Directory lib/export/

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westram 2017-10-21 12:40 Rev.: 16564

* reintegrates 'io' into 'trunk'
- implements #691
* adds: log:branches/io@16436:16510,16513:16514,16517,16533:16535,16537:16563

3 lines of code changed in 1 file:

• lib/export: fasta_wacc.eft (+3 -3)

westram 2015-01-21 15:21 Rev.: 13424

* remove extra space at end of last sequence line

1 lines of code changed in 1 file:

• lib/export: embl.eft (+1 -1)

westram 2015-01-21 15:10 Rev.: 13423

* fix embl export filter (#638):
- print base count on right side of sequence (uses 'numright' added with [13420])

1 lines of code changed in 1 file:

• lib/export: embl.eft (+1 -1)

westram 2012-04-19 08:13 Rev.: 8607

merge from e4fix [8135] [8136] [8137] [8138] [8139] [8140] [8141] [8142] [8143] [8144] [8222]
(this revives the reverted patches [8129] [8130] [8131] [8132]; see [8133])

* fixes
- some free/delete mismatches
- wrong definition of ORF objects (Level was no bit value)
- amino consensus (failed for columns only containing 'C')
* rename
- AA_sequence_term -> orf_term
- ED4_sequence_terminal_basic -> ED4_abstract_sequence_terminal
* cleaned up hierarchy dumps
* tweaked is_terminal()/to_terminal()

0 lines of code changed in 1 file:

• lib/export: nexus.eft (changed)

westram 2010-10-25 18:47 Rev.: 7046

* refactored CONVERTALN (merges [6885] [6886] [6888] [6889] [6890] [6891] [6894] [6906] [6907] [6908] [6910] [6911] [6914] [6915] [6916] [6917] [6918] [6922] [6923] [6925] [6927] [6928] [6929] [6930] [6931] [6933] [6934] [6935] [6937] [6945] [6950] [6956] [6961] [6962] [6963] [6964] [6965] [6967] [6968] [6972] [6973] [6974] [6975] [6976] [6977] [6979] [6980] [6981] [6982] [6983] [6985] [6986] [6987] [6988] [6990] [6991] [6992] [6993] [6994] [6995] [6996] [6997] [6998] [6999] [7002] [7003] [7008] [7009] [7010] [7011] [7012] [7025] [7026] [7027] [7029] [7030] [7031] [7032] [7034] [7035] [7036])
- build arb_convert_aln in ARB standard way
- added unit-test
- fixed various date bugs (even Y2K)
- fixed conversion MACKE -> GCG.
- fixed crash in conversions EMBL/GENBANK -> GCG
- fixed SWISSPROT->MACKE conversion
- dropped conversion support for ALMA
- removed completely unused "formats" NBRF and STADEN
- removed 1x1 sequence conversions for interleaved formats
- converter is more picky (fails instead of doing nonsense)
- added self conversions for all input formats
- proper formatting of 3/5 info
- proper line wrapping
- fixed acc broken by genbank reader
- fixed broken IDs (short-names)
- fixed embl reader (added number @ EOL to sequence data)
- errors now refer to the input file + linenumber
- abort with error if sequence data contains invalid characters
- removed C-interface for FileBuffer (CONVERTALN was the only client)

4 lines of code changed in 2 files:

• lib/export: nexus.eft (new 4), paup.eft (del)

westram 2009-07-01 16:19 Rev.: 6096

* Again allow display of hidden files in filter list (reverts part of [6082])
* renamed all rarely-used import filters into .importfilter
- user has to click on 'Show hidden files' to show these filters or to use them in AUTODETECT
* moved a few sub-filters to nonformats
* added .fasta_contextual_data_1_03.ift (thx to Renzo, Joerg and Frank Oliver)
* added fasta_wacc import/export filters (thx to Harald)

9 lines of code changed in 1 file:

• lib/export: fasta_wacc.eft (new 9)

westram 2009-06-13 10:19 Rev.: 6051

* RN entry was missing

1 lines of code changed in 1 file:

• lib/export: embl.eft (+1)

westram 2009-06-13 09:09 Rev.: 6048

produced wrong feature table when exporting field 'strain'

previous output:
{{{
FT strain=abcd
}}}

current output:
{{{
FT source 1..1188
FT /strain=DSM 2039
}}}

or
{{{
FT source 1..1188
}}}

if no strain present (hope a single source line is ok)

2 lines of code changed in 1 file:

• lib/export: embl.eft (+2 -1)

westram 2008-12-28 15:54 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.

1 lines of code changed in 2 files:

• lib/export: ae2.eft (+1 -1), xml.eft (-1)

westram 2008-06-06 13:23 Rev.: 5390

- TAB-Ex

21 lines of code changed in 12 files:

• lib/export: ae2.eft (+3 -3), embl.eft (+1 -1), fasta.eft (+2 -2), fasta_NCBI_sequin.eft (+1 -1), fasta_wide.eft (+2 -2), gcg.eft (+1 -1), genbank.eft (+1 -1), genbank_list.eft (+1 -1), paup.eft (+3 -3), phylip.eft (+3 -3), pir.eft (+2 -2), xml.eft (+1 -1)

westram 2007-01-27 13:29 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 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 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 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 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 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 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 Rev.: 4292

- changed suffix (PHYL->AE2)

1 lines of code changed in 1 file:

• lib/export: ae2.eft (+1 -1)

westram 2006-01-05 14:13 Rev.: 3993

- export filter for NCBI sequin

4 lines of code changed in 1 file:

• lib/export: fasta_NCBI_sequin.eft (new 4)

westram 2004-11-09 14:37 Rev.: 3360

- like fasta_noalign.eft, but all data in one line

0 lines of code changed in 1 file:

• lib/export: fasta_wide_noalign.eft (new)

westram 2004-11-09 14:37 Rev.: 3359

- like fasta.eft, but all data in one line

4 lines of code changed in 1 file:

• lib/export: fasta_wide.eft (new 4)

westram 2004-11-09 14:37 Rev.: 3358

- fasta export filter (removes alignment from sequence)

0 lines of code changed in 1 file:

• lib/export: fasta_noalign.eft (new)

westram 2004-11-09 14:37 Rev.: 3357

- renamed into fasta_noalign.eft

0 lines of code changed in 1 file:

• lib/export: fastacompressed.eft (del)

westram 2002-06-14 18:46 Rev.: 642

some bugfixes for import/export

6 lines of code changed in 1 file:

• lib/export: genbank.eft (+6 -7)

westram 2001-04-05 09:14 Rev.: 151

Changes (mostly for GENEMAP)

3 lines of code changed in 1 file:

• lib/export: xml.eft (new 3)

oldcode 2000-11-23 10:41 Rev.: 2

Initial revision

56 lines of code changed in 9 files:

• lib/export: ae2.eft (new 3), fasta.eft (new 4), fastacompressed.eft (new), gcg.eft (new 16), genbank.eft (new 16), genbank_list.eft (new 6), paup.eft (new 3), phylip.eft (new 3), pir.eft (new 5)