#
# ChangeLog for mds-and-trees
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# Generated by Trac 1.2.1
# 03/11/25 13:53:43
Sat, 07 Oct 2017 14:29:23 GMT Maciej Komosinski [713]
* mds-and-trees/tree-genealogy.py (modified)
Made error message more specific
Fri, 06 Oct 2017 17:07:47 GMT Maciej Komosinski [712]
* mds-and-trees/tree-genealogy.py (modified)
Improved status and error messages
Fri, 06 Oct 2017 15:08:12 GMT konrad [711]
* mds-and-trees/tree-genealogy.py (modified)
Logs without [BORN] entries (only [OFFSPRING]) should load properly
now
Fri, 06 Oct 2017 14:06:17 GMT konrad [710]
* mds-and-trees/tree-genealogy.py (modified)
Added multi-input-file support (eg. ./tree-genealogy.py -i file1.out ...
Sat, 30 Sep 2017 22:06:54 GMT konrad [709]
* mds-and-trees/tree-genealogy.py (modified)
tree-genealogy.py should now work correctly with the order of events ...
Sat, 30 Sep 2017 17:39:25 GMT Maciej Komosinski [708]
* mds-and-trees/tree-genealogy.py (modified)
Improved diagnostic message
Sat, 30 Sep 2017 12:53:15 GMT konrad [707]
* mds-and-trees/tree-genealogy.py (modified)
Added a warning message about merging nodes with a virtual parent
node.
Fri, 29 Sep 2017 17:20:26 GMT konrad [706]
* mds-and-trees (modified)
No more svn ignore on mds-and-trees
Fri, 29 Sep 2017 16:26:48 GMT konrad [705]
* mds-and-trees (modified)
* mds-and-trees/tree_colormaps.conf (added)
Added an example of configuration file with colormaps
Thu, 21 Sep 2017 13:05:17 GMT konrad [702]
* mds-and-trees/tree-genealogy.py (modified)
Non-normalized step values for cmap can now extend outside the range ...
Wed, 20 Sep 2017 13:29:50 GMT konrad [701]
* mds-and-trees/tree-genealogy.py (modified)
Fixed a bug that could occur for trees with a lot of crossover ...
Tue, 19 Sep 2017 13:45:07 GMT konrad [700]
* mds-and-trees/tree-genealogy.py (modified)
Colors support matplotlib cmaps now. 'color' property in config file ...
Tue, 05 Sep 2017 16:33:17 GMT Maciej Komosinski [697]
* mds-and-trees/tree-genealogy.py (modified)
More legible and consistent notation of ranges
Tue, 05 Sep 2017 14:14:41 GMT konrad [696]
* mds-and-trees/tree-genealogy.py (modified)
Changes to formating of min/max values of properties
Tue, 05 Sep 2017 14:08:58 GMT konrad [695]
* mds-and-trees/tree-genealogy.py (modified)
Using matplotlib's color package to interpret colors. Color can be ...
Mon, 04 Sep 2017 14:28:03 GMT konrad [694]
* mds-and-trees/tree-genealogy.py (modified)
Some improvements in behavior for big trees
Mon, 04 Sep 2017 00:52:52 GMT konrad [690]
* mds-and-trees/tree-genealogy.py (modified)
Better (but not ideal) behavior for very big trees
Sun, 03 Sep 2017 16:22:55 GMT Maciej Komosinski [689]
* mds-and-trees/tree-genealogy.py (modified)
More informative message
Sun, 03 Sep 2017 16:21:10 GMT Maciej Komosinski [688]
* mds-and-trees/tree-genealogy.py (modified)
More informative message
Sun, 03 Sep 2017 15:37:43 GMT konrad [687]
* mds-and-trees/tree-genealogy.py (modified)
Using "inherited' to decide horizontal distance from the parent
Sun, 03 Sep 2017 14:23:17 GMT Maciej Komosinski [686]
* mds-and-trees/tree-genealogy.py (modified)
Made loop iteration variable implicit ("enumerate")
Sun, 03 Sep 2017 14:14:47 GMT Maciej Komosinski [685]
* mds-and-trees/tree-genealogy.py (modified)
Displays progress as convenient percentage
Sun, 03 Sep 2017 13:57:13 GMT Maciej Komosinski [684]
* mds-and-trees/tree-genealogy.py (modified)
Minor optimization
Sun, 03 Sep 2017 13:51:24 GMT Maciej Komosinski [683]
* mds-and-trees/tree-genealogy.py (modified)
Slightly more helpful error message
Sat, 02 Sep 2017 12:12:51 GMT konrad [682]
* mds-and-trees/tree-genealogy.py (modified)
Broken last lines in input logs will not crash the script anymore ...
Mon, 28 Aug 2017 16:43:30 GMT konrad [681]
* mds-and-trees/tree-genealogy.py (modified)
Improved the compute_depth function so now it works much faster for ...
Sun, 27 Aug 2017 18:05:45 GMT konrad [680]
* mds-and-trees/tree-genealogy.py (modified)
Fixed the "ValueError: max() arg is an empty sequence" error ...
Sun, 27 Aug 2017 17:48:02 GMT konrad [679]
* mds-and-trees/tree-genealogy.py (modified)
compute_adepth no longer uses recursion (so it should work better ...
Sun, 27 Aug 2017 13:11:36 GMT konrad [678]
* mds-and-trees/tree-genealogy.py (modified)
Fixed a bug attempting to normalize a list of lists
Sun, 27 Aug 2017 13:06:39 GMT konrad [677]
* mds-and-trees/tree-genealogy.py (modified)
Fixed a bug with an incorrect order of assigning placement to nodes
Wed, 23 Nov 2016 16:58:33 GMT konrad [633]
* mds-and-trees/tree-genealogy.py (modified)
Added measure of progress (based on regression of time-distances ...
Thu, 27 Oct 2016 14:38:57 GMT konrad [628]
* mds-and-trees/tree-genealogy.py (modified)
Fixed printing texts in svg and added support for additional ...
Wed, 26 Oct 2016 17:13:26 GMT konrad [627]
* mds-and-trees/tree-genealogy.py (modified)
tree-genealogy.py is now supporting multiple virtual parents (they ...
Mon, 24 Oct 2016 13:01:12 GMT konrad [626]
* mds-and-trees/tree-genealogy.py (modified)
Added multisampling (antialiasing) option for raster output
Fri, 21 Oct 2016 21:40:42 GMT konrad [625]
* mds-and-trees/Vera.ttf (added)
Font for tree-genealogy.py
Fri, 21 Oct 2016 17:45:07 GMT konrad [624]
* mds-and-trees/tree-genealogy.py (modified)
* mds-and-trees/tree.conf (added)
New, faster, more flexible and refactored version of the tree- ...
Tue, 11 Oct 2016 15:19:04 GMT konrad [623]
* mds-and-trees/tree-genealogy.py (modified)
Some minor changes
Tue, 11 Oct 2016 14:48:23 GMT konrad [622]
* mds-and-trees/tree-genealogy.py (modified)
Added an option to restrict the tree to first X nodes.
Mon, 10 Oct 2016 15:18:52 GMT konrad [621]
* mds-and-trees/tree-genealogy.py (modified)
Rewritten prepos_children to the iterative form + Turned on some ...
Fri, 30 Sep 2016 00:43:38 GMT konrad [620]
* mds-and-trees/tree-genealogy.py (modified)
The parameters should not be case specific anymore, also added some ...
Fri, 23 Sep 2016 13:06:58 GMT konrad [619]
* mds-and-trees/tree-genealogy.py (modified)
Changed spine and skeleton drawing methods from recurrent to ...
Fri, 23 Sep 2016 11:09:55 GMT konrad [618]
* mds-and-trees/tree-genealogy.py (modified)
Removed the recurrent version of the tree-drawing method, fixed and ...
Wed, 21 Sep 2016 15:52:27 GMT konrad [617]
* mds-and-trees/tree-genealogy.py (modified)
Added non-recurrent verion of tree drawing function, ...
Wed, 14 Sep 2016 22:07:27 GMT Maciej Komosinski [616]
* mds-and-trees/mds_plot.py (modified)
Introduced an option to swap (exchange) X and Y axes
Sun, 11 Sep 2016 20:52:34 GMT Maciej Komosinski [615]
* mds-and-trees/tree-genealogy.py (modified)
Improved descriptions
Sun, 11 Sep 2016 20:45:46 GMT Maciej Komosinski [614]
* mds-and-trees/tree-genealogy.py (modified)
Fixed typos
Sun, 11 Sep 2016 01:59:38 GMT Maciej Komosinski [613]
* mds-and-trees/mds_plot.py (modified)
Introduced options to flip (invert, negate) X and/or Y axes
Thu, 01 Sep 2016 22:06:41 GMT Maciej Komosinski [609]
* mds-and-trees/mds_plot.py (modified)
Labels can have colors dependent on label text
Thu, 01 Sep 2016 15:01:37 GMT Maciej Komosinski [608]
* mds-and-trees/mds_plot.py (modified)
Displays the fraction of variance preserved after MDS
Thu, 01 Sep 2016 14:39:23 GMT Maciej Komosinski [607]
* mds-and-trees/mds_plot.py (modified)
Updated for new format of dissimilarity matrix (with the optional two ...
Tue, 30 Aug 2016 15:08:10 GMT Maciej Komosinski [604]
* mds-and-trees/mds_plot.py (modified)
Made the amount of jitter a continuous, adjustable parameter
Sun, 28 Aug 2016 16:34:15 GMT oriona [603]
* mds-and-trees/mds_plot.py (modified)
Integer command line arguments converted to ints in main call.
Sun, 28 Aug 2016 15:00:05 GMT Maciej Komosinski [602]
* mds-and-trees/mds_plot.py (modified)
- More flexible reading of distance matrices from files
- Can also ...
Sun, 28 Aug 2016 13:04:25 GMT oriona [600]
* mds-and-trees/mds_plot.py (modified)
Number of returned dimensions set to minimum of desired number and ...
Thu, 25 Aug 2016 15:48:45 GMT oriona [599]
* mds-and-trees/mds_plot.py (modified)
Function for computing variances removed.
Thu, 25 Aug 2016 15:44:00 GMT oriona [598]
* mds-and-trees/mds_plot.py (modified)
MDS algorithm changed to cmdscale. Coordinates export to file added.
Wed, 24 Aug 2016 01:54:42 GMT Maciej Komosinski [597]
* mds-and-trees/mds_plot.py (modified)
No longer ignores "jitter" and "outname" parameters
Wed, 24 Aug 2016 01:52:38 GMT Maciej Komosinski [596]
* mds-and-trees/mds_plot.py (modified)
Uncomment to make it work with no graphical backend
Tue, 23 Aug 2016 16:13:31 GMT konrad [594]
* mds-and-trees/tree-genealogy.py (modified)
Fixed drawing the spine and the skeleton for the tree-genealogy.py
Fri, 19 Aug 2016 21:59:09 GMT konrad [589]
* mds-and-trees/tree-genealogy.py (modified)
Fixed dark lines inside lines in tree-genealogy.py
Thu, 18 Aug 2016 20:01:16 GMT konrad [586]
* mds-and-trees/tree-genealogy.py (modified)
Tiny refactoring of tree-genealogy.py
Thu, 18 Aug 2016 19:58:00 GMT konrad [585]
* mds-and-trees/tree-genealogy.py (modified)
Added an option for defining colors of crossover / mutation lines ...
Tue, 09 Aug 2016 17:38:35 GMT konrad [577]
* mds-and-trees/tree-genealogy.py (modified)
Supporting coloring edges and nodes by type, scalable dots
Tue, 09 Aug 2016 16:30:33 GMT konrad [576]
* mds-and-trees/tree-genealogy.py (modified)
Simple scale
Mon, 08 Aug 2016 18:13:29 GMT konrad [572]
* mds-and-trees/tree-genealogy.py (modified)
Added crossover and support for Inheritance table (but the table ...
Mon, 08 Aug 2016 14:10:18 GMT konrad [571]
* mds-and-trees/tree-genealogy.py (modified)
Additional options in tree-genealogy.py, dots and jitter
Sat, 06 Aug 2016 00:16:56 GMT konrad [566]
* mds-and-trees/tree-genealogy.py (modified)
Added REAL time option for tree-genealogy.py, renamed previous REAL ...
Fri, 05 Aug 2016 23:27:20 GMT oriona [565]
* mds-and-trees/mds_plot.py (added)
Script for plotting results of the MDS added.
Fri, 05 Aug 2016 21:25:02 GMT konrad [564]
* mds-and-trees/tree-genealogy.py (modified)
some changes to drawing style + non-random dissimilarity + assertion
Fri, 05 Aug 2016 21:15:07 GMT konrad [563]
* mds-and-trees/tree-genealogy.py (modified)
updated to the new input format
Fri, 05 Aug 2016 18:23:52 GMT Maciej Komosinski [562]
* mds-and-trees (added)
* mds-and-trees/tree-genealogy.py (added)
Added a script to draw genealogical trees based on parent-child ...