December 2008 Commit Log

Number of Commits:
83
Number of Active Developers:
2
westram 2008-12-31 14:52 Rev.: 5710


* fix #149
- Decompress *.ps.gz to /tmp/...ps, instead of piping into gv

26 lines of code changed in 1 file:

westram 2008-12-31 13:27 Rev.: 5709


- made depends for [5708]

778 lines of code changed in 48 files:

westram 2008-12-31 13:24 Rev.: 5708


* backtrace gets printed to console from
- GB_internal_error
- SIGSEGV (currently GB_login installs the handler using GBK_install_SIGSEGV_handler. Most likely needs to be called manually for some executables)
- GBK_terminate
* added GBK_dump_backtrace, GBK_terminate and GBK_assert_msg
* Default assertion dumps backtrace now
* added -rdynamic and --export-dynamic compiler/linker flags, leaving symbols in code. This raises size of executables by approx. 8%, but we will get meaningful backtraces from users.
* removed old inactive SIGSEGV code
* replaced GB_CORE either by xx_assert() or GBK_terminate()
* removed GBS_do_core (was used conditionally together with GB_CORE)
* disabled crash provoked via arb_panic (using 'core' as savename)
* Linkage changed:
- The future plan is to try some kind of emergency save on open DBs when GBK_terminate or similar is called.
- Since arb_assert calls GBK_terminate this affects ALL applications.
- The drawback is all executables have to be linked vs ARBDB (done with: arb_help2xml and arb_convert_aln, all others already had ARBDB linked)
- Molphy uses #define SIMPLE_ARB_ASSERT before including arb_assert.h
* renamed define GBL_INCLUDED -> ADLOCAL_H
* added arbdb_base.h (defining some types and including ad_k_prot.h, which contains all GBK_*-functions). Intended as minimal and seldom changed interface to libARBDB as needed by arb_assert(), to keep build dependencies low.
* arb_assert.h now automatically includes arbdb_base.h
* trigger compilation of test functions in parsimony via define

538 lines of code changed in 53 files:

westram 2008-12-30 19:14 Rev.: 5707

* added '-c comment' switch to aisc_mkpt (writes comment to header)
* removed patchlev.h (really not used)
* less calls to (f)printf/fputs

107 lines of code changed in 8 files:

westram 2008-12-30 07:38 Rev.: 5706

* added gbs_vglobal_string_copy and used it to simplify GBS_global_string_copy and GB_warning
* free oversized GBS_strstruct's
* skip unneeded call to strlen in GBS_strnprintf

49 lines of code changed in 1 file:

westram 2008-12-29 18:06 Rev.: 5705

- removed more outdated code

0 lines of code changed in 54 files:

westram 2008-12-29 17:34 Rev.: 5704


- removed demo and test targets (completely out of date)

3 lines of code changed in 21 files:

westram 2008-12-28 23:02 Rev.: 5703


- target 'proto' now only updates if necessary
- updated prototypes

2 lines of code changed in 2 files:

westram 2008-12-28 22:27 Rev.: 5702


- dead "code"

0 lines of code changed in 1 file:

boehnel 2008-12-28 20:30 Rev.: 5701

* Increasing QUERYHITSHASHSIZE to avoid realloc() (needed for SSUParc'95, cttgtacacaccgcccgt, 5 mismatches)

1 lines of code changed in 1 file:

boehnel 2008-12-28 17:55 Rev.: 5700

* Removing OpenDataBase() from main to LoadSpecies(). Arbdb access is
* now only needed in LoadSpecies() and since we can't close arbdb, this
* saves us lots of memory when we're not building the tree.

7 lines of code changed in 2 files:

boehnel 2008-12-28 17:25 Rev.: 5699

* Removing #ifdef DEVEL_JB and making the code default

17 lines of code changed in 1 file:

westram 2008-12-28 17:09 Rev.: 5698


- fixed syntax for error messages created by GB_export_IO_error()
- redesign comment

21 lines of code changed in 5 files:

boehnel 2008-12-28 17:04

* removing COMPRESSSEQUENCEWITHDOTSANDHYPHENS #ifdefs and making it default

5 lines of code changed in 6 files:

westram 2008-12-28 16:54 Rev.: 5695


* added functions to handle temporary files
- GB_unique_filename (used pid of current process. before in most cases $ARB_PID was used, but that is only useful for arb_panic and arb_clean functionality. For normal tempfiles pid is the better choice - otherwise two processes of one ARB instance could generate the same tempfile name)
- GB_create_tempfile
- GB_fopen_tempfile
- GB_is_privatefile (function for testing whether tempfiles have correct permissions - especially those tempfiles pre-generated by GB_create_tempfile and overwritten later by a shell script)
* added GB_read_fp (similar to GB_read_file, but works on open filepointer)
* added GB_append_suffix
* added GB_remove_on_exit (removes files at program exit)
* rewrote all functions creating temporary files. Files are opened in private mode (user only read/write) now and are properly removed after usage or when program exits.
* bug-fixes:
- GB_size_of_file(NULL)
- GB_split_full_path (returned name as suffix if no suffix was present. Now returns NULL)
- awt_get_selected_fullname returned /print.ps (instead of using cwd)
* replaced String() by strdup() in GDE
* fixed several calls to GB_unlink()
* removed GB_getuid / GB_getpid
* tweaked arb_panic (panicfile is private now! modified output and added cmd killall)
* help-search now ignores comment lines in helpfiles
* rewrote exporter (cause it was impossible to correctly handle tmp-files). Automatically appends suffix to outputfilename.
* improved error handling in several functions
* file selection boxes refresh automatically if directory modtime changes
* When exporting frequencies from arb_phylo, dont write 3 files to tmp (of which 2 were always empty) - write only the one with content. I dont know what the file is good for, but since it is removed on exit now, it doesnt do any harm.

1666 lines of code changed in 30 files:

boehnel 2008-12-28 16:11 Rev.: 5694

Bugfix

1 lines of code changed in 1 file:

boehnel 2008-12-28 15:38 Rev.: 5693

* changed return type of CompressSequenceWithDotsAndHyphens
* removed use of CacheLoadData when compiling with COMPRESSSEQUENCEWITHDOTSANDHYPHENS to reduce memory usage
* introduced ALLOWDOTSINMATCH


127 lines of code changed in 6 files:

westram 2008-12-28 14:23 Rev.: 5692


* distinguish between create_all_awars() in ARB_NT and ARB_PARS
* describe where to create awars

36 lines of code changed in 4 files:

westram 2008-12-28 13:38 Rev.: 5691


- create local input mask directory w/o warning

9 lines of code changed in 1 file:

westram 2008-12-28 13:17 Rev.: 5690


- fail on slow hash (but not for very small hashes)

4 lines of code changed in 1 file:

westram 2008-12-27 22:41 Rev.: 5689

- first init gb_main, then use it to open transaction :)

2 lines of code changed in 1 file:

westram 2008-12-27 22:40 Rev.: 5688

- ignore bin dir

1 lines of code changed in 1 file:

boehnel 2008-12-27 17:31 Rev.: 5687

Fixed indentation

743 lines of code changed in 1 file:

boehnel 2008-12-26 23:56 Rev.: 5686

Bugfix for databases without Ecoli Sequences.


21 lines of code changed in 2 files:

boehnel 2008-12-26 23:40 Rev.: 5685

Added a comment.

4 lines of code changed in 1 file:

boehnel 2008-12-26 23:34 Rev.: 5684

Save full names of Species and Ecoli alignment into *.arb.pan file, to
avoid arbdb access when not building tree. Saves lots of Memory

75 lines of code changed in 3 files:

boehnel 2008-12-26 21:42 Rev.: 5683

Fixed indentation.

32 lines of code changed in 1 file:

boehnel 2008-12-26 20:38 Rev.: 5682

Fixed indentation

13 lines of code changed in 1 file:

boehnel 2008-12-26 20:28 Rev.: 5681

Removed checkpointing when compiling with
COMPRESSSEQUENCEWITHDOTSANDHYPHENS

2 lines of code changed in 1 file:

boehnel 2008-12-26 20:26 Rev.: 5680

Removed checkpointing when compiling with
COMPRESSSEQUENCEWITHDOTSANDHYPHENS

18 lines of code changed in 4 files:

boehnel 2008-12-26 18:19 Rev.: 5679

Added a comment
Removed #ifdef DEVEL_JB #else (...) #endif - GBS_stropen(...) works
very well

4 lines of code changed in 1 file:

boehnel 2008-12-26 18:13

Changeing COMPRESSSEQUENCEWITHDOTSANDHYPHENS to speed up building
process and reduce memory consumption

23 lines of code changed in 2 files:

westram 2008-12-25 16:31 Rev.: 5676


* fixed bug in GBS_read_dir (produced wrong paths)
* Select add. field: 'None' -> 'None (only 'acc')'

6 lines of code changed in 2 files:

westram 2008-12-25 14:03 Rev.: 5675


- removed automatic timestamps (the best they were good for, were vc-conflicts)

0 lines of code changed in 159 files:

westram 2008-12-23 10:05 Rev.: 5674


- gcc 4.3.2 fix

1 lines of code changed in 1 file:

westram 2008-12-23 09:37 Rev.: 5673


* added GBS_global_string_to_buffer + GBS_last_global_string_size
* avoid intense buffer usage in path functions (introduced by [5648])
* GBS_global_string_copy: use GB_strduplen with size generated by gbs_vglobal_string
* aw_str_2_label:
- always called twice with same arguments (due to macro-callers)
- store result internally and reuse it
* store config in NTREE-NDS now only stores current 10 entries

96 lines of code changed in 5 files:

westram 2008-12-23 07:35 Rev.: 5672


* fixed target 'bclean' and renamed into 'binclean'
* added target 'objclean'
* spelling in 'help'

18 lines of code changed in 1 file:

westram 2008-12-22 19:52 Rev.: 5671


* dont create existing directories

10 lines of code changed in 1 file:

westram 2008-12-22 19:40 Rev.: 5670

* fix GB_split_full_path:
- path w/o trailing '/'
- name w/o trailing '.'
- suffix w/o leading '.'
* rewrote GB_create_directory(): use POSIX instead of shell

26 lines of code changed in 2 files:

westram 2008-12-22 17:44 Rev.: 5669


* fixed compare of floats

3 lines of code changed in 1 file:

westram 2008-12-22 17:34 Rev.: 5668


* added GB_system (returning GB_ERROR)
* replaced all occurances of system in ARBDB
* force results to be used for some functions using GB_system (unused result warnings not fixed yet)

73 lines of code changed in 6 files:

westram 2008-12-22 15:54 Rev.: 5667


- added transfig

2 lines of code changed in 1 file:

westram 2008-12-22 15:53 Rev.: 5666


- any existing arb*test*.c[xx] file is automatically compiled. Use this to write quick test programs w/o the need to change the Makefile

3 lines of code changed in 1 file:

westram 2008-12-22 14:48 Rev.: 5665

- removed test code

0 lines of code changed in 3 files:

westram 2008-12-21 16:02 Rev.: 5664

* Removed arb_ale relicts
* Removed useless scripts in util

16 lines of code changed in 37 files:

westram 2008-12-21 15:20 Rev.: 5663


- added new target 'relocation'. Make it to fix things w/o complete rebuild, after you have relocated the ARBHOME directory.

8 lines of code changed in 1 file:

westram 2008-12-19 12:57 Rev.: 5662


* fixed memleak introduced with [5661]

4 lines of code changed in 1 file:

westram 2008-12-19 12:23 Rev.: 5661


* added GB_split_full_path()
* AWT_append_suffix and AWT_get_suffix: renamed, made local, rewritten
* changed a few filename generations



70 lines of code changed in 6 files:

westram 2008-12-18 18:43 Rev.: 5660


- generally use GBT_read_name() where possible
- recoded several functions

551 lines of code changed in 40 files:

westram 2008-12-18 17:53 Rev.: 5659


- moved DB access for experiments to ARBDB

91 lines of code changed in 11 files:

westram 2008-12-18 13:10 Rev.: 5658

rm empty dirs

0 lines of code changed in 22 files:

westram 2008-12-18 13:07 Rev.: 5657


byebye SEER

3 lines of code changed in 6 files:

westram 2008-12-18 00:24 Rev.: 5656


elmar:

awt_add_new_changekey_to_keypath gibt eine Warnung als GB_ERROR zurueck.
Seit r5625 loest ein GB_ERROR einen rollback aus, d.h. z.B. import und
merge gehen nicht mehr.

4 lines of code changed in 1 file:

westram 2008-12-17 11:58 Rev.: 5655


* GBT_read_name:
- returns 'const char *' now
- never returns NULL (instead returns '<unnamed species>' etc.)
* GB_read_key_pntr/GB_read_key:
- never returns NULL (instead returns '<invalid key quark=##>')
- same for GB_read_key()

155 lines of code changed in 13 files:

boehnel 2008-12-16 11:36 Rev.: 5654

changing prefix from "PT_" to "PP_" (for PtPan)


6 lines of code changed in 1 file:

westram 2008-12-16 11:35 Rev.: 5653


MAXBOND erwartet laut PT.aisc ein double, kein int. Der Wert wird IIRC
ohnehin nicht beachtet, aber er sollte schon die richtige groesse haben.
Sonst GB_CORE in AISC/C/client.c:645.

thx 2 elmar

1 lines of code changed in 1 file:

boehnel 2008-12-16 10:57 Rev.: 5652

Prefixed some functions with "PT_" to avoid same name.

removed a TODO

7 lines of code changed in 1 file:

westram 2008-12-16 10:37 Rev.: 5651


* cleanup

0 lines of code changed in 1 file:

westram 2008-12-16 10:37 Rev.: 5650


* added warning

3 lines of code changed in 1 file:

westram 2008-12-16 10:36 Rev.: 5649


* for some unknown reason makedepend left a Makefile.bak in ptpan. added code to remove it
* dont mask known makedepend flags

3 lines of code changed in 2 files:

westram 2008-12-16 10:34 Rev.: 5648


* moved AWT_get_full_path() + AWT_concat_full_path() to ARBDB
* rewrote GBS_read_dir() using opendir/readdir (instead of calling 'ls')
* changed result of GB_is_...(): int -> GB_BOOL, added GB_is_readablefile()
* added GB_path_in_ARBLIB() + GB_path_in_ARBHOME()
* removed GBS_free_names() (same as GBT_free_names())
* Pressing 'Auto detect' again, selects next matching import filter. added some advices


564 lines of code changed in 18 files:

westram 2008-12-15 14:15 Rev.: 5647


* typo
* updated prototypes

4 lines of code changed in 2 files:

westram 2008-12-15 13:00 Rev.: 5646


* replaced GB_mergesort() and GBT_quicksort() by GB_sort()
* implemented GB_sort() using qsort(). current qsort is implemented as intronsort, which has mean AND worst case complexity O(N*log N), w/o the memory complexity of mergesort.
* fixed constness of compare function type (hash and array)
* added and using standard comparators (GB_string_comparator, GBS_HCF_sortedByKey)
* fixed/reimplemented several custom comparators


207 lines of code changed in 19 files:

boehnel 2008-12-14 11:02 Rev.: 5645

save compressed aligment of species (with dots and hyphens) to speed up
probe_match

increaced filename buffer


12 lines of code changed in 1 file:

boehnel 2008-12-14 10:56 Rev.: 5644

Fixing calculation of ps_SeqDataCompressedSize
removing debug output

2 lines of code changed in 1 file:

boehnel 2008-12-14 10:43

save compressed aligment of species (with dots and hyphens) to speed up
probe_match


218 lines of code changed in 4 files:

boehnel 2008-12-14 10:43 Rev.: 5639

save compressed aligment of species (with dots and hyphens) to speed up
probe_match

150 lines of code changed in 1 file:

westram 2008-12-10 12:41 Rev.: 5638


- make perl was broken since [5637]

11 lines of code changed in 1 file:

westram 2008-12-06 13:06 Rev.: 5637

* write-protect generated ARB.xs to protect myself from changing it
* type-fix

4 lines of code changed in 2 files:

westram 2008-12-06 12:40 Rev.: 5636

* added handcoded perl replacements for GBT_read_int + GBT_read_float
* added "generated"-note to ARB.xs

42 lines of code changed in 2 files:

westram 2008-12-06 01:52 Rev.: 5635

* class GB_transaction:
* replaced abort() by close(error). close() is similar to GB_end_transaction()

106 lines of code changed in 19 files:

westram 2008-12-05 18:50 Rev.: 5634


* Added __ATTR__USERESULT
* attributed some functions in ARBDB with __ATTR__USERESULT.
Should be done with all functions returning GB_ERROR, to fix error handling
* Removed some useless GB_ERROR return types (always returning NULL)

62 lines of code changed in 11 files:

westram 2008-12-05 12:04 Rev.: 5633


* svnignore .a
* fixed depends

214 lines of code changed in 1 file:

westram 2008-12-04 15:09 Rev.: 5632


awt_scanner_scan_rek uses GBS_strstruct

32 lines of code changed in 1 file:

westram 2008-12-04 15:09 Rev.: 5631


added ctags, removed indent

1 lines of code changed in 1 file:

westram 2008-12-04 15:08 Rev.: 5630


* fixed a few gcc 4.3.2 warnings

43 lines of code changed in 12 files:

westram 2008-12-04 14:42 Rev.: 5629


* removed redundant sections
* added PTPAN=2 (compile both, use old)


44 lines of code changed in 2 files:

westram 2008-12-03 19:53 Rev.: 5628


* removed functions GBT_search_[string,int,float]. They implemented mostly the same as
GBT_read_[string,int,float]2.
* changed GBT_read_[string,int,float]2 to GBT_readOrCreate_[string,int,float]
* Added GB_searchOrCreate_[string,int,float] = find db entry or create one with default
* GBT_write_[string,int,float] now asserts that the DB field is singular (i.e. no other field
with the same key exists in the fields container).
Avoids a common error: Not testing whether the field already exists, creating a duplicate of
the field, but continue reading the first instance of the field.
* changed result type of GBT_read_int and GBT_readOrCreate_int from 'long' to 'long*'. Usage needs
additional deferenciation, but transports error-status by returning 0. Not handling such an error
results in SIGSEGV now.
Same for GBT_read_float, GBT_readOrCreate_float (double -> double*).
* added GBT_readOrCreate_char_pntr, GBT_read_char_pntr and GBT_read_as_string
* reimplemented GBT_create_species, GBT_create_species_rel_species_data, and GBT_create_SAI
using new function GBT_create_item.
* GBT_set_default_alignment did not do anything if "presets/use" was missing. fixed
* removed local function gbt_save_entry (same as GBT_write_string)
* gb_search() returns NULL and sets error when field to create exists with a different type.
Before it deleted the old field and created a new one.

546 lines of code changed in 19 files:

westram 2008-12-03 19:52 Rev.: 5627

static scope

1 lines of code changed in 2 files:

westram 2008-12-03 19:10 Rev.: 5626

static scope

4 lines of code changed in 3 files:

westram 2008-12-03 13:58 Rev.: 5625

* added convenience functions:
- GB_end_transaction()
- GB_end_transaction_show_error()
- AW_window::hide_or_notify()
* improved error handling in several functions
* cleaned up obsolete code

1940 lines of code changed in 54 files:

boehnel 2008-12-02 08:33 Rev.: 5624

changing indentation of probe match results (for species ids >99999)

3 lines of code changed in 1 file:

boehnel 2008-12-02 08:12 Rev.: 5623

Fixed sorting bug (rounding error)
Added some asserts

12 lines of code changed in 1 file:

November 2008 »

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