December 2013 Commit Log

Number of Commits:
10
Number of Active Developers:
1
westram 2013-12-26 12:48 Rev.: 11401


* reintegrates 'tree' into 'trunk':
- consensus trees:
* support for merging partial trees ("worked" before, but results were crap; implements #65)
* generated trees are automatically re-rooted and -ordered
* always list source trees in consensus-tree-comment; show info about partial trees
* fixed progress bar
- made GBT_TREE a base class of other tree classes (implements #31)
- save tree properties in properties (not in DB)
- new functions 'Remove zombies/marked from ALL trees'
- tree load/save: layout fixes
- unit tests
* added tests for basic tree modifications (PARSIMONY)
- performance:
* compute_tree updates tree information in one traversal
* tree generators are now capable to generate any type of tree (w/o needing to copy it once)
- bugfixes:
* NNI (of marked species) was also always performed for colored species
* centered beautify-order is stable now
* improved 'search optimal root'
* adds:
- log:branches/tree@10500:10534,10542:11182,11184:11186,11188:11400
- log:branches/treeTests@11198:11335

3866 lines of code changed in 113 files:

westram 2013-12-21 17:05 Rev.: 11380


* fix JUMP button behavior
- no strange zoom-reset in radial view (fixes #111)
- scroll display in radial view. Actually NT_jump_cb() now uses same code for all views
- if selected species is outside logical zoom, do not reset zoom unconditionally
* instead set logical zoom to common ancestor, but only if group unfolding is permitted (i.e. if jump-button was pressed)
- when jump button is pressed again, also center horizontally
- fixed several cases where strange messages appeared

109 lines of code changed in 3 files:

westram 2013-12-21 14:59 Rev.: 11379


* LIST/DENDRO:
- pressing JUMP button when species is already visible -> center species vertically

34 lines of code changed in 5 files:

westram 2013-12-21 13:41 Rev.: 11378


- rename misleading member

40 lines of code changed in 5 files:

westram 2013-12-14 15:35 Rev.: 11354


* fix several cppcheck warnings

86 lines of code changed in 10 files:

westram 2013-12-12 16:15 Rev.: 11339


* fix detection of "required by"-annotations (gcc 4.8.x)

1 lines of code changed in 1 file:

westram 2013-12-12 16:15 Rev.: 11338


* suppress "invalid suffix on literal" warnings (cause is in perl-headers)

1 lines of code changed in 1 file:

westram 2013-12-03 10:28 Rev.: 11284


* removed the possibility to separately perform
- removal of unused and
- registration of unregistered fields.
* 'Refresh fields' does "both" (see #306)
* deleted obsolete helpfile
* updated help

33 lines of code changed in 9 files:

westram 2013-12-02 13:04 Rev.: 11283


* fixed some issues related to [11278]
- added missing help
- disable for non-experts
- some logical fixes
* do timer callback only (once) after need_recalc was set
* checking 'auto calc' now instantly performs the calculation (if needed)
* happens even automatically after ARB_DIST startup (if saved with properties)
* if 'matrix autocalc' is checked, but neither 'tree autocalc' is checked nor matrix windows is shown (or would auto-popup) => only forget matrix

158 lines of code changed in 4 files:

westram 2013-12-01 16:49 Rev.: 11278


* added two automation toggles to ARB_DIST
- 'Auto recalculate' (for matrix) and
- 'Auto calculate tree'
* new trigger for recalculation:
- one of the trees involved in sorting itself has changed (not only treename)
* fixed glitches:
- when user matrix is unsupported for selected correction
* do not fail and abort
* instead warn and just do not use it
- if no sort tree given, warn only once

254 lines of code changed in 5 files:

November 2013 »

Generated by StatSVN 0.7.0