# # ChangeLog for mds-and-trees # # Generated by Trac 1.2.1 # 12/22/24 09:00:37 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 ...