[PART 1] GUI: Fix reconciliation button graying out bug (#218)

* Fix reconciliation button graying out bug

As documented in #180, sometimes `View reconciliations` and `View p-value histogram` buttons become unexpectedly grayed out after setting the transfer cost to 1.5,  clicking compute reconciliations, and then set the number of cluster.

This happens because our code says we will gray out the compute reconciliation button and other buttons when an action happens to the three cost boxes (duplication, transfer, loss). The problem with this is that when we click on `View solution space` -> `Clusters`, the event `focusout` and `focusin` are triggered by the input boxes, graying out the button. The fix is to have the gray out command run only on `key` event, which is triggered on text change.

Resolve #180

* Fix cluster bug (#219)

empress_gui.py

@@ -205,7 +205,7 @@ def init_view_reconciliations(self):
             *self.view_reconciliations_options, command=self.select_from_view_reconciliations_dropdown)
         self.view_reconciliations_dropdown.configure(width=15)
         self.view_reconciliations_dropdown.configure(state=tk.DISABLED)
-        self.view_reconciliations_dropdown['menu'].entryconfigure("One per cluster", state = "disabled")
+        self.view_reconciliations_dropdown['menu'].entryconfigure("One per cluster", state="disabled")
         self.view_reconciliations_dropdown.grid(row=5, column=0)
 
     def init_view_pvalue_histogram(self):
@@ -331,6 +331,7 @@ def close_unnecessary_windows_if_opened(self):
     def disable_unaccessable_widgets(self):
         self.view_solution_space_dropdown.configure(state=tk.DISABLED)
         self.view_reconciliations_dropdown.configure(state=tk.DISABLED)
+        self.view_reconciliations_dropdown['menu'].entryconfigure("One per cluster", state=tk.DISABLED)
         self.view_pvalue_histogram_btn.configure(state=tk.DISABLED)
 
     def load_input_files(self, event):
@@ -510,7 +511,7 @@ def create_dtl_costs_boxes(self):
         # self.trans_input is tk.DoubleVar(), initialized to be 1.00
         self.trans_entry_box = CustomEntry(self.costs_frame, width=4, textvariable=self.trans_input)
         self.trans_entry_box.set_border_color("green")
-        self.trans_entry_box.validate(validate="all", validatecommand=trans_vcmd)
+        self.trans_entry_box.validate(validate="key", validatecommand=trans_vcmd)
         self.trans_entry_box.grid(row=1, column=1, sticky="w")
         self.validate_trans_input(str(self.trans_entry_box.get()))  # validate for the initialization of self.trans_input to be 1.0
 
@@ -522,7 +523,7 @@ def create_dtl_costs_boxes(self):
         # self.loss_input is tk.DoubleVar(), initialized to be 1.00
         self.loss_entry_box = CustomEntry(self.costs_frame, width=4, textvariable=self.loss_input)
         self.loss_entry_box.set_border_color("green")
-        self.loss_entry_box.validate(validate="all", validatecommand=loss_vcmd)
+        self.loss_entry_box.validate(validate="key", validatecommand=loss_vcmd)
         self.loss_entry_box.grid(row=2, column=1, sticky="w")
         self.validate_loss_input(str(self.loss_entry_box.get()))  # validate for the initialization of self.loss_input to be 1.00
 
@@ -694,7 +695,7 @@ def set_num_clusters(self):
         self.num_cluster_entry_box = CustomEntry(self.set_num_cluster_frame, width=3, textvariable=self.num_cluster_input)
         self.num_cluster_entry_box.set_border_color("green")
         self.num_cluster_entry_box.validate(validate="key", validatecommand=num_cluster_vcmd)
-        self.validate_num_cluster_input(1)
+        self.validate_num_cluster_input(self.num_cluster_entry_box.get())
         self.num_cluster_label.grid(row=0, column=0, sticky="e")
         self.num_cluster_entry_box.grid(row=0, column=1, sticky="w")
         self.num_cluster_error.grid(row=0, column=2)
@@ -703,7 +704,7 @@ def validate_num_cluster_input(self, input_after_change: str):
         """The number of clusters is only allowed to be an integer that >= 1 and <= the number of MPRs."""
         try:
             val = int(input_after_change)
-            if val >= 1 and val <= self.recon_count:
+            if 1 <= val <= self.recon_count:
                 self.num_cluster = val
                 self.num_cluster_entry_box.set_border_color("green")
                 self.enter_num_clusters_btn.configure(state=tk.NORMAL)
@@ -719,14 +720,14 @@ def validate_num_cluster_input(self, input_after_change: str):
         if self.num_cluster is not None:
             self.num_cluster_entry_box.set_border_color("green")
             self.enter_num_clusters_btn.configure(state=tk.NORMAL)
-            self.view_reconciliations_dropdown.configure(state=tk.NORMAL)
-            self.view_reconciliations_dropdown['menu'].entryconfigure("One per cluster", state=tk.NORMAL)
         return True # return True means allowing the change to happen
 
     def click_on_enter_num_clusters_btn(self):
         """Compute cluster histograms and median reconciliations, and open a new tkinter window to show the solution space."""
         self.compute_recon_solutions()
         self.open_window_solution_space()
+        self.view_reconciliations_dropdown.configure(state=tk.NORMAL)
+        self.view_reconciliations_dropdown['menu'].entryconfigure("One per cluster", state=tk.NORMAL)
 
     def compute_recon_solutions(self):
         """Compute cluster histograms and median reconciliations and store them in variables to draw later."""
@@ -735,17 +736,14 @@ def compute_recon_solutions(self):
         # App.clusters_list[0] contains App.recon_graph.cluster(1) and so on
         # Each App.clusters_list[num] is a list of ReconGraph
         App.clusters_list = []
-        for num in range(self.num_cluster):
-            App.clusters_list.append(App.recon_graph.cluster(num+1))
+        for cluster_size in range(1, self.num_cluster + 1):
+            App.clusters_list.append(App.recon_graph.cluster(cluster_size))
 
         # Compute medians for a specific self.num_cluster
+        clusters = App.clusters_list[-1]
         App.medians = []
-        if self.num_cluster == 1:
-            App.medians.append(App.recon_graph.median())
-        else:
-            clusters = App.recon_graph.cluster(self.num_cluster)
-            for i in range(len(clusters)):
-                App.medians.append(clusters[i].median())
+        for recongraph in clusters:
+            App.medians.append(recongraph.median())
 
         if self.solution_space_for_clusters_window is not None and self.solution_space_for_clusters_window.winfo_exists():
             self.solution_space_for_clusters_window.destroy()
@@ -787,19 +785,16 @@ def select_from_view_reconciliations_dropdown(self, event):
 
     def open_window_reconciliations(self):
         """Pop up new tkinter windows to display one reconciliation per cluster."""
-        if self.num_cluster is not None:
-            solution_number = 1
-            for solution_index, solution in enumerate(App.medians):
-                self.view_reconciliations_for_clusters_window  = tk.Toplevel(self.master)
-                self.view_reconciliations_for_clusters_window .geometry("800x800")
-                self.view_reconciliations_for_clusters_window .title("View reconciliations " + str(solution_index + 1))
-                # Bring the new tkinter window to the front
-                # https://stackoverflow.com/a/53644859/13698076
-                self.view_reconciliations_for_clusters_window .attributes('-topmost', True)
-                self.view_reconciliations_for_clusters_window .focus_force()
-                self.view_reconciliations_for_clusters_window .bind('<FocusIn>', self.bring_to_front)
-                ReconciliationsOnePerClusterWindow(self.view_reconciliations_for_clusters_window , solution)
-                solution_number = solution_number + 1
+        for solution_index, solution in enumerate(App.medians):
+            self.view_reconciliations_for_clusters_window = tk.Toplevel(self.master)
+            self.view_reconciliations_for_clusters_window.geometry("800x800")
+            self.view_reconciliations_for_clusters_window.title("View reconciliations " + str(solution_index + 1))
+            # Bring the new tkinter window to the front
+            # https://stackoverflow.com/a/53644859/13698076
+            self.view_reconciliations_for_clusters_window.attributes('-topmost', True)
+            self.view_reconciliations_for_clusters_window.focus_force()
+            self.view_reconciliations_for_clusters_window.bind('<FocusIn>', self.bring_to_front)
+            ReconciliationsOnePerClusterWindow(self.view_reconciliations_for_clusters_window , solution)
 
     def open_window_pvalue_histogram(self):
         """Pop up a new tkinter window to display the p-value histogram."""