Directory PHYLO/

Directory Created:
2000-11-23 11:41
Total Files:
11
Deleted Files:
4
Lines of Code:
2152

[root]/PHYLO

Lines of Code

PHYLO/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 416 (100.0%) 7399 (100.0%) 17.7
westram 397 (95.4%) 4754 (64.3%) 11.9
oldcode 13 (3.1%) 2434 (32.9%) 187.2
meierh 1 (0.2%) 200 (2.7%) 200.0
epruesse 2 (0.5%) 5 (0.1%) 2.5
yadhu 1 (0.2%) 4 (0.1%) 4.0
boehnel 1 (0.2%) 2 (0.0%) 2.0
baderk 1 (0.2%) 0 (0.0%) 0.0

Most Recent Commits

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:

  • PHYLO: Makefile (+2)
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

1 lines of code changed in 1 file:

  • PHYLO: PH_filt.cxx (+1 -1)
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

3 lines of code changed in 1 file:

  • PHYLO: Makefile (+3)
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:

  • PHYLO: PH_main.cxx (-9)
westram 2017-11-28 19:22 Rev.: 16766


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

17 lines of code changed in 4 files:

  • PHYLO: PH_display.cxx (+12 -24), PH_display.hxx (+1 -1), PH_filt.cxx (+3 -6), PH_main.cxx (+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

48 lines of code changed in 6 files:

  • PHYLO: PH_data.cxx (+6 -6), PH_display.cxx (+1 -1), PH_filt.cxx (+6 -6), PH_main.cxx (+12 -12), PH_root.cxx (+2 -2), phylo.hxx (+21 -21)
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

2 lines of code changed in 1 file:

  • PHYLO: PH_main.cxx (+2 -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

2 lines of code changed in 1 file:

  • PHYLO: PH_filt.cxx (+2 -2)
westram 2017-07-04 17:25 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

8 lines of code changed in 1 file:

  • PHYLO: PH_main.cxx (+8 -6)
westram 2016-08-30 14:26 Rev.: 15256


* replace redundant data {{{AW_font_limits::height}}} with {{{get_height()}}}

3 lines of code changed in 1 file:

  • PHYLO: PH_display.cxx (+3 -3)
westram 2016-08-30 12:30 Rev.: 15254


* depends for [15253]

3 lines of code changed in 1 file:

  • PHYLO: Makefile (+3)
westram 2016-08-11 11:05 Rev.: 15176


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

15 lines of code changed in 4 files:

  • PHYLO: Makefile (+5), PH_data.cxx (+2 -2), PH_filt.cxx (+5 -7), PH_main.cxx (+3 -3)
westram 2016-07-15 15:48 Rev.: 15064


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

2 lines of code changed in 1 file:

  • PHYLO: PH_main.cxx (+2 -2)
westram 2016-06-15 13:35 Rev.: 14943


* merge 2 WINDOW-modifications from 'color' into 'trunk'
* adds: log:branches/color@14929,14940

0 lines of code changed in 1 file:

  • PHYLO: PH_main.cxx (-2)
westram 2016-05-24 15:53 Rev.: 14862


* use separate GCs for bottom area (changed basename -> 'ARB_PHYLO_BOTTOM') => no longer uses canvas background color in gtk-version
* define lightgrey background for bottom area (workaround problem described in #433)
* change default colors (background, marker)

4 lines of code changed in 1 file:

  • PHYLO: PH_main.cxx (+4 -4)
westram 2016-05-24 14:07 Rev.: 14860


* DRY phylo display code

19 lines of code changed in 1 file:

  • PHYLO: PH_display.cxx (+19 -41)
westram 2016-05-24 14:00 Rev.: 14859


* fix wrong {{{base_drag}}}s passed to {{{AW_manage_GC}}} (see [14857])
* use meaningful names for GCs
* headline of bottom-section was not visible in motif-version. fixed.

27 lines of code changed in 3 files:

  • PHYLO: PH_display.cxx (+16 -15), PH_main.cxx (+2 -2), phylo.hxx (+9 -3)
westram 2016-05-12 09:58 Rev.: 14838


* no longer pseudo-hide gc-manager-object
- {{{aw_gc_manager}}} -> {{{AW_gc_manager}}}
- use pointers to {{{AW_gc_manager}}} instead of pointer-typedef

13 lines of code changed in 1 file:

  • PHYLO: PH_main.cxx (+13 -11)
westram 2015-12-16 16:13 Rev.: 14622


* reintegrates 'ui' into 'trunk'
- implements #656
- adds instant update for
* next neighbour search
* branch analysis (mark functions)
* arb-phylo (filter setup)
* adds: log:branches/ui@14588:14621

127 lines of code changed in 6 files:

  • PHYLO: PH_display.cxx (+6 -3), PH_display.hxx (+2 -2), PH_filt.cxx (+92 -58), PH_filter.hxx (-14), PH_main.cxx (+13 -21), phylo.hxx (+14 -11)
westram 2015-12-11 16:05 Rev.: 14604


* reintegrates 'cleanup' into 'trunk'
- eliminates ~10k dead code
* adds: log:branches/cleanup@14598:14603

92 lines of code changed in 9 files:

  • PHYLO: Makefile (-15), PH_data.cxx (+1 -197), PH_display.cxx (+44 -123), PH_display.hxx (+24 -25), PH_filt.cxx (-41), PH_filter.hxx (+9 -6), PH_main.cxx (+1 -5), needs_libs (-1), phylo.hxx (+13 -81)
westram 2015-11-11 13:40 Rev.: 14490


* change callbacktype used to trigger refresh after GCs changed
- pass what has been changed (font,color only,use of color groups)
* added standard callback ({{{AWT_GC_changed_cb}}})
* {{{AWAR_COLOR_GROUPS_USE}}}
- remove client callback triggering refresh (installed by TREEDISP)
- add general callback calling {{{GcChangedCallback}}} passed to {{{AW_manage_GC}}}
- hide awar inside {{{AW_preset.cxx}}}
* effects:
- EDIT4 does refresh now when toggling use of color groups
- (several) canvases just do "expose" in case of color change (instead of "resize/zoom reset" which is needed for font changes)

18 lines of code changed in 1 file:

  • PHYLO: PH_main.cxx (+18 -4)
westram 2015-11-04 10:57 Rev.: 14453


* do not cast AW_POPDOWN

1 lines of code changed in 1 file:

  • PHYLO: PH_filt.cxx (+1 -1)
westram 2015-10-28 11:58 Rev.: 14425


* reintegrates 'consensus' into 'trunk'
- fixes #663 (consistent consensus calculation)
- allow to load SAI into existing EDIT4 config
- tweaked "View differences"
- minor fixes for SAI MAX_FREQUENCY
* adds:
- log:branches/addtest@14319:14326
- log:branches/consensus@14276:14424

1 lines of code changed in 1 file:

  • PHYLO: PH_data.cxx (+1 -1)
westram 2015-09-07 17:58 Rev.: 14269


* sync menu entry 'Frame settings' (and mark motif only where missing)
* merge some gtk-only application code into trunk (not compiled there)

9 lines of code changed in 1 file:

  • PHYLO: PH_main.cxx (+9)
westram 2015-07-17 16:18 Rev.: 14046


* use one help for all "Colors and fonts"

2 lines of code changed in 1 file:

  • PHYLO: PH_main.cxx (+2 -2)
westram 2015-04-19 16:17 Rev.: 13754


* add config manager to PHYL filter settings
* minor layout fixes

28 lines of code changed in 3 files:

  • PHYLO: Makefile (+1), PH_filt.cxx (+21 -3), PH_main.cxx (+6 -6)
westram 2015-01-23 15:19 Rev.: 13443


* reintegrates 'vectorize' into 'trunk'
- adds vectorization check for gcc 4.9.x / NDEBUG compile
* adds:
- log:branches/vectorize@13428:13442

1 lines of code changed in 1 file:

  • PHYLO: Makefile (+1 -1)
westram 2014-10-13 17:34 Rev.: 13044


* revert [13041:13043]
- instead forbid gcc 4.8.0

2 lines of code changed in 2 files:

  • PHYLO: PH_data.cxx (+1 -1), PH_filt.cxx (+1 -1)
westram 2014-10-12 17:18 Rev.: 13043


* ~~harden patches [13041:13042]~~
- ~~add safebool (=bool for non 4.8.0)~~
- ~~use in all bool-arrays~~

(reverted by [13044])

2 lines of code changed in 2 files:

  • PHYLO: PH_data.cxx (+1 -1), PH_filt.cxx (+1 -1)
westram 2014-08-14 12:18 Rev.: 12757


* unify selectionlist creator names
* awt_create_selection_list_on_pt_servers
- remove param 'popup', instead split into two function (button and list) as done for SAIs

2 lines of code changed in 1 file:

  • PHYLO: PH_main.cxx (+2 -2)
westram 2014-05-17 15:02 Rev.: 12273


- no magic exit codes

1 lines of code changed in 1 file:

  • PHYLO: PH_main.cxx (+1 -1)
westram 2014-05-12 15:22 Rev.: 12205


* inlined default param for create_option_menu

4 lines of code changed in 1 file:

  • PHYLO: PH_filt.cxx (+4 -4)
westram 2014-05-12 12:38 Rev.: 12192


* do not use more than 1 parameter in calls to create_option_menu
- 2nd parameter 'label' is dominated by a previous call to label (use direct label calls instead)
- 3rd parameter 'mnemonic' is w/o function in motif and is superfluous in gtk anyway
* reset 'gone_tree_name'

8 lines of code changed in 1 file:

  • PHYLO: PH_filt.cxx (+8 -4)
westram 2014-05-09 17:23 Rev.: 12189


* added 'fallback2default' to awt_create_selection_list_on_sai
* pass false (=disable fallback2default) for
- SAI/Create/Consensus
- SAI/Create/Max. Frequency
- SAI/Create/Positional variability + Column statistic
- ARB_PHYLO/File/Export Filter
- ARB_PHYLO/File/Export Frequencies
* fixes #520

1 lines of code changed in 1 file:

  • PHYLO: PH_main.cxx (+1 -1)
westram 2014-04-16 16:13 Rev.: 12043


* reintegrates 'fix' into 'trunk' (fixes #519)
- this patch wasn't really straightforward, instead each change caused new unexpected side effects. It's quite likely that i didn't detect all of them.
* adds:
- log:branches/fix@12023,12027:12042

2 lines of code changed in 1 file:

  • PHYLO: PH_data.cxx (+2 -2)
westram 2014-02-20 17:54 Rev.: 11645


* fix missing/duplicated/invalid mnemonics in rest of arb (completes [11643])

1 lines of code changed in 1 file:

  • PHYLO: PH_main.cxx (+1 -1)
westram 2014-01-10 20:16 Rev.: 11464


- un-dummy-fied transaction (renames only)

1 lines of code changed in 1 file:

  • PHYLO: PH_display.cxx (+1 -1)
westram 2013-11-26 19:39 Rev.: 11236


* inlined PH_matr.cxx

11 lines of code changed in 4 files:

  • PHYLO: Makefile (+5 -28), PH_main.cxx (+6 -2), PH_matr.cxx (del), phylo.hxx (-1)
westram 2013-11-26 19:12 Rev.: 11235


- no need to save in properties (overwritten anyway)

1 lines of code changed in 1 file:

  • PHYLO: phylo.hxx (+1 -1)
westram 2013-11-26 19:08 Rev.: 11234


* eliminate unneeded includes

2 lines of code changed in 2 files:

  • PHYLO: Makefile (-5), PH_matr.cxx (+2 -7)

(192 more)

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