January 2007 Commit Log

Number of Commits:

42

Number of Active Developers:

2

westram 2007-01-27 13:47 #42 Rev.: 4306

- trailing backslashes

2 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: export_format.hlp (+2)

westram 2007-01-27 13:47 #41 Rev.: 4305

- description of new parameter 'forcenl' for cmd 'format'
- help for 'split', 'streams', 'trace', 'define', 'do'

38 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: commands.hlp (+38 -4)

westram 2007-01-27 13:46 #40 Rev.: 4304

- description of new export parameters

15 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: arb_export.hlp (+15 -5)

westram 2007-01-27 13:31 #39 Rev.: 4303

- depends updated

17 lines of code changed in 4 files:

• ARB_GDE: Makefile (+1)
• AWTI: Makefile (+4)
• EDIT4: Makefile (+10)
• WINDOW: Makefile (+2)

westram 2007-01-27 13:30 #38 Rev.: 4302

- 'tmp'->'ambig'

2 lines of code changed in 1 file:

• lib/sellists: mod_fields.sellst (+2 -2)

westram 2007-01-27 13:30 #37 Rev.: 4301

- new gui elements (compression, filter, ...)

26 lines of code changed in 1 file:

• lib/pictures/awt: export_db.fig (+26 -18)

westram 2007-01-27 13:30 #36 Rev.: 4300

- 'medline'->'medline_id', 'gene_pos'->'nuc_rp', 'pubmed'->'pubmed_id'

20 lines of code changed in 9 files:

• lib/import: ebi_mod.ift (+2 -2), ebi_old.ift (+2 -2), ebi_old2.ift (+3 -3), genbank.ift (+3 -3), genbank_multi.ift (+3 -3), genbank_old.ift (+1 -1), genbank_prot_from_translation_field.ift (+1 -1), rdp.ift (+2 -2)
• lib/import/nonformats: longebi.ift (+3 -3)

westram 2007-01-27 13:29 #35 Rev.: 4299

- suffix lowercase

2 lines of code changed in 2 files:

• lib/export: paup.eft (+1 -1), phylip.eft (+1 -1)

westram 2007-01-27 13:29 #34 Rev.: 4298

- export more datafields
- conditional export (skip entry if field not present in DB)

14 lines of code changed in 1 file:

• lib/export: genbank.eft (+14 -11)

westram 2007-01-27 13:29 #33 Rev.: 4297

- old gcg format (but no longer pseudo embl format)

23 lines of code changed in 1 file:

• lib/export: gcg_8x.eft (new 23)

westram 2007-01-27 13:29 #32 Rev.: 4296

- was a strange kind of embl export
- now exports "new" gcg 9.x++ format

4 lines of code changed in 1 file:

• lib/export: gcg.eft (+4 -11)

westram 2007-01-27 13:29 #31 Rev.: 4295

- no longer necessary (remove gaps supported generally)

0 lines of code changed in 2 files:

• lib/export: fasta_noalign.eft (del), fasta_wide_noalign.eft (del)

westram 2007-01-27 13:28 #30 Rev.: 4294

- use 'export_sequence'-ACIfunction

7 lines of code changed in 4 files:

• lib/export: fasta.eft (+2 -2), fasta_NCBI_sequin.eft (+1 -1), fasta_wide.eft (+2 -2), pir.eft (+2 -2)

westram 2007-01-27 13:27 #29 Rev.: 4293

- wrote embl exporter (previously only pseudo-embl-export gcg.eft existed)

34 lines of code changed in 1 file:

• lib/export: embl.eft (new 34)

westram 2007-01-27 13:27 #28 Rev.: 4292

- changed suffix (PHYL->AE2)

1 lines of code changed in 1 file:

• lib/export: ae2.eft (+1 -1)

westram 2007-01-27 13:26 #27 Rev.: 4291

- aw_status(0.0) now restarts the timer

3 lines of code changed in 1 file:

• WINDOW: AW_status.cxx (+3)

westram 2007-01-27 12:49 #26 Rev.: 4290

- removed virtual destructor
- added rewind
- removed is_EOL (no longer used)
- FILE_BUFFER_read() returns length of read line

11 lines of code changed in 1 file:

• SL/FILE_BUFFER: FileBuffer.h (+11 -9)

westram 2007-01-27 12:49 #25 Rev.: 4289

- use memchr to search for EOL in input buffer.
- added method rewind()
- cleaned up C->C++ interface functions

65 lines of code changed in 1 file:

• SL/FILE_BUFFER: FileBuffer.cxx (+65 -19)

westram 2007-01-27 12:49 #24 Rev.: 4288

- added list of common database fields

26 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: sp_info.hlp (+26 -3)

westram 2007-01-27 12:37 #23 Rev.: 4287

- prototypes updated

46 lines of code changed in 1 file:

• CONVERTALN: prototypes.h (+46 -35)

westram 2007-01-27 12:37 #22 Rev.: 4286

- small helper functions (allocation related)

42 lines of code changed in 1 file:

• CONVERTALN: convert.c (new 42)

westram 2007-01-27 12:37 #21 Rev.: 4285

- rewrote Fgetline() using FileBuffer (~ 6.5 x old speed)
Now aborts with error if line is too long - instead of spitting a
warning, which normally isn't recognized by the user.

13 lines of code changed in 1 file:

• CONVERTALN: util.c (+13 -32)

westram 2007-01-27 12:36 #20 Rev.: 4284

- use FileBuffer instead of plain files
- avoid repetitive calculation of sequencedata length.

39 lines of code changed in 1 file:

• CONVERTALN: printable.c (+39 -47)

westram 2007-01-27 12:36 #19 Rev.: 4283

- use FileBuffer instead of plain files
- avoid repetitive calculation of sequencedata length.
- single characters were printed with fprintf [sic]
- overall performance for GENBANK->PHYLIP conversion: ~85 x old speed

56 lines of code changed in 1 file:

• CONVERTALN: phylip.c (+56 -68)

westram 2007-01-27 12:36 #18 Rev.: 4282

- use realloc_sequence_data() / free_sequence_data()
- use FileBuffer instead of plain files
- single characters were printed with fprintf [sic]
- avoid repetitive calculation of sequencedata length.
For alignments with 400000 positions, the conversion spent
more than 98% of time in length calculation.
- overall performance for GENBANK->PAUP conversion: ~180 x old speed

67 lines of code changed in 1 file:

• CONVERTALN: paup.c (+67 -103)

westram 2007-01-27 12:35 #17 Rev.: 4281

- skipped NOP-rewind

1 lines of code changed in 1 file:

• CONVERTALN: main.c (+1 -1)

westram 2007-01-27 12:35 #16 Rev.: 4280

- use FileBuffer instead of plain files
- single characters were printed with fprintf [sic]

41 lines of code changed in 1 file:

• CONVERTALN: macke.c (+41 -48)

westram 2007-01-27 12:34 #15 Rev.: 4279

- initialize new elements of global struct 'data'

92 lines of code changed in 1 file:

• CONVERTALN: fconv.c (+92 -89)

westram 2007-01-27 12:34 #14 Rev.: 4278

- global struct 'data' [sic] now contains information
about lengths of handled sequences and about allocated space.

20 lines of code changed in 1 file:

• CONVERTALN: convert.h (+20 -12)

westram 2007-01-25 16:30 #13 Rev.: 4277

- use FileBuffer instead of plain files

276 lines of code changed in 6 files:

• CONVERTALN: alma.c (+137 -152), embl.c (+62 -63), gcg.c (+23 -23), genbank.c (+30 -35), mg.c (+21 -18), swissprot.c (+3 -3)

westram 2007-01-25 16:29 #12 Rev.: 4276

- link FILE_BUFFER.a
- depends updated
- added convert.o

22 lines of code changed in 1 file:

• CONVERTALN: Makefile (+22 -2)

westram 2007-01-25 16:28 #11 Rev.: 4275

- added awars defs for export

10 lines of code changed in 1 file:

• AWTI: awti_exp_local.hxx (+10 -3)

westram 2007-01-25 16:28 #10 Rev.: 4274

- defaults for export awars
- new gui elements in export:
marked/all, compress gaps, filter, cut stop-codon
- added class export_sequence_data: provides compressed
and filtered sequence data for export. Also caches the resulting
sequence, since it often is used several times from the eft's.
- hook ACI command 'export_sequence' to export_sequence()
- XML export now only exports current alignment. GapCompression and
filtering possible.
- If an error occurs while writing to export file, the (partial) file
gets deleted.
- removed invalid+duplicated free's
- join lines ending with a '\' with next line. This allows to write
export filters which skip entries if they are not present in the
database (see embl.eft).

503 lines of code changed in 1 file:

• AWTI: AWTI_export.cxx (+503 -135)

westram 2007-01-25 16:28 #9 Rev.: 4273

- assertion to avoid wrong use of awt_create_select_filter().
Some comments about usage.

14 lines of code changed in 1 file:

• AWT: AWT_filter.cxx (+14 -3)

westram 2007-01-25 16:28 #8 Rev.: 4272

- updated

1 lines of code changed in 1 file:

• ARBDB: arbdb.h (+1)

westram 2007-01-25 16:28 #7 Rev.: 4271

- prototypes updated (now contains GEN_* functions)

39 lines of code changed in 1 file:

• ARBDB: ad_prot.h (+39)

westram 2007-01-25 16:28 #6 Rev.: 4270

- minor change

23 lines of code changed in 1 file:

• ARBDB: adstring.c (+23 -13)

westram 2007-01-25 16:28 #5 Rev.: 4269

- added ACI tracing
- GB_command_interpreter returned "<NULL>" if no output stream left, now it
returns "". Needed for self-eliminating expressions used by export filters.

42 lines of code changed in 1 file:

• ARBDB: adquery.c (+42 -12)

westram 2007-01-25 16:27 #4 Rev.: 4268

- added new command 'export_sequence' used by Exporter
This functions is only available if hooked by calling
GB_set_export_sequence_hook()
- new parameter 'forcenl' for functions 'format' and 'format_sequence'.
Defines characters where a LF is forced
- rewrote gbl_format_sequence (needs approx. 20% of time)
- 'trace' (dump action to stdout)
- 'define' + 'do' (ACI macros)
- 'count' and 'len' returned a number with trailing space, now they dont.
- 'split' (stream splitting)

449 lines of code changed in 1 file:

• ARBDB: adlang1.c (+449 -121)

westram 2007-01-25 16:27 #3 Rev.: 4267

*** empty log message ***

8 lines of code changed in 1 file:

• arb_CHANGES.txt (+8 -1)

westram 2007-01-10 18:05 #2 Rev.: 4266

- changed importancy of files (additional files now least important)
- abort if only other/additional files were found
- declared group of ACI/SRT containing extensions

10 lines of code changed in 1 file:

• SOURCE_TOOLS: grepx.pl (+10 -8)

yadhu 2007-01-04 13:47 #1 Rev.: 4265

Changes to ProtView Module
1. Added REFRESH button to ProtView Dialog in order to refresh the translated display while inserting and deleting columns in the editor.
2. Added new Refresh, close and help icons for button drawing.

155 lines of code changed in 7 files:

• EDIT4: ED4_ProteinViewer.cxx (+14 -126)
• lib/pictures: proteinViewer.fig (+2 -1)
• lib/pixmaps: close_text.xpm (new 27), help_text.xpm (new 28), refresh.xpm (+26 -41), refreshText.xpm (new 32), refresh_text.xpm (new 26)

December 2006 »