Directory UNIT_TESTER/run/

Directory Created:
2010-02-18 08:12
Total Files:
39
Deleted Files:
3
Lines of Code:
17711

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Lines of Code

UNIT_TESTER/run/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
westram 118 (100.0%) 21343 (100.0%) 180.8

Most Recent Commits

westram 2019-09-17 14:13 Rev.: 18088


* reintegrates 'fts' into 'trunk'
* adds:
- log:branches/fts@17653,17655:17717,17724:18087
- [17925/branches/gui]

3508 lines of code changed in 3 files:

  • UNIT_TESTER/run: TEST_fields_ascii.arb (new 2089), TEST_fields_cloned_expected.arb (new 848), TEST_fields_xferred_expected.arb (new 571)
westram 2019-07-12 13:08 Rev.: 17956


* implement GB_copy_overlay
- works like GB_copy_std if destination is empty container.
- completely overwrites existing entries including protection + marks.
- added unittests (overlay onto empty container + onto filled container). both reproduce original database ("TEST_copy.arb").
- adds an assertion vs accidently overwriting temp entries (doing so currently is "undefined behavior").

2 lines of code changed in 1 file:

  • UNIT_TESTER/run: TEST_copy_noProtect.arb (+2 -2)
westram 2019-07-08 09:26 Rev.: 17953


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

3133 lines of code changed in 8 files:

  • UNIT_TESTER/run: AB735678_expected.arb (+346 -346), TEST_arbdbserver_save_expected.arb (+78 -78), TEST_copy.arb (+79 -79), TEST_copy_noProtect.arb (+79 -79), TEST_loadsave_ascii.arb (+78 -78), TEST_opti_ascii_in.arb (+1162 -1162), TEST_opti_ascii_renamed_expected.arb (+1162 -1162), TEST_pt_cleaned_expected.arb (+149 -149)
westram 2019-04-29 13:44 Rev.: 17836


* reintegrates 'clone' into 'trunk'
* adds: log:branches/clone@17813:17835

234 lines of code changed in 2 files:

  • UNIT_TESTER/run: TEST_copy.arb (new 117), TEST_copy_noProtect.arb (new 117)
westram 2019-03-04 19:39 Rev.: 17641


* reintegrates 'mix' into 'trunk'
- improve git/svn interoperability
* adds: log:branches/mix@17637:17640

2 lines of code changed in 1 file:

  • UNIT_TESTER/run: .gitignore (new 2)
westram 2018-09-03 12:19 Rev.: 17348


* applying ACI to groupname only had an effect together with overwrite mode {{{KEEP_OLD_NAMES}}}. fixed.

4 lines of code changed in 1 file:

  • UNIT_TESTER/run: group_xfer_32_li.log.expected (+4 -4)
westram 2018-08-30 16:24 Rev.: 17342


* reintegrates 'group' into 'trunk'
- implements #780
* adds: log:branches/group@17162:17190,17261:17341

98 lines of code changed in 6 files:

  • UNIT_TESTER/run: group_xfer_11.log.expected (new 14), group_xfer_21.log.expected (new 14), group_xfer_32.log.expected (new 17), group_xfer_32_li.log.expected (new 18), group_xfer_32_rc.log.expected (new 17), group_xfer_32_rel.log.expected (new 18)
westram 2018-06-15 12:08 Rev.: 17110


* reintegrates 'tree' into 'trunk'
- implements #735
* adds:
- log:branches/addtest@17040:17044
- log:branches/tree@16921:17109

0 lines of code changed in 1 file:

  • UNIT_TESTER/run: TEST_trees.arb (changed)
westram 2018-02-15 11:51 Rev.: 16861


* reintegrates 'unittest' into 'trunk'
- fixed non-deterministic behavior of add-species:
* 2 sequences in test-DB were identical (changed 1 bp)
* {{{AP_tree_edge}}} cannot be used to store insert-positions (uses pair of {{{AP_tree_nlen}}} instead)
* corrected some undefined behavior (results did depend on compiler version+flags):
- general order of inserts was undefined
- order of initial-insert was undefined (used by complete tree reconstruction)
- bugs fixed:
* not all possible insert-positions were tested
* sometimes species were added at wrong positions
* if multiple species were inserted at the same position, the following optimization
- did modify topology
- now optimizes all multi-inserts globally
- at leaf-positions: includes the leaf (Note: this does not modify the original topology)
* insert order now is "longest sequence first" (was "shortest sequence first")
- fixed unwanted behavior when testing for content of generated files
* adds: log:branches/unittest@16807:16860

0 lines of code changed in 1 file:

  • UNIT_TESTER/run: TEST_trees.arb (changed)
westram 2017-09-18 18:57 Rev.: 16383


* reintegrates 'aci' into 'trunk'
- split TEST_GB_command_interpreter (too big, esp. for sanitizer)
- fix undefined behavior in {{{GBS_regreplace}}}
- reduce test DB
* adds: log:branches/aci@16376:16382

85 lines of code changed in 1 file:

  • UNIT_TESTER/run: TEST_aci.arb (new 85)
westram 2017-07-10 11:29 Rev.: 16119


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

1667 lines of code changed in 1 file:

  • UNIT_TESTER/run: TEST_prot_tiny.arb (new 1667)
westram 2017-07-04 16:25 Rev.: 16077


* reintegrates 'fix' into 'trunk'
- adds markerline to load/save-test-DB (bitstring data)
- store encoding in cached bitstring entries (to avoid cache-hit returns wrong encoding; fixes #760)
* adds: log:branches/fix@16072:16076

18 lines of code changed in 4 files:

  • UNIT_TESTER/run: TEST_arbdbserver_save_expected.arb (+9), TEST_loadsave.arb (changed), TEST_loadsave_ascii.arb (+9), TEST_loadsave_quick.a00 (changed)
westram 2017-05-03 14:31 Rev.: 15876


* reintegrates 'fix' into 'trunk'
- automatically deletes field 'group_name' at root of tree
- done while loading tree
- provides workaround for #753
* adds: log:branches/fix@15870:15875

0 lines of code changed in 1 file:

  • UNIT_TESTER/run: TEST_nuc_seqcompr_exp.arb (changed)
westram 2017-01-25 17:54 Rev.: 15624


* reintegrates 'db' into 'trunk'
- fixes #742
* adds: log:branches/db@15618:15623

100 lines of code changed in 3 files:

  • UNIT_TESTER/run: TEST_opti_ascii_in.arb (+50), TEST_opti_ascii_renamed_expected.arb (+50), TEST_opti_expected.arb (changed)
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

18 lines of code changed in 4 files:

  • UNIT_TESTER/run: TEST_arbdbserver_save_expected.arb (+9 -17), TEST_loadsave.arb (changed), TEST_loadsave_ascii.arb (+9 -1), TEST_loadsave_quick.a00 (changed)
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 7 files:

  • UNIT_TESTER/run: AB735678_expected.arb (-9), TEST_gpt.arb.expected (changed), TEST_loadsave.arb (changed), TEST_nuc_seqcompr_exp.arb (changed), TEST_opti_ascii_in.arb (-10), TEST_opti_ascii_renamed_expected.arb (-10), TEST_opti_expected.arb (changed)
westram 2015-07-31 10:43 Rev.: 14116


* adds a "no color" entry to colorset in test DB (as generated by pre-[14094] versions)
* auto-remove such entries in rename-session

1 lines of code changed in 2 files:

  • UNIT_TESTER/run: TEST_opti_ascii_in.arb (+1 -1), TEST_opti_expected.arb (changed)
westram 2015-07-31 10:21 Rev.: 14115


* correct stored colorsets when committing rename-session (fixes #660)
* summarize failures when restoring a colorset

1 lines of code changed in 1 file:

  • UNIT_TESTER/run: TEST_opti_ascii_renamed_expected.arb (+1 -1)
westram 2015-07-31 09:22 Rev.: 14114


* add a colorset to test DB

35 lines of code changed in 3 files:

  • UNIT_TESTER/run: TEST_opti_ascii_in.arb (+18), TEST_opti_ascii_renamed_expected.arb (+17), TEST_opti_expected.arb (changed)
westram 2015-07-04 13:00 Rev.: 13970


* reintegrates 'ptsfix' into 'trunk'
- fixes #659
* adds:
- log:branches/ptsfix@13960:13969

16 lines of code changed in 4 files:

  • UNIT_TESTER/run: TEST_pt.arb.pt.expected (changed), TEST_pt_cleaned_expected.arb (+2 -2), TEST_pt_src.arb (+2 -2), index_pt.dump.expected (+12 -12)
westram 2015-03-29 11:47 Rev.: 13625


* reintegrates 'pars' into 'trunk'
- fixes #528, #609, #620, #631, #633, #640, #641
- implements #619, #627
* adds:
- log:branches/addtest@13123:13260,13523:13551,13570
- log:branches/check@13365:13375,13450:13457
- log:branches/check2@13458:13465
- log:branches/fix@13522:13588
- log:branches/fixres@13270:13277,13279:13293,13295:13326
- log:branches/pars@12938:13280,13282:13325,13327:13387,13389:13527,13530:13624

83 lines of code changed in 3 files:

  • UNIT_TESTER/run: TEST_prot.arb (+80 -42), TEST_realign.arb (+3 -3), TEST_trees.arb (changed)
westram 2014-11-17 15:42 Rev.: 13191


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

9 lines of code changed in 2 files:

  • UNIT_TESTER/run: TEST_pt_cleaned_expected.arb (+4), TEST_pt_src.arb (+5 -1)
westram 2014-08-04 16:25 Rev.: 12667


* reintegrates 'alilink' into 'trunk'
- fixes #419, #145, #563
* adds:
- log:branches/addtest@12468:12472
- log:branches/alilink@12419:12421,12423:12429,12431:12432,12437:12601,12603:12666
- log:branches/oldrealign@12499,12501,12537,12541,12548,12595,12607,12612,12616,12620,12625,12628,12634,12641

1376 lines of code changed in 1 file:

  • UNIT_TESTER/run: TEST_realign.arb (new 1376)
westram 2014-04-14 16:07 Rev.: 12020


* reintegrates 'tree' into 'trunk'
- fixing #507
* adds:
- log:branches/tree@12004:12019

0 lines of code changed in 1 file:

  • UNIT_TESTER/run: TEST_trees.arb (changed)
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

0 lines of code changed in 1 file:

  • UNIT_TESTER/run: TEST_trees.arb (changed)
westram 2013-11-03 14:42 Rev.: 11060


* reintegrates 'ptsfix' into 'trunk':
* adds:
- log:branches/ptsdump@8966:9000
- log:branches/ptsfix@8965:9012,9014:9017,9019:9023,9025:9046,9048:9089,9091:9114,9116:9132,9134:9139,9141:9145,9147:9151,9153:9158,9160:9379,9381:11059
- log:branches/ptsstartup@9160:9235,9237:9278,9280:9336,9339:9361,9363:9446
- log:branches/ptsundef@9061:9358

3597 lines of code changed in 4 files:

  • UNIT_TESTER/run: TEST_gpt.arb.pt.expected (changed), TEST_pt.arb.pt.expected (changed), index_gpt.dump.expected (new 195), index_pt.dump.expected (new 3402)
westram 2013-09-09 12:41 Rev.: 10559


* added unit test for rename-session
- does not use nameserver (just tests renaming of species and correction of names in trees and configs)

1400 lines of code changed in 1 file:

  • UNIT_TESTER/run: TEST_opti_ascii_renamed_expected.arb (new 1400)
westram 2013-09-09 12:23 Rev.: 10558


- added species configurations to test DB

22 lines of code changed in 2 files:

  • UNIT_TESTER/run: TEST_opti_ascii_in.arb (+22 -1), TEST_opti_expected.arb (changed)
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

0 lines of code changed in 1 file:

  • UNIT_TESTER/run: corrupted.tree (del)
westram 2013-07-16 12:23 Rev.: 10282


* added unit test reading corrupted tree file
- checks for proper failure
- failed till [10278]; succeeds now

72 lines of code changed in 1 file:

  • UNIT_TESTER/run: corrupted.tree (new 72)
westram 2013-07-11 16:13 Rev.: 10269


* added a unit test for genome file importer (currently disabled because it segfaults)
- test uses flatfile attached to #335
- expected test result has been generated with [7813] where importer still worked

953 lines of code changed in 2 files:

  • UNIT_TESTER/run: AB735678.txt (new 509), AB735678_expected.arb (new 444)
westram 2013-04-04 10:20 Rev.: 9804


- added unit-test for GB_optimize

1378 lines of code changed in 2 files:

  • UNIT_TESTER/run: TEST_opti_ascii_in.arb (new 1378), TEST_opti_expected.arb (new)
westram 2012-09-27 13:02 Rev.: 8962


* added auto-update-code for normal ptserver
* inserted '...' behind 'GUUUGAUCAAGUCGAGCGGU' in ptserver-test-source-DB
- probe has exactly two occurrances in the middle of the sequence data
- updated test-results for changed data
* ran TEST_SLOW_find_unmatched_probes to check for further index-errors
- no additional errors caused
- i.e. index-errors seem to occur only on 3'-end

4 lines of code changed in 3 files:

  • UNIT_TESTER/run: TEST_pt.arb.pt.expected (changed), TEST_pt_cleaned_expected.arb (+2 -2), TEST_pt_src.arb (+2 -2)
westram 2012-09-13 14:32 Rev.: 8877


* added unit-tests for sequence compression (by master-sequences)
- shows input-restrictions of g_b_put_number2

0 lines of code changed in 1 file:

  • UNIT_TESTER/run: TEST_nuc_seqcompr_exp.arb (new)
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 3 files:

  • UNIT_TESTER/run: TEST_nuc.arb (changed), TEST_prot.arb (changed), TEST_pt.arb.pt.expected (changed)
westram 2012-03-21 17:44 Rev.: 8516


* replace other uses of literal main-container-names
* arb_gene_probe generates species_data with correct protection
- updated test result
* fixed locals in arb_prm_read()

0 lines of code changed in 1 file:

  • UNIT_TESTER/run: TEST_gpt.arb.expected (changed)
westram 2012-03-18 20:02 Rev.: 8499


* several changes to quark-functions
- split GB_key_2_quark into GB_find_existing_quark + GB_find_or_create_quark
- replaced weird gb_key_2_quark
* by gb_find_or_create_NULL_quark (one occurrance)
* by gb_find_or_create_quark
- several functions unnecessarily created new quarks
* gb_find_internal (when searching for non-existing keys)
* GB_first_marked/GB_following_marked (when iterating over non-existant keys)
* GB_has_key (when checking for non-existant key)
* updated some binary test-databases (patch slighty changed order of system keys)

0 lines of code changed in 3 files:

  • UNIT_TESTER/run: TEST_gpt.arb.expected (changed), TEST_loadsave.arb (changed), TEST_loadsave_quick.a00 (changed)
westram 2012-02-02 09:57 Rev.: 8352


- change result expected by unit-test (according to [8351])

37 lines of code changed in 1 file:

  • UNIT_TESTER/run: TEST_pt_cleaned_expected.arb (+37)
westram 2011-10-17 13:21 Rev.: 8101


merge from ptpan_back [8065] [8066]
* rewrote arb_db_server + added tests

113 lines of code changed in 1 file:

  • UNIT_TESTER/run: TEST_arbdbserver_save_expected.arb (new 113)
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)

593 lines of code changed in 6 files:

  • UNIT_TESTER/run: TEST_gpt.arb.expected (new), TEST_gpt.arb.pt.expected (new), TEST_gpt_src.arb (new 81), TEST_pt.arb (del), TEST_pt_cleaned_expected.arb (new 220), TEST_pt_src.arb (new 292)

(12 more)

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