'

4 lines of code changed in 1 file:

westram 2009-04-21 10:26 Rev.: 5832


* result params 'removed' and 'groups_removed' are optional now (GBT_remove_leafs)

5 lines of code changed in 1 file:

westram 2009-04-21 10:12 Rev.: 5831


- one case less where GB_dump() crashes

4 lines of code changed in 1 file:

westram 2009-04-21 08:25 Rev.: 5830

* moved remove_leafs() to GBT_remove_leafs() (NT_extern.cxx -> adtools.c)

136 lines of code changed in 5 files:

westram 2009-04-19 18:36 Rev.: 5829


* included some patches for OSX (thx to Matt Cottrell)
* added global switch LINK_STATIC
* added script which checks for tools needed to compile ARB
* typo CCPLIB->CPPLIB

198 lines of code changed in 23 files:

westram 2009-04-19 18:35 Rev.: 5828


* changed ulong->ULONG and uint->UINT (ulong/uint are missing under OSX)

52 lines of code changed in 13 files:

westram 2009-04-18 11:33 Rev.: 5827

* GBS_hash_do_loop() and GBS_hash_do_sorted_loop() now always take a 'client_data' param
* fixed error handling in several functions
* fixed memory leaks in GBS_merge_tagged_strings and GBS_string_eval_tagged_string
* removed several globals
- gbs_save_hash_strstruct
- g_bs_merge_result, g_bs_merge_sub_result, g_bs_collect_tags_hash
- gbs_scan_db_data
- isits (parsimony)
- st_delete_species_st_ml
* global 'nt' -> GLOBAL_NT
* global_combineCount -> AP_sequence::global_combineCount
* filter params changed from AW_CL to adfiltercbstruct* where possible

644 lines of code changed in 42 files:

arb_build 2009-04-16 14:29 Rev.: 5826

Auto version upgrade to 4.30 by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2009-04-16 14:21 Rev.: 5825


* replaced GB_entry/GB_create/GB_search+GB_read_XXX by GBT_read_XXX
* improved error handling in many functions

1173 lines of code changed in 69 files:

westram 2009-04-16 08:47 Rev.: 5824

* renamed GB_expect_error into GB_await_error
- GB_expect_error was too similar to GB_export_error
- GB_await_error now clears the error buffer!
* declared GB_get_error() deprecated
- Problem is: after calling GB_get_error it is undefined, whether the error message belongs to the caller or still to the error buffer
- GB_have_error() and GB_await_error() - maybe combined - are the recommended replacement

47 lines of code changed in 17 files:

westram 2009-04-15 13:58 Rev.: 5823

* more uniform function names
- EXP_create_experiment_rel_experiment_data -> EXP_find_or_create_experiment_rel_exp_data
- EXP_find_experiment_rel_experiment_data -> EXP_find_experiment_rel_exp_data
- GBT_create_SAI -> GBT_find_or_create_SAI
- GBT_create_item -> GBT_find_or_create_item_rel_item_data
- GBT_create_species -> GBT_find_or_create_species
- GBT_create_species_rel_species_data -> GBT_find_or_create_species_rel_species_data

64 lines of code changed in 20 files:

westram 2009-04-15 13:13 Rev.: 5822


* prototypes for [5821]

6 lines of code changed in 1 file:

westram 2009-04-15 11:41 Rev.: 5821

* added GBT_find_item_rel_item_data() and GBT_create_unique_item_identifier()
* GBT_check_alignment
- fixed error handling
- failsafe name generation (now creates 'autoname.###' instead of 'unknown_###')

144 lines of code changed in 1 file:

westram 2009-04-14 19:30 Rev.: 5820

* changed type of GBT_read_gene_sequence_and_length's result param (int->size_t)

4 lines of code changed in 3 files:

westram 2009-04-14 19:20 Rev.: 5819

* primer design and probe design still used old way to access gene sequence

107 lines of code changed in 2 files:

westram 2009-04-14 19:19 Rev.: 5818


* removed dead code

0 lines of code changed in 1 file:

westram 2009-04-14 19:15 Rev.: 5817

* AWT_pro_a_nucs_convert: changed param types int->size_t

5 lines of code changed in 2 files:

westram 2009-04-14 18:39 Rev.: 5816

* fixed status-gauge in consensus calculation (ED4-startup)

29 lines of code changed in 5 files:

westram 2009-04-13 21:44 Rev.: 5815


* GBT_get_configuration_names_and_count() now automatically repairs configurations w/o legal name
- simplified awt_create_selection_list_on_configurations_cb() and awt_create_string_on_configurations()
* nt_rename_configuration: fixed double free
* aw_string_selection: possible to pass NULL for param 'value_list'

54 lines of code changed in 4 files:

westram 2009-04-13 11:47 Rev.: 5814


* fixed memory leak (GEN_positionPtr used free() instead of GEN_free_position())
* cleanup static dynamic data (after import)

32 lines of code changed in 4 files:

westram 2009-04-13 11:41 Rev.: 5813


* debug output

3 lines of code changed in 1 file:

westram 2009-04-13 11:41 Rev.: 5812


* refuse to import flatfiles containing 'CONTIG'. Maybe will be added in the future..

17 lines of code changed in 2 files:

westram 2009-04-13 11:37 Rev.: 5811


* fixed undefined behavior at EOF (when testing for DOS linefeed)

5 lines of code changed in 1 file:

westram 2009-04-13 11:35 Rev.: 5810


* free->delete[]

2 lines of code changed in 1 file:

westram 2009-04-13 11:35 Rev.: 5809


* added template custom_dealloc_ptr<> providing smartpointers with custom deallocation function
* fixed compilation of smartpointer trace code

44 lines of code changed in 1 file:

westram 2009-04-12 19:53 Rev.: 5808

* forgot try/catch

12 lines of code changed in 1 file:

westram 2009-04-12 19:50 Rev.: 5807

* no longer misuse exceptions to return result (in parseCounter)
* added non-throwing methods to Parser

60 lines of code changed in 2 files:

westram 2009-04-12 18:31 Rev.: 5806

* Feature::addQualifiedEntry throws error, if value is "\"" (should no longer occur, but just in case)
* quoted multiline qualifier entries are now detected even if first line only contains the opening quotes
* type: expection -> exception

40 lines of code changed in 3 files:

westram 2009-04-11 14:55 Rev.: 5805


* genome importer
- fixed status display during import
- show file only once in import-warnings
- added 'REMARK' to genbank description (imported into field 'refremark')
- EMBL-RX ids are now parsed in detail (and rejected if they are unknown)

103 lines of code changed in 6 files:

westram 2009-04-11 14:54 Rev.: 5804


* assert correct gauge

2 lines of code changed in 1 file:

westram 2009-04-11 14:52 Rev.: 5803


* added C++-Wrapper for regular expressions (REGEXPR.a)

239 lines of code changed in 6 files:

westram 2009-04-11 14:47 Rev.: 5802


* FileBuffer: added toggle to suppress output of filename

26 lines of code changed in 2 files:

westram 2009-04-11 14:44 Rev.: 5801


* GBS_read_dir() now only returns files

7 lines of code changed in 1 file:

westram 2009-04-10 19:15 Rev.: 5800


* translate_gene_sequence() defaults to EMBL table 1 (if no codon table specified) and to codon_start 0
* added fixEmptyQualifiers():
- searches for empty data and replaces it by '<empty>' (currently only done for qualifier 'replace')
- called before writing features to DB
* silently skip empty lines before or after sections

46 lines of code changed in 7 files:

westram 2009-04-10 19:14 Rev.: 5799


- 'up does 'checks' and 'links'

2 lines of code changed in 1 file:

westram 2009-04-10 09:52 Rev.: 5798


- finishes [5797]

3 lines of code changed in 1 file:

westram 2009-04-10 09:47 Rev.: 5797

* rewrote parts of internal buffer code (GB_get_buffer)
- removed direct access
- renamed a few functions

150 lines of code changed in 8 files:

westram 2009-04-10 09:04 Rev.: 5796


* fixed #160
- put actual question into awar and bind button in aw_question windows to that awar (should be no problem, cause only one question can be active at a time)
- optimized question-window-hash: different messages of same length reuse one question window.

32 lines of code changed in 1 file:

westram 2009-04-09 14:41 Rev.: 5795


* searching for duplicate entries now searches for unique entries, if 'that dont match the query' is selected

38 lines of code changed in 2 files:

westram 2009-04-09 12:45 Rev.: 5794


- cosmetic

4 lines of code changed in 3 files:

westram 2009-04-09 12:44 Rev.: 5793


* #156: fixed broken tree-size display (introduced with [5285])

1 lines of code changed in 1 file:

westram 2009-04-09 11:01 Rev.: 5792

* removed adReference.c link

0 lines of code changed in 1 file:

arb_build 2009-04-09 10:56 Rev.: 5791

Auto version upgrade to 4.29 by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2009-04-09 10:56 Rev.: 5790

* when searching for duplicates in other DB (merge tool), respect the setting of 'that match/that dont match'

11 lines of code changed in 2 files:

westram 2009-04-09 10:30 Rev.: 5789

* completely removed GB_STRDUP (as started in [5725])
* removed dead code

18 lines of code changed in 8 files:

westram 2009-04-09 09:57 Rev.: 5788

* rewrote regular expression code using POSIX extended regular expressions (from glibc)
- removed GBS_regsearch(), cause GBS_regmatch() does no longer return a heap-copy of the match. Instead it returns a pointer to the match and the length of the match.
- added functions for matching with precompiled regexpr (GBS_compile_regexpr,GBS_regmatch_compiled) or precompiled matcher (GBS_compile_matcher, GBS_string_matches_regexp)

666 lines of code changed in 19 files:

westram 2009-04-08 09:49 Rev.: 5787

* moved string match/replace related functions from adstring.c to admatch.c

883 lines of code changed in 11 files:

arb_build 2009-04-03 12:24 Rev.: 5786

Auto version upgrade to 4.28 by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2009-04-03 11:56 Rev.: 5785



* ACI and regular expressions now usable in query expressions
* track hit information (why something came into hitlist)
* improved query
- analyze query at start, simpler code at search
- !(A op B op C) -> (!A op' !B op' !C); needed for proper hit-info; allows early-stop
- query stops early (e.g. if A is false in (A and B), B is no longer tested)
- added '[all fields]' pseudo field (needed for completeness; !('any field'=='*a*') <=> 'all fields'!='*a*')
* fixed a bug in merge tool (when searching for duplicate fields/words of species listed in left hitbox): if identical content was found for a not-listed item, other listed items were not even tested, whether they contain the same content.
* regexpr search bugfix
- searching for /Halo/ after searching for /Halof/ did not recompile the regexpr
* fixed ticket #10
* implemented ticket #147
* replaced AW_window::selection_list_to_species_set by more flexible method selection_list_to_hash which as well allows access to text of selection boxes
- removed type GBDATA_SET + functions (now unused)
* documentation
- general help page for searching; linked to this page from species- and gene-search helppages
- help for "find duplicated fields" (normal and in merge tool); linked to from main search-/merge-page

1165 lines of code changed in 22 files:

westram 2009-04-02 17:43 Rev.: 5784


* mark long branches
- allow to specify a minimum absolute diff

47 lines of code changed in 4 files:

westram 2009-04-02 13:22 Rev.: 5783


* added 2 taxonomy ACIs

3 lines of code changed in 1 file:

westram 2009-04-01 16:58 Rev.: 5782


* fixed spelling of 'occurrence'

71 lines of code changed in 30 files:

March 2009 »

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