Directory NTREE/

Directory Created:
2000-11-23 11:41
Total Files:
43
Deleted Files:
39
Lines of Code:
18071

[root]/NTREE

Lines of Code

NTREE/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 2575 (100.0%) 60786 (100.0%) 23.6
westram 2421 (94.0%) 45832 (75.4%) 18.9
oldcode 35 (1.4%) 9712 (16.0%) 277.4
yadhu 54 (2.1%) 3232 (5.3%) 59.8
richter 23 (0.9%) 1336 (2.2%) 58.0
meierh 8 (0.3%) 471 (0.8%) 58.8
murban 5 (0.2%) 123 (0.2%) 24.6
epruesse 16 (0.6%) 63 (0.1%) 3.9
huberj 4 (0.2%) 9 (0.0%) 2.2
baderk 6 (0.2%) 4 (0.0%) 0.6
boehnel 1 (0.0%) 3 (0.0%) 3.0
brettske 1 (0.0%) 1 (0.0%) 1.0
artemov 1 (0.0%) 0 (0.0%) 0.0

Most Recent Commits

westram 2019-07-17 16:27 Rev.: 17982


* reduced use of GB_change_my_security:
- use GB_securityLevel instead of manually fiddling around with GB_change_my_security.
- inspected and accepted leftover uses (see comments).

1 lines of code changed in 1 file:

  • NTREE: NT_extern.cxx (+1 -1)
westram 2019-07-17 16:22 Rev.: 17980


* use security objects instead of manually calling GB_push/pop_my_security.
* eliminate GB_push/pop_my_security.
* fix scoping using a TA object.

8 lines of code changed in 3 files:

  • NTREE: NT_dbrepair.cxx (+1 -2), NT_extern.cxx (+2 -4), NT_main.cxx (+5 -8)
westram 2019-07-02 14:45 Rev.: 17944


* FIXES crash in RELEASE version (when invalid color group occurs in database).
* add assertions against
- invalid color_groups and
- invalid unshaded GCs.
* ARBDB color-group interface:
- define number of allowed color groups in ARBDB
- fix interface types (long->int)
- report error when color_group passed to {{{GBT_set_color_group}}} is out-of-range.
- {{{GBT_get_color_group}}} does range check. returns 0 if out-of-range.

1 lines of code changed in 2 files:

  • NTREE: Makefile (+1), NT_extern.cxx (-1)
westram 2019-05-10 13:57 Rev.: 17877


* reintegrates 'gcc' into 'trunk'
* adds: log:branches/gcc@17850:17876

2 lines of code changed in 1 file:

  • NTREE: ad_spec.cxx (+2 -2)
westram 2019-04-29 14:44 Rev.: 17836


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

6 lines of code changed in 5 files:

  • NTREE: NT_concatenate.cxx (+1 -1), NT_join.cxx (+1 -1), NT_tree_cmp.cxx (+1 -1), ad_ext.cxx (+2 -2), ad_spec.cxx (+1 -1)
westram 2019-04-05 19:32 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:

  • NTREE: AP_consensus.cxx (+1 -1)
westram 2019-04-04 16:47 Rev.: 17742


* fix unnecessary typos.

1 lines of code changed in 1 file:

  • NTREE: NT_tree_cmp.cxx (+1 -1)
westram 2019-04-01 17:41 Rev.: 17724


* partial merge from 'fts' into 'trunk'
- {{{ConfigMapping}}}:
* cleanup
* add missing tests
* fix config bug: trailing backslash at end of values did cause wrong read of data
* adds: log:branches/fts@17718:17723

9 lines of code changed in 3 files:

  • NTREE: Makefile (+9), NT_edconf.cxx (-1), NT_group_search.cxx (-1)
westram 2019-03-07 18:30 Rev.: 17651


* reintegrates 'cleanup' into 'trunk'
* adds: log:branches/cleanup@17627:17650

4 lines of code changed in 1 file:

  • NTREE: NT_concatenate.cxx (+4 -4)
westram 2018-10-31 10:52 Rev.: 17593


* reintegrates 'fix' into 'trunk'
- performs #798
* adds genetic code tables (24-31)
* adds combined amino acid J (I or L)
* improved translate and/or realign
- handle optional start-/stop-codons
- improve recognition of nuc-triples containing IUPAC-codes
* error messages now always list EMBL table numbers
* adds:
- log:branches/fix@17480:17485,17491:17492,17494:17507,17509:17528,17534:17592
- log:branches/optional@17481:17568

9 lines of code changed in 1 file:

  • NTREE: AP_consensus.cxx (+9 -9)
westram 2018-10-17 11:00 Rev.: 17478


* reintegrates 'svalues' into 'trunk'
- implements #614
* adds: log:branches/svalues@17357:17419,17428:17464,17469,17471:17477

11 lines of code changed in 2 files:

  • NTREE: NT_extern.cxx (-1), ad_trees.cxx (+11 -18)
westram 2018-10-02 16:08 Rev.: 17428


* partial merge from 'svalues' into 'trunk'
- root branches always need to have identical remarks (associated with the root-edge)
* condition previously implicit, now hardened by tests/assertions/...
* fixed several bugs that violated this condition
* adds: log:branches/svalues@17420:17427

3 lines of code changed in 1 file:

  • NTREE: NT_tree_cmp.cxx (+3 -2)
westram 2018-09-20 18:43 Rev.: 17396


* reintegrates 'fix' into 'trunk'
- elim dead code
- use const hash loop
* adds: log:branches/fix@17380,17388:17395

22 lines of code changed in 4 files:

  • NTREE: NT_edconf.cxx (+17 -18), NT_extern.cxx (+1 -1), ad_trees.cxx (+4 -4), ad_trees.h (-1)
westram 2018-09-07 09:22 Rev.: 17356


* add ticket number

4 lines of code changed in 1 file:

  • NTREE: NT_tree_cmp.cxx (+4 -4)
westram 2018-09-03 13:57 Rev.: 17349


* add + document configs for
- reporting transfer quality
- restoring original name (after quality has been reviewed)

4 lines of code changed in 2 files:

  • NTREE: NT_group_search.cxx (+2), ad_trees.cxx (+2)
westram 2018-09-03 13:19 Rev.: 17348


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

22 lines of code changed in 2 files:

  • NTREE: NT_tree_cmp.cxx (+21 -15), ad_trees.cxx (+1 -1)
westram 2018-08-30 17:24 Rev.: 17342


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

1133 lines of code changed in 5 files:

  • NTREE: Makefile (+5), NT_species_set.h (+87 -30), NT_tree_cmp.cxx (+606 -193), NT_tree_cmp.h (+150 -5), ad_trees.cxx (+285 -82)
westram 2018-08-30 10:58 Rev.: 17336


* typos
- some had ''two'' good language skills ;-)
- fix some plural forms

1 lines of code changed in 1 file:

  • NTREE: NT_main.cxx (+1 -1)
westram 2018-07-23 16:52 Rev.: 17262


* partial merge from 'group' into 'trunk'
- fixes to arb_progress
* adds:
- log:branches/group@17191:17218,17220:17260
- log:branches/progress@17195:17216,17218:17259

13 lines of code changed in 6 files:

  • NTREE: AP_consensus.cxx (+2 -2), NT_dbrepair.cxx (+4 -4), NT_extern.cxx (+4 -4), NT_main.cxx (+1 -1), ad_spec.cxx (+1 -1), ad_trees.cxx (+1 -1)
westram 2018-07-10 16:48 Rev.: 17178


* reintegrates 'gcc' into 'trunk'
- complete arb port to gcc 8.1
- fixes NDEBUG-related issues (not handled by [16986])
* adds: log:branches/gcc@17164:17177

2 lines of code changed in 1 file:

  • NTREE: ad_spec.cxx (+2 -2)
westram 2018-07-06 16:02 Rev.: 17160


* reintegrates 'group' into 'trunk'
- misc. cleanup:
* group related functions now all accessible via menu of 1st ntree window
* DRY selection of 2 trees
* warn if annotated tree isnt visible
* fix mnemonics
* fix error handling (compare taxonomy)
* unittest comments added to tree remarks
* names
* adds: log:branches/group@17139:17159

299 lines of code changed in 9 files:

  • NTREE: Makefile (+1), NT_extern.cxx (+22 -15), NT_group_search.cxx (+25 -9), NT_local_proto.h (+6), NT_species_set.h (+18 -18), NT_taxonomy.cxx (+88 -81), NT_tree_cmp.cxx (+59 -56), NT_tree_cmp.h (+1 -1), ad_trees.cxx (+79 -44)
westram 2018-06-15 13:08 Rev.: 17110


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

135 lines of code changed in 11 files:

  • NTREE: NT_edconf.cxx (+3 -3), NT_extern.cxx (+4), NT_group_search.cxx (+5 -5), NT_local_proto.h (+1), NT_sort.cxx (+1 -1), NT_species_set.h (+1 -1), NT_taxonomy.cxx (+7 -7), NT_tree_cmp.cxx (+31 -27), ScrollSynchronizer.cxx (+1 -1), ad_trees.cxx (+80 -3), tree_position.h (+1 -1)
westram 2018-05-04 18:06 Rev.: 16986


* reintegrates 'gcc' into 'trunk'
- ports arb to gcc 8.1 (fixing warnings)
* adds: log:branches/gcc@16965:16985

Update: continued by [17178]

5 lines of code changed in 3 files:

  • NTREE: Makefile (+1), NT_extern.cxx (+1 -1), NT_group_search.cxx (+3 -2)
westram 2018-05-02 11:32 Rev.: 16961


* partial merge from 'fix' into 'trunk'
- refactored {{{AW_device}}} text output
* reduces calls to strlen (using {{{SizedCstr}}})
* eliminated/modernized several parameters/functions (esp. in {{{TextOverlayCallback}}}s)
* adds: log:branches/fix@16939:16960

14 lines of code changed in 2 files:

  • NTREE: Makefile (+12), ScrollSynchronizer.cxx (+2 -2)
westram 2018-04-30 18:27 Rev.: 16936


* reintegrates 'cleanup' into 'trunk'
- performs #762 (shrink 3.7 k)
* adds: log:branches/cleanup@16924:16935

0 lines of code changed in 1 file:

  • NTREE: NT_extern.cxx (-12)
westram 2018-04-20 13:04 Rev.: 16904


* reintegrates 'pvp' into 'trunk'
- fixes #782
- implements #701
* adds: log:branches/pvp@16882:16903

71 lines of code changed in 5 files:

  • NTREE: AP_pos_var_pars.cxx (+17 -320), AP_pos_var_pars.h (del), Makefile (+1 -3), ad_trees.cxx (+52 -49), needs_libs (+1)
westram 2018-01-26 17:12 Rev.: 16828


* fix progress assertion (in error case)

2 lines of code changed in 1 file:

  • NTREE: NT_main.cxx (+2)
westram 2017-11-28 19:22 Rev.: 16766


* reintegrates 'gcc' into 'trunk'
- mostly cosmetics changes
* adds: log:branches/gcc@16655,16741:16743,16752:16765

13 lines of code changed in 5 files:

  • NTREE: AP_pos_var_pars.cxx (+1 -1), NT_extern.cxx (+4 -6), NT_validNameParser.cxx (+4 -7), ScrollSynchronizer.cxx (+1 -2), ad_trees.cxx (+3 -6)
westram 2017-11-28 18:09 Rev.: 16763


* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751

372 lines of code changed in 30 files:

  • NTREE: AP_consensus.cxx (+5 -5), AP_pos_var_pars.cxx (+7 -7), AP_pos_var_pars.h (+1 -1), ColumnStat_2_gnuplot.cxx (+21 -21), NT_branchAnalysis.cxx (+4 -4), NT_cb.cxx (+3 -3), NT_concatenate.cxx (+30 -28), NT_dbrepair.cxx (+31 -30), NT_edconf.cxx (+26 -26), NT_extern.cxx (+61 -61), NT_group_search.cxx (+21 -21), NT_import.cxx (+3 -3), NT_ins_col.cxx (+16 -16), NT_join.cxx (+4 -4), NT_local.h (+4 -4), NT_main.cxx (+27 -27), NT_shadeTree.cxx (+2 -2), NT_sort.cxx (+4 -4), NT_taxonomy.cxx (+5 -5), NT_trackAliChanges.cxx (+4 -4), NT_tree_cmp.cxx (+17 -17), NT_validManual.cxx (+3 -3), NT_validNameParser.h (+9 -9), NT_validNames.cxx (+5 -5), ScrollSynchronizer.cxx (+3 -3), ScrollSynchronizer.h (+3 -3), ad_ext.cxx (+12 -12), ad_spec.cxx (+11 -10), ad_transpro.cxx (+2 -2), ad_trees.cxx (+28 -28)
westram 2017-11-19 16:19 Rev.: 16683


* full update from child 'gcc' into 'trunk'
- more warning fixes
- fix bug in prettyprint
* adds: log:branches/gcc@16668:16682

3 lines of code changed in 2 files:

  • NTREE: ColumnStat_2_gnuplot.cxx (+2 -1), NT_main.cxx (+1 -1)
westram 2017-11-17 13:54 Rev.: 16668


* full update from child 'gcc' into 'trunk'
- fix/suppress (new) compiler warnings
- skip vectorizer notes
* adds: log:branches/gcc@16656:16667

10 lines of code changed in 2 files:

  • NTREE: NT_edconf.cxx (+8), ad_trees.cxx (+2 -2)
westram 2017-11-12 15:53 Rev.: 16649


* partial merge from 'gcc' into 'trunk'
- handles #770 by reducing optimizations of several bleeding test functions
* adds: log:branches/gcc@16636:16648

1 lines of code changed in 1 file:

  • NTREE: ad_trees.cxx (+1 -1)
westram 2017-11-06 14:54 Rev.: 16628


* reintegrates 'vectorize' into 'trunk'
- fixes #700
* documented vectorization-checks
* fine-grained check based on gcc-version
- drops old gcc-versions (<4.4.3)
- new attribute {{{__ATTR__DONT_VECTORIZE}}}
* disabled vectorization of {{{POS_TREE2::init_static()}}} for newer gcc-versions (generated code fails tests)
- added a bunch of new vectorization-checks (probably irrelevant to overall performance)
* adds: log:branches/vectorize@15531:16585,16595:16627

4 lines of code changed in 4 files:

  • NTREE: AP_pos_var_pars.cxx (+1 -1), NT_concatenate.cxx (+1 -1), NT_tree_cmp.cxx (+1 -1), ad_spec.cxx (+1 -1)
westram 2017-10-27 19:04 Rev.: 16576


* painful merge from 'alilink' into 'trunk'
- attempt to eliminate existing conflicts by merging log:branches/alilink@12782,12786:12787 (=creation of conflicting files)
- also merged back already resolved conflicts (done in alilink)
- a dozen of manual merges :-(
* adds: log:branches/alilink@12782,12786:12787,13999,14004

7 lines of code changed in 2 files:

  • NTREE: Makefile (+1 -5), ad_transpro.cxx (+6 -1768)
westram 2017-10-21 13:40 Rev.: 16564


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

8 lines of code changed in 2 files:

  • NTREE: NT_import.cxx (+3 -3), NT_main.cxx (+5 -6)
westram 2017-10-08 15:54 Rev.: 16508


* reintegrates 'macros' into 'trunk'
- introduce generic input prompt (related #179)
- use it instead of locally generated windows:
* species (rename + create)
* alignment (rename, copy + create)
* experiments (rename, copy + create)
* genes (rename, copy + extract)
* mergetool (rename SAI + configs)
* SAIviz color translation (copy + create)
- fixed bugs in mergetool ([16503],[16504])
* adds: log:branches/macros@16484:16507

4 lines of code changed in 2 files:

  • NTREE: NT_concatenate.cxx (+1 -1), ad_trees.cxx (+3 -3)
westram 2017-10-03 18:26 Rev.: 16469


* reintegrates 'textedit' into 'trunk'
- fixes #586
* editor now always started asynchronously
* uses inotify to track file changes
- ~~also use inotify to track directory updates (in order to update file selections when needed)~~\\(./) by [16515] ff.; merged by [16551]
* adds: log:branches/textedit@16448:16468

2 lines of code changed in 1 file:

  • NTREE: Makefile (+2)
westram 2017-09-23 14:03 Rev.: 16425


* reintegrates 'aci' into 'trunk'
- extends ACI language (implementing #707)
* boolean operators: {{{And}}},{{{Or}}},{{{Not}}}
* numeric comparison: {{{isAbove}}},{{{isBelow}}},{{{isEqual}}}
* floating point arithmetic: {{{fplus}}},{{{fminus}}},{{{fmult}}},{{{fdiv}}}
* misc: {{{round}}},{{{inRange}}},{{{isEmpty}}}
- enforce parameter checks in ACI function code
- case of commands completely ignored
* adds: log:branches/aci@16385,16391:16424

1 lines of code changed in 1 file:

  • NTREE: Makefile (+1)
westram 2017-09-19 14:40 Rev.: 16391


* full update from child 'aci' into 'trunk'
- allow to view console from inside ARB
- slightly tweaked ACI trace
* adds: log:branches/aci@16386:16390

4 lines of code changed in 2 files:

  • NTREE: NT_extern.cxx (+3 -1), NT_group_search.cxx (+1 -1)
westram 2017-09-18 15:23 Rev.: 16374


* reintegrates 'aci' into 'trunk'
- refactored wide parts of ACI code (incl. SRT+REG)
* added more test
* ACI tracing
- more complete and readable
- automatically turned off when done with expression
* improved error messages (esp. diagnostics)
* documentation (updated, added missing)
* fixed a bunch of bugs (incl. SEGV and deadlock)
* ACI now runs inside execution environment
- ACI language may be extended with custom commands (implements #756)
* added ACI extension for group-batch-rename
* adds:
- log:branches/aci@16170:16373
- log:branches/addtest@16193:16316

28 lines of code changed in 4 files:

  • NTREE: Makefile (+1), NT_group_search.cxx (+24 -17), ad_spec.cxx (+1 -5), ad_trees.cxx (+2 -2)

(1033 more)

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