Added functions to save and load selections + explanation in help menu

snub/gui/help/loading_data.md

@@ -4,4 +4,4 @@ To open a SNUB project, go to File > Open Project, navigate to the project direc
 
 ## Reload a project
 
-If a project is already open and its files have been modified outside of SNUB, the project can be reloaded in the SNUB GUI by going to File > Reload Project.
+If a project is already open and its files have been modified outside of SNUB, the project can be reloaded in the SNUB GUI by going to File > Reload Project.

snub/gui/help/selections.md

@@ -6,6 +6,10 @@ Selections can be used to show relationships between data-views (such intervals
 * Use command/control+drag to deselect points and intervals.
 * Use Edit > Deselect All to deselect everything
 
+### Saving and loading selections
+
+The start/end times of all currently selected intervals can be saved to an external file using File > Save Selections. The file is in csv format with two columns containing the start and end times respectively. Selections can also be loaded using File > Load Selections. Note that when you load selections from a file, all current selections are cleared. 
+
 ## Rank variables by enrichment
 
 ### Scatter plot

snub/gui/main.py

@@ -2,6 +2,7 @@
 from PyQt5.QtWidgets import *
 from PyQt5.QtGui import *
 import sys, os, json
+import numpy as np
 from functools import partial
 from snub.gui.utils import IntervalIndex, CheckBox
 from snub.gui.stacks import PanelStack, TrackStack
@@ -339,12 +340,15 @@ def __init__(self, args):
         reload_data.setShortcut("Ctrl+R")
         reload_data.triggered.connect(self.reload_data)
 
+        save_selection = QAction("Save Selection", self)
+        save_selection.triggered.connect(self.save_selection)
+
+        load_selection = QAction("Load Selection", self)
+        load_selection.triggered.connect(self.load_selection)
+
         deselect_all = QAction("&Deselect All", self)
         deselect_all.triggered.connect(self.deselect_all)
 
-        save_layout = QAction("&Layout", self)
-        save_layout.triggered.connect(self.save_layout)
-
         self.set_layout_to_rows = QAction("&Rows", self)
         self.set_layout_to_cols = QAction("&Columns", self)
         self.set_layout_to_rows.setCheckable(True)
@@ -362,6 +366,8 @@ def __init__(self, args):
         fileMenu = mainMenu.addMenu("&File")
         fileMenu.addAction(open_project)
         fileMenu.addAction(reload_data)
+        fileMenu.addAction(save_selection)
+        fileMenu.addAction(load_selection)
 
         editMenu = mainMenu.addMenu("&Edit")
         editMenu.addAction(deselect_all)
@@ -401,8 +407,6 @@ def open(self, *args, project_directories=None):
         error_directories = []
         for project_dir in project_directories:
             if len(project_dir) > 0:
-                # if project_dir.endswith('config.json'):
-                #     project_dir = os.path.dirname(project_dir)
                 if os.path.exists(os.path.join(project_dir, "config.json")):
                     self.load_project(project_dir)
                 else:
@@ -426,9 +430,6 @@ def reload_data(self):
         self.close_tab(current_index)
         self.load_project(project_dir)
 
-    def save_layout(self):
-        print("save")
-
     def load_project(self, project_directory):
         name = project_directory.strip(os.path.sep).split(os.path.sep)[-1]
         project_tab = ProjectTab(project_directory)
@@ -458,6 +459,76 @@ def getExistingDirectories(self):
             str(),
         ]
 
+    def load_selection(self):
+        current_index = self.tabs.currentIndex()
+        if current_index == -1:
+            QMessageBox.warning(self, "Error: No project is open")
+            return  # no tab
+
+        # get path of file to load
+        options = QFileDialog.Options()
+        options |= QFileDialog.DontUseNativeDialog
+        file_name, _ = QFileDialog.getOpenFileName(
+            self,
+            "Load Selection",
+            "",
+            "All Files (*);;CSV Files (*.csv)",
+            options=options,
+        )
+
+        print(file_name)
+
+        if file_name:
+            try:
+                intervals = np.loadtxt(file_name, delimiter=",", skiprows=1)
+                if len(intervals) > 0:
+                    is_selected = np.ones(len(intervals)) > 0
+                    self.tabs.currentWidget().update_selected_intervals(
+                        intervals, is_selected
+                    )
+            except Exception as e:
+                QMessageBox.warning(
+                    self, "Error", f"Failed to load selection: {str(e)}"
+                )
+
+    def save_selection(self):
+        current_index = self.tabs.currentIndex()
+        if current_index == -1:
+            QMessageBox.warning(self, "Error: No project is open")
+            return  # no tab
+
+        selected_intervals = self.tabs.currentWidget().selected_intervals.intervals
+        if len(selected_intervals) == 0:
+            QMessageBox.warning(self, "Error: Nothing is selected")
+            return  # no tab
+
+        # get path of file to save
+        options = QFileDialog.Options()
+        options |= QFileDialog.DontUseNativeDialog
+        file_name, _ = QFileDialog.getSaveFileName(
+            self, "Save Selection", "", "CSV Files (*.csv)", options=options
+        )
+
+        if file_name:
+
+            if not file_name.lower().endswith(".csv"):
+                file_name += ".csv"
+
+            try:
+                # generate csv text
+                text = ["start,end"]
+                for s, e in selected_intervals:
+                    text.append(f"{s},{e}")
+                text = "\n".join(text) + "\n"
+
+                # write to file
+                with open(file_name, "w") as file:
+                    file.write(text)
+            except Exception as e:
+                QMessageBox.warning(
+                    self, "Error", f"Failed to save selection: {str(e)}"
+                )
+
 
 def run():
     app = QApplication(sys.argv)