Directory PARSIMONY/

Directory Created:
2000-11-23 11:41
Total Files:
19
Deleted Files:
10
Lines of Code:
8889

[root]/PARSIMONY

Lines of Code

PARSIMONY/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 760 (100.0%) 26588 (100.0%) 34.9
westram 732 (96.3%) 18976 (71.4%) 25.9
oldcode 21 (2.8%) 7371 (27.7%) 351.0
meierh 1 (0.1%) 233 (0.9%) 233.0
yadhu 1 (0.1%) 4 (0.0%) 4.0
epruesse 2 (0.3%) 2 (0.0%) 1.0
boehnel 1 (0.1%) 1 (0.0%) 1.0
baderk 2 (0.3%) 1 (0.0%) 0.5

Most Recent Commits

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.

2 lines of code changed in 1 file:

  • PARSIMONY: PARS_main.cxx (+2 -2)
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.

2 lines of code changed in 1 file:

  • PARSIMONY: Makefile (+2)
westram 2019-05-10 13:57 Rev.: 17877


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

1 lines of code changed in 1 file:

  • PARSIMONY: PARS_main.cxx (+1 -1)
westram 2019-04-29 14:44 Rev.: 17836


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

1 lines of code changed in 1 file:

  • PARSIMONY: PARS_main.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

2 lines of code changed in 1 file:

  • PARSIMONY: Makefile (+2)
westram 2018-10-24 15:58 Rev.: 17534


* partial merge from 'fix' into 'trunk'
- globally define what are "gaps"
- kept behavioral changes to a minimum:
* defaults for (user-defined) gap-definition in EDIT4 changed
* EDIT sequence search also uses user-defined gaps
* adds: log:branches/fix@17529:17533

10 lines of code changed in 2 files:

  • PARSIMONY: Makefile (+1), PARS_main.cxx (+9 -8)
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

4 lines of code changed in 3 files:

  • PARSIMONY: AP_tree_edge.cxx (+1 -1), AP_tree_nlen.cxx (+1 -1), PARS_dtree.cxx (+2 -2)
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

33 lines of code changed in 4 files:

  • PARSIMONY: AP_buffer.hxx (+4), AP_tree_edge.cxx (+6 -1), AP_tree_nlen.cxx (+14 -1), PARS_main.cxx (+9 -3)
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

4 lines of code changed in 1 file:

  • PARSIMONY: PARS_main.cxx (+4 -5)
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:

  • PARSIMONY: AP_tree_edge.cxx (+1 -1)
westram 2018-07-24 08:36 Rev.: 17263


* refer to ticket

4 lines of code changed in 2 files:

  • PARSIMONY: PARS_dtree.cxx (+1 -1), PARS_main.cxx (+3 -3)
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

61 lines of code changed in 2 files:

  • PARSIMONY: PARS_dtree.cxx (+39 -35), PARS_main.cxx (+22 -12)
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

68 lines of code changed in 8 files:

  • PARSIMONY: AP_buffer.cxx (+1 -1), AP_buffer.hxx (+2 -1), AP_main.cxx (+1 -1), AP_tree_edge.cxx (+13 -13), AP_tree_nlen.cxx (+36 -60), PARS_dtree.cxx (+2 -2), PARS_main.cxx (+10 -10), ap_tree_nlen.hxx (+3 -5)
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

6 lines of code changed in 1 file:

  • PARSIMONY: Makefile (+6)
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:

  • PARSIMONY: PARS_main.cxx (-5)
westram 2018-04-11 16:48 Rev.: 16880


* reintegrates 'multicore' into 'trunk'
- derive sequence classes able to be combined from new class {{{AP_combinableSeq}}}
* elim dummy functions from rest of hierarchy
- implements non-writing combine for add-species (speedup: 25-35%)
- introduce type {{{Mutations}}} => uses long everywhere (before mostly, but not always used float)
- allows use of {{{future}}}s
* nucleotide combine is able to calculate async (disabled via define atm -> {{{NEVER_COMBINE_ASYNC}}}; needs more work on calling algorithm)
* adds: log:branches/multicore@16769:16879

146 lines of code changed in 10 files:

  • PARSIMONY: AP_buffer.cxx (+1 -1), AP_buffer.hxx (+3 -3), AP_tree_edge.cxx (+10 -10), AP_tree_nlen.cxx (+25 -25), PARS_dtree.cxx (+22 -22), PARS_main.cxx (+58 -42), PerfMeter.h (+8 -8), ap_tree_nlen.hxx (+14 -11), pars_main.hxx (+1 -1), test_env.h (+4 -4)
westram 2018-02-15 12:51 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

366 lines of code changed in 3 files:

  • PARSIMONY: PARS_main.cxx (+360 -169), ap_tree_nlen.hxx (+6), test_env.h (-10)
westram 2017-11-28 19:22 Rev.: 16766


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

27 lines of code changed in 5 files:

  • PARSIMONY: AP_tree_edge.cxx (+1 -2), AP_tree_nlen.cxx (+4 -8), PARS_klprops.cxx (+1 -1), PARS_main.cxx (+20 -29), test_env.h (+1 -2)
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

173 lines of code changed in 12 files:

  • PARSIMONY: AP_buffer.cxx (+4 -4), AP_buffer.hxx (+3 -3), AP_main.cxx (+3 -3), AP_tree_edge.cxx (+25 -25), AP_tree_nlen.cxx (+32 -32), PARS_dtree.cxx (+15 -15), PARS_main.cxx (+69 -64), ap_main.hxx (+6 -6), ap_main_type.hxx (+4 -4), ap_tree_nlen.hxx (+6 -6), pars_main.hxx (+1 -1), test_env.h (+5 -5)
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

1 lines of code changed in 1 file:

  • PARSIMONY: PARS_dtree.cxx (+1 -1)
westram 2017-11-14 15:36 Rev.: 16653


* reintegrates 'gcc' into 'trunk' (fixes defect part of #752)
- allow compilation with gcc 7.x series (accepting 2 clang-test-results for gcc 7.x)
- vectorization:
* in {{{SL/CONSENSUS/chartable.cxx}}} works again with gcc 7.x (broken for 6.x series)
- checker: added syntax to exclude a range of versions
* check new 7.x vectorizations + fix vectorization-counts
* adds: log:branches/gcc@16578:16635,16649:16652

18 lines of code changed in 2 files:

  • PARSIMONY: PARS_main.cxx (+14 -4), test_env.h (+4 -1)
westram 2017-06-29 15:18 Rev.: 16043


* reintegrates 'fix' into 'trunk'
- valgrind fixes
* generally repaired valgrinding (external tools)
* {{{group_scaling}}} was not initialized correct (RUI)
- DRYed code to run external tools from unittests
* adds: log:branches/fix@16037:16042

10 lines of code changed in 3 files:

  • PARSIMONY: PARS_dtree.cxx (+1 -1), ap_tree_nlen.hxx (+2 -2), test_env.h (+7 -1)
westram 2017-03-28 15:32 Rev.: 15703


* reintegrates 'group' into 'trunk'
- implements #709
* adds: log:branches/group@15693:15702

6 lines of code changed in 1 file:

  • PARSIMONY: Makefile (+6)
westram 2017-03-26 17:00 Rev.: 15691


* reintegrates 'keys' into 'trunk'
- implements part of #687 (species traversal via keys)
- adds temp. unfolding of selected species
- several fixes to [15665] (PARSIMONY)
* adds: log:branches/keys@15591:15690

67 lines of code changed in 3 files:

  • PARSIMONY: PARS_dtree.cxx (+1 -1), PARS_main.cxx (+63 -60), test_env.h (+3 -1)
westram 2017-03-23 14:58 Rev.: 15665


* reintegrates 'refactor' into 'trunk'
- refactored AWT_graphic
* now have explicit states with different permissions
1. update model + request view/DB updates (AWT_auto_refresh)
- always preceeded by DB->model up-to-date-check
- automatically updates the view on destruction
2. update (DB and view) from model
3. neither
- benefits
* saves several view-updates
* unproblematic nesting of functions requesting view-updates
* will allow
- delayed view-updates and
- easier modification of update logic
- fixes a bunch of update-issues (found on the way)
* adds: log:branches/refactor@15613:15615,15627:15637,15639:15664

16 lines of code changed in 5 files:

  • PARSIMONY: AP_tree_nlen.cxx (+4 -3), PARS_dtree.cxx (+2 -2), PARS_main.cxx (+8 -14), ap_tree_nlen.hxx (+1 -2), test_env.h (+1 -1)
westram 2017-01-16 12:17 Rev.: 15579


* reintegrates 'unittest' into 'trunk'
- activates unittests under OSX (performs #740)
* disabled a few tests + accepted a few modified results (see #741)
* {{{RegExpr}}} no longer uses exception
* fix quoting of {{{char*}}} (in reported test result)
- fixes several compiler flags unknown under OSX/clang
- fix usability of compile log (make now prints directory)
* adds: log:branches/unittest@15534:15578
* removes: [15520/branches/warnings]

21 lines of code changed in 1 file:

  • PARSIMONY: PARS_main.cxx (+21 -2)
westram 2017-01-13 08:55 Rev.: 15559


* reintegrates 'random' into 'trunk'
- replaces random number generator by portable version (using boost)
- approve changed test results (PARSIMONY: mix protein tree; CONSENSUS: random regression test)
- accept one unstable test result
* adds: log:branches/random@15551:15558

20 lines of code changed in 1 file:

  • PARSIMONY: PARS_main.cxx (+20 -13)
westram 2017-01-09 16:10 Rev.: 15529


* reintegrates 'warnings' into 'trunk'
- use gnu++14-standard for gcc>=6
- use gnu++0x-standard for gcc<4.7 (bugfix)
- defines many inlines as constexpr
* adds: log:branches/warnings@15515:15522,15525:15528

1 lines of code changed in 1 file:

  • PARSIMONY: AP_tree_nlen.cxx (+1 -1)
westram 2017-01-04 18:06 Rev.: 15513


* reintegrates 'warnings' into 'trunk'
- activate additional warnings (gcc 5.x++)
- Cxx11-forward final (classes+methods)
- fix tag problems caused by using preprocessor
* adds: log:branches/warnings@15486:15489,15491:15501,15506:15512

3 lines of code changed in 2 files:

  • PARSIMONY: ap_tree_nlen.hxx (+2 -2), test_env.h (+1 -1)
westram 2016-12-30 13:31 Rev.: 15484


* reintegrates 'warnings' into 'trunk'
- fixes compiler warnings (gcc 5.x)
* adds: log:branches/warnings@15468,15471,15473,15477,15481:15483

2 lines of code changed in 1 file:

  • PARSIMONY: AP_tree_edge.cxx (+2)
westram 2016-12-28 19:15 Rev.: 15459


* reintegrates 'pars' into 'trunk'
- performs #643
* adds: log:branches/pars@15428:15450,15452:15458

350 lines of code changed in 6 files:

  • PARSIMONY: AP_buffer.hxx (+2), AP_tree_nlen.cxx (+39 -62), PARS_dtree.cxx (+3 -3), PARS_main.cxx (+289 -151), ap_tree_nlen.hxx (+3 -7), test_env.h (+14 -1)
westram 2016-11-23 13:46 Rev.: 15374


* reintegrates 'tree' into 'trunk'
- implements #578
- tree display
* new options: triangle, attach points
* optimized placement: folded group names, bootstrap values
* split config window (too big)
* adds: log:branches/tree@15347:15373

8 lines of code changed in 2 files:

  • PARSIMONY: PARS_dtree.cxx (+3 -3), PARS_main.cxx (+5 -5)
westram 2016-11-23 11:47 Rev.: 15372


* fix "insufficient data" warning
- inner node count was wrong
- show what "low" means

4 lines of code changed in 1 file:

  • PARSIMONY: PARS_main.cxx (+4 -2)
westram 2016-10-06 12:52 Rev.: 15306


* derive {{{TREE_canvas}}} from {{{AWT_canvas}}}
- move {{{awar_tree}}} -> {{{TREE_canvas}}}
- use {{{TREE_canvas}}} where required
- remove dummy-param from {{{AWT_canvas}}}-ctor
* rename {{{NT_canvas_registry}}} -> {{{TREE_canvas_registry}}}
* remove unused param from {{{AP_user_push_cb}}}

23 lines of code changed in 1 file:

  • PARSIMONY: PARS_main.cxx (+23 -23)
westram 2016-10-05 12:39 Rev.: 15301


* full update from child 'sync' into 'trunk'
- register all NTREE canvases
- provide canvas selection list
- pass awar to canvas (not its name; expect awar already exists); no awar for non-tree-canvases
* adds: log:branches/sync@15292:15300

1 lines of code changed in 1 file:

  • PARSIMONY: PARS_main.cxx (+1 -1)
westram 2016-08-30 12:30 Rev.: 15254


* depends for [15253]

6 lines of code changed in 1 file:

  • PARSIMONY: Makefile (+6)
westram 2016-08-17 20:39 Rev.: 15198


* remove {{{virtual}}} if {{{OVERRIDE}}} is present
- OVERRIDE implies 'implicit virtual' (if code compiles as C++11 <- tested on build server!)

1 lines of code changed in 1 file:

  • PARSIMONY: ap_tree_nlen.hxx (+1 -1)
westram 2016-08-11 11:05 Rev.: 15176


* reintegrates 'fixres' into 'trunk'
- fixes #715
* adds: log:branches/fixres@15127:15175

12 lines of code changed in 4 files:

  • PARSIMONY: AP_tree_edge.cxx (+1 -1), AP_tree_nlen.cxx (+4 -4), Makefile (+6), PARS_main.cxx (+1 -1)
westram 2016-07-15 15:48 Rev.: 15064


* remove parameter {{{base_gc}}} from {{{AW_manage_GC}}} (always zero)

1 lines of code changed in 1 file:

  • PARSIMONY: PARS_dtree.cxx (+1 -1)
westram 2016-07-14 15:15 Rev.: 15054


* reintegrates 'color' into 'trunk'
- implements #443 (+parts of #444)
* adds: log:branches/color@14920:14921,14923:14928,14930:14939,14941:14951,14954:14956,14958:14959,14961:14964,14968,14970:14981,14985,14988,14990:14992,14994:14999,15001:15004,15007,15009,15012:15026,15028:15035,15037:15039,15041:15053

8 lines of code changed in 3 files:

  • PARSIMONY: Makefile (+1 -5), PARS_dtree.cxx (+2 -1), PARS_main.cxx (+5 -4)

(330 more)

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