Directory UNIT_TESTER/run/tools/

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westram 2020-04-06 14:18 Rev.: 18437

* reintegrates 'io' into 'trunk'
* adds: log:branches/io@18428:18436

0 lines of code changed in 1 file:

• UNIT_TESTER/run/tools: export_newick.arb (new)

westram 2019-07-08 09:26 Rev.: 17953

* fix number of tabs between key and data (ASCII DB format)
- auto-updated all databases.

96 lines of code changed in 3 files:

• UNIT_TESTER/run/tools: dnarates_expected.arb (+15 -15), exseq_ascii.arb.expected (+40 -40), read_tree_out_expected.arb (+41 -41)

westram 2019-04-05 18:32 Rev.: 17748

* remove hardcoded 'markCreated==true' from
- GBT_find_or_create_species_rel_species_data and
- GBT_find_or_create_species.
* hardcode 'markCreated==false' in GBT_find_or_create_SAI.
- changes result DB.
- increase diff buf size (result DB has loooong lines).

1 lines of code changed in 1 file:

• UNIT_TESTER/run/tools: dnarates_expected.arb (+1 -1)

westram 2018-06-25 16:04 Rev.: 17121

* reintegrates 'saiexport' into 'trunk'
- no longer expand dangerous ranges (e.g. {{{--pass allbut .-=012345}}})
* adds: log:branches/saiexport@17112:17120

40 lines of code changed in 2 files:

• UNIT_TESTER/run/tools: exflt_DNA_pvp_g05.fasta.expected (new 20), exflt_DNA_pvp_gaps.fasta.expected (new 20)

westram 2017-08-21 13:47 Rev.: 16234

* reintegrates 'saiexport' into 'trunk'
* adds: log:branches/saiexport@16229:16233

5 lines of code changed in 1 file:

• UNIT_TESTER/run/tools: exflt_DNA_mfpvp.fasta.expected (+5 -5)

westram 2017-07-10 11:29 Rev.: 16119

* reintegrates 'saiexport' into 'trunk'
- implements #743
* adds: log:branches/saiexport@16023:16118

132 lines of code changed in 9 files:

• UNIT_TESTER/run/tools: exflt_AMI_mf.fasta.expected (new 20), exflt_AMI_skipShort.fasta.expected (new 10), exflt_AMI_unfiltered.fasta.expected (new 20), exflt_DNA_mf.fasta.expected (new 20), exflt_DNA_mfpvp.fasta.expected (new 20), exflt_DNA_partial.fasta.expected (new 2), exflt_DNA_pvp.fasta.expected (new 20), exflt_DNA_unfiltered.fasta.expected (new 20), exflt_empty.fasta.expected (new)

westram 2016-05-07 09:07 Rev.: 14833

* reintegrates 'fixwarn' into 'trunk'
* adds: log:branches/fixwarn@14815:14832

60 lines of code changed in 2 files:

• UNIT_TESTER/run/tools: probeset.data.expected (new 2), probeset.out.expected (new 58)

westram 2016-01-28 08:33 Rev.: 14682

* merge [14675:14681] from 'gde' into 'trunk'
- change DB interface function concerned with GB_FLOAT from double -> float
- introduce more stable ascii <-> float conversion
* adds: log:branches/gde@14676:14681

9 lines of code changed in 1 file:

• UNIT_TESTER/run/tools: exseq_ascii.arb.expected (+9 -1)

westram 2015-11-27 19:31 Rev.: 14556

* reintegrates 'dbsave' into 'trunk'
- implements #665
* adds: log:branches/dbsave@14521:14555

0 lines of code changed in 3 files:

• UNIT_TESTER/run/tools: dnarates_expected.arb (-13), exseq_ascii.arb.expected (-9), read_tree_out_expected.arb (-9)

westram 2014-11-17 15:42 Rev.: 13191

* reintegrates 'slv' into 'trunk'
* performs #624
* adds:
- log:branches/slv@13152:13190

85 lines of code changed in 5 files:

• UNIT_TESTER/run/tools: acc.list (new 1), exseq.fasta.expected (new 6), exseq_ascii.arb.expected (new 63), exseq_via_eft.fasta.expected (new 2), min_template.arb (new 13)

westram 2014-10-09 17:48 Rev.: 13018

* merge a bunch of fixes from 'gcc' into 'trunk'
- detected using !AddressSanitizer
- fixing #613, #580 and other (undetected) bugs
* adds:
- log:branches/gcc@12996,13001:13003,13005:13006,13010:13014,13016

3 lines of code changed in 3 files:

• UNIT_TESTER/run/tools: dnarates.arb (new), dnarates_expected.arb (+2 -2)

westram 2014-01-20 16:08 Rev.: 11488

* reintegrates 'tree' into 'trunk'
- implements #417 (multifurcate tree)
- tree display
* adds MULTIFURC MODE
* reordered modes (synchronizes NTREE and PARSIMONY)
- branch analysis
* display number of multifurcations in 'mark long branches'
* display "in-tree-distance" and "per-species-distance"
- added function to toggle '100%' bootstraps
- document bug in GBT_remove_leafs (#452)
* adds:
- log:branches/tree@11425:11487

1 lines of code changed in 1 file:

• UNIT_TESTER/run/tools: read_tree_out_expected.arb (+1 -1)

westram 2013-08-25 14:09 Rev.: 10482

* Tree IO (patch reintegrates branch 'tree')
- added unit test (!TreeReader, export/import consistency for most export-parameters combinations)
- refactorings: moved more behavior into !TreeReader; deny access to class internals
- improved error messages/warnings
* show error-position in input data when bailing out
* warn about unused data behind tree
* trees < 2 species produce error now
- behavior
* fixed export/import of bootstrap values (expect ':' as separator; avoiding misinterpretation of group names starting with digits)
* auto-name unnamed nodes
* supports bootstrap values specified as percent (e.g. '12.5%')
* no longer interpret {{{''}}} as escape sequence for a single {{{'}}}
* no longer remove leading '_' from leaf-/groupnames (no idea why this was done)
- fixes:
* export+import of tree using double quotes often resulted in leaf-/groupnames enclosed in double-quotes (or more often failed to load completely)
* name of root-node was lost after import.
* better support for single-node subtrees, e.g. '(leafname)'. Nodes were skipped.
* deadlock occurring when tree file was truncated somewhere in the middle.
* leaks stuffed

11 lines of code changed in 1 file:

• UNIT_TESTER/run/tools: read_tree_out_expected.arb (+11 -1)

westram 2012-05-05 06:57 Rev.: 8704

- fix test-result changed by [8699]

6 lines of code changed in 1 file:

• UNIT_TESTER/run/tools: read_tree_out_expected.arb (+6)

westram 2012-03-21 16:21 Rev.: 8514

* create main containers with delete protection (only affects new DBs)

2 lines of code changed in 4 files:

• UNIT_TESTER/run/tools: dnarates_expected.arb (new), read_tree_out_expected.arb (new)

westram 2011-10-07 13:39 Rev.: 8041

merge from dev [7990] [7991] [7992] [7993] [7994] [7995] [7996] [7998] [8001] [8003] [8005] [8006] [8007] [8008] [8009] [8011] [8012] [8019]
* added a faked ecoli to ptserver test-db
* added unit-tests for gene-ptserver
* rename ptserver testdb
* ptserver db-cleanup
- size of mapfile for SSUREF108 is reduced by 85% (3,4Gb -> 519Mb)
* ptserver
- refactored
* prefix tree builders
* probe_input_data
- removed ptnd_new_match (dead code)

47 lines of code changed in 3 files:

• UNIT_TESTER/run/tools: arb_replace.in (new 47), gene_probe.arb (del), gene_probe_expected.arb (del)

westram 2011-02-26 10:40 Rev.: 7201

- test-result for arb_gene_probe no longer depends on ARBDB memory layout

0 lines of code changed in 1 file:

• UNIT_TESTER/run/tools: gene_probe_expected.arb (changed)

westram 2011-02-23 16:17 Rev.: 7189

merges [7108] [7146] [7147] [7148] [7150] [7151] [7152] [7153] [7155] [7156] [7161] [7162] [7163] from refactor
* arb_dnarates
- may read from file (instead of STDIN)
- if dbname is given on command line, expect dbsavename as following argument and save db with that name.
- removed old debug code
- adds a SAI counter to DB
- no longer uses PID for SAI name, instead uses counter
- no longer overwrites existing SAIs
* arb_swap_rnastr (unused, uncommented -> unlinked)
* arb_read_tree
- command line options may appear anywhere / in any order
- new option -db to specify db (load/save).
* arb_export_rates
- new option -d to specify db.
- handle more errors
* arb_export_tree
- optional CLI-argument 'DBNAME' (to specify a DB for unittests)
* arb_gene_probe
- error handling fixes
- do not write debugging-data to gene-ptserver-db (+fixed expected result-db)
* arb_primer
- optional CLI-argument 'dbname'
- replaced scattered exit()-calls by proper error-handling
* arb_probe
- forward errors to top level, to enable error check in unit-test
- allow usage of TEST_SERVER_ID if compiled with UNIT_TESTS==1
* added unit tests for mosts tools in TOOLS. Tests do not try to test complete functionality - they only check that one or a few calls to the tools do not fail.
* fixed sourcefile list

1 lines of code changed in 2 files:

• UNIT_TESTER/run/tools: gene_probe_expected.arb (+1)