Made 'centroid' the default decomposition, rather than 'longest'

Author: mtholder

run_sate_gui.py

@@ -216,7 +216,7 @@ def OnSatePresets(self, event):
         #wx.MessageBox("Preset Selected (Binding 1)", "Info")
         preset_selection = self.cb_sate_presets.GetValue()
         if preset_selection != "(custom)":
-            self.cb_decomp.SetValue("Longest")
+            self.cb_decomp.SetValue("Centroid")
             self.blindmode.SetValue(1)
             self.cb_apply_stop_rule.Enable()
             self.checkbox_stop_time.SetValue(False)
@@ -421,7 +421,7 @@ def _create_sate_settings_sizer(self):
                            ])
 
         strategy_list = ["Centroid", "Longest"]
-        self.cb_decomp = wx.ComboBox(self, -1, "Longest", choices=strategy_list, style=wx.CB_READONLY)
+        self.cb_decomp = wx.ComboBox(self, -1, "Centroid", choices=strategy_list, style=wx.CB_READONLY)
 
         self.ctrls.append(self.cb_decomp)
         self.sate_settings_ctrl_list = []

sate/__init__.py

@@ -12,7 +12,7 @@
 PROGRAM_NAME = "SATe"
 PROGRAM_AUTHOR = ["Jiaye Yu", "Mark T. Holder", "Jeet Sukumaran", "Siavash Mirarab", "Jamie Oaks"]
 PROGRAM_LICENSE = "GNU General Public License, version 3"
-PROGRAM_VERSION = "2.2.2"
+PROGRAM_VERSION = "2.2.3"
 PROGRAM_YEAR = "2009-2012"
 PROGRAM_DESCRIPTION = "Simultaneous Alignment and Tree Estimation"
 PROGRAM_WEBSITE = "http://phylo.bio.ku.edu/software/sate/sate.html"

sate/mainsate.py

@@ -87,7 +87,7 @@ def get_auto_defaults_from_summary_stats(datatype, ntax_nchar_tuple_list, total_
         'tree_estimator' : 'fasttree',
         'aligner' : 'mafft',
         'merger' : 'muscle',
-        'break_strategy' : 'longest',
+        'break_strategy' : 'centroid',
         'move_to_blind_on_worse_score' : True,
         'start_tree_search_from_current' : True,
         'after_blind_iter_without_imp_limit' : 1,

sate/settings.py

@@ -74,7 +74,7 @@ def __init__(self):
         self.sate.add_option('aligner', StringUserSetting(name='aligner', default='mafft', short_name=None, help='The name of the alignment program to use for subproblems.', subcategory='tools'))
         self.sate.add_option('merger', StringUserSetting(name='merger', default='muscle', short_name=None, help='The name of the alignment program to use to merge subproblems.', subcategory='tools'))
         self.sate.add_option('tree_estimator', StringUserSetting(name='tree_estimator', default='fasttree', short_name=None, help='The name of the tree inference program to use to find trees on fixed alignments.', subcategory='tools'))
-        self.sate.add_option('break_strategy', ChoiceUserSetting(name='break_strategy', default='longest', choices=['centroid', 'longest'], multiple_choices=True, short_name=None, help='The method for choosing an edge when bisecting the tree during decomposition', subcategory='decomposition'))
+        self.sate.add_option('break_strategy', ChoiceUserSetting(name='break_strategy', default='centroid', choices=['centroid', 'longest'], multiple_choices=True, short_name=None, help='The method for choosing an edge when bisecting the tree during decomposition', subcategory='decomposition'))
         self.sate.add_option('max_subproblem_size', IntUserSetting(name='max_subproblem_size', default=3, min=0, max=None, short_name=None, help='The maximum size (number of leaves) of subproblems.  When a subproblem contains this number of leaves (or fewer), then it will not be decomposed further.', subcategory='decomposition'))
         self.sate.add_option('max_subproblem_frac', FloatUserSetting(name='max_subproblem_frac', default=0.5, min=0.0, max=None, short_name=None, help='The maximum size (number of leaves) of subproblems specified in terms as a proportion of the total number of leaves.  When a subproblem contains this number of leaves (or fewer), then it will not be decomposed further.', subcategory='decomposition'))
         self.sate.add_option('start_tree_search_from_current', BoolUserSetting(name='start_tree_search_from_current', default='False', short_name=None, help='If selected that the tree from the previous iteration will be given to the tree searching tool as a starting tree.', subcategory='searching'))

sate_ui.xml

@@ -122,7 +122,7 @@
 	<string-option name="tree_estimator" default="fasttree" category="sate" subcategory="tools">
 		<help>The name of the tree inference program to use to find trees on fixed alignments.</help>
 	</string-option>
-	<choice-option name="break_strategy" default="longest" multichoice="True" category="sate" subcategory="decomposition">
+	<choice-option name="break_strategy" default="centroid" multichoice="True" category="sate" subcategory="decomposition">
 		<choice value="centroid"><help>The edge that comes closest to dividing the tree into two equally sized subtrees (in terms of the number of leaves).</help></choice>
 		<choice value="longest" ><help>Longest edge in the tree</help></choice>
 		<help>The method for choosing an edge when bisecting the tree during decomposition</help>