Trees in a dataset should be named
Bug #1378075 reported by
Jon Hill
This bug affects 1 person
Affects | Status | Importance | Assigned to | Milestone | |
---|---|---|---|---|---|
Supertree Toolkit |
Fix Released
|
Critical
|
Unassigned |
Bug Description
Each tree element should have a name, generated automatically, that is immutable. Currently, they are numbered and hence change when added to or deleted from.
This makes automatic processing (and the overlap) easier and more understandable.
To do:
- write function to automatically name a tree (based on what is there when imported)
- add the name to the schema - make it non-editable?
- add info to the manual
- check the tutorial
Related branches
lp:~jon-hill/supertree-toolkit/tree_names
- Jon Hill: Approve
-
Diff: 2151 lines (+404/-208)35 files modifieddoc/gui.rst (+18/-8)
schema/phylo_storage.rnc (+2/-2)
schema/phylo_storage.rng (+6/-9)
stk/stk_import_export.py (+1/-0)
stk/supertree_toolkit.py (+69/-23)
stk/test/_import_export.py (+2/-0)
stk/test/_schema_validation.py (+11/-1)
stk/test/_supertree_toolkit.py (+15/-3)
stk/test/data/input/awkward_subs.phyml (+5/-5)
stk/test/data/input/check_data_ind.phyml (+10/-10)
stk/test/data/input/check_data_summary.phyml (+6/-6)
stk/test/data/input/check_fossils.phyml (+6/-6)
stk/test/data/input/check_overlap_ok.phyml (+6/-6)
stk/test/data/input/check_taxa.phyml (+6/-6)
stk/test/data/input/clean_data.phyml (+12/-12)
stk/test/data/input/create_matrix.phyml (+6/-6)
stk/test/data/input/full_tree.phyml (+6/-6)
stk/test/data/input/lots.xml (+1/-1)
stk/test/data/input/non_unique_names.phyml (+8/-8)
stk/test/data/input/old_stk_input.phyml (+40/-40)
stk/test/data/input/old_stk_input_data_summary_test.phyml (+21/-21)
stk/test/data/input/permute_trees.phyml (+9/-9)
stk/test/data/input/single_name.xml (+1/-1)
stk/test/data/input/single_source.phyml (+2/-2)
stk/test/data/input/single_source_no_names.phyml (+67/-0)
stk/test/data/input/sub_taxa.phyml (+3/-3)
stk/test/data/input/two_names.xml (+2/-2)
stk/test/data/input/weighted_trees.phyml (+3/-3)
stk/test/data/output/full_tree.phyml (+3/-3)
stk/test/data/output/lots.xml (+1/-1)
stk/test/data/output/single_name.xml (+1/-1)
stk/test/data/output/two_names.xml (+2/-2)
stk_gui/gui/gui.glade (+11/-0)
stk_gui/plugins/phyml/import_tree.py (+1/-0)
stk_gui/stk_gui/interface.py (+41/-2)
Changed in supertree-toolkit: | |
status: | In Progress → Fix Committed |
Changed in supertree-toolkit: | |
status: | Fix Committed → Fix Released |
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Other issues here:
- existing tests check tree names, etc, but these are not in the data right now. Do we add the names to each Phyml in the dataset?
- Do we hack a function in that checks if tree names are set and if not, set's them? This covers old data
- _clean_data needs to add the names - we *should* load all existing datasets in, clean them (maybe not those designed to test clean_data...) and add the names. A user can do this.
- Also, a name_all_trees function would be useful for a user to run without cleaning data. Jaime will find it useful when generating Phyml's from the database too