Add Recent Files Menu and Improve Recent Sessions

src/main/java/org/broad/igv/prefs/Constants.java

@@ -42,6 +42,7 @@ private Constants() {
 
     //
     public static final String RECENT_SESSIONS = "IGV.Session.recent.sessions";
+    public static final String RECENT_URLS = "IGV.Session.recent.urls";
     public static final String LAST_EXPORTED_REGION_DIRECTORY = "LAST_EXPORTED_REGION_DIRECTORY";
     public static final String LAST_TRACK_DIRECTORY = "LAST_TRACK_DIRECTORY";
     public static final String LAST_SNAPSHOT_DIRECTORY = "LAST_SNAPSHOT_DIRECTORY";

src/main/java/org/broad/igv/prefs/IGVPreferences.java

@@ -44,9 +44,7 @@
 import org.broad.igv.renderer.SequenceRenderer;
 import org.broad.igv.sam.mods.BaseModificationColors;
 import org.broad.igv.track.TrackType;
-import org.broad.igv.ui.IGV;
-import org.broad.igv.ui.IGVMenuBar;
-import org.broad.igv.ui.UIConstants;
+import org.broad.igv.ui.*;
 import org.broad.igv.ui.color.ColorUtilities;
 import org.broad.igv.ui.color.PaletteColorTable;
 import org.broad.igv.ui.util.MessageUtils;
@@ -280,7 +278,7 @@ public void put(String key, String value) {
             // Explicitly setting removes override
             overrideKeys.remove(key);
 
-            if (value == null || value.trim().length() == 0) {
+            if (value == null || value.isBlank()) {
                 userPreferences.remove(key);
             } else {
                 userPreferences.put(key, value);
@@ -297,7 +295,7 @@ public void put(String key, boolean b) {
 
     public void putAll(Map<String, String> updatedPrefs) {
         for (Map.Entry<String, String> entry : updatedPrefs.entrySet()) {
-            if (entry.getValue() == null || entry.getValue().trim().length() == 0) {
+            if (entry.getValue() == null || entry.getValue().isBlank()) {
                 remove(entry.getKey());
             } else {
                 put(entry.getKey(), entry.getValue());
@@ -610,14 +608,28 @@ public Rectangle getApplicationFrameBounds() {
      * @param recentSessions
      */
     public void setRecentSessions(String recentSessions) {
+        remove(RECENT_SESSIONS);
         put(RECENT_SESSIONS, recentSessions);
     }
 
 
-    public String getRecentSessions() {
-        return get(RECENT_SESSIONS, null);
+    public RecentFileSet getRecentSessions() {
+        String sessionsString = get(RECENT_SESSIONS, null);
+        return RecentFileSet.fromString(sessionsString, UIConstants.NUMBER_OF_RECENT_SESSIONS_TO_LIST);
     }
 
+    public void setRecentUrls(String recentUrls) {
+        remove(RECENT_URLS);
+        put(RECENT_URLS, recentUrls);
+    }
+
+
+    public RecentUrlsSet getRecentUrls() {
+        String sessionsString = get(RECENT_URLS, null);
+        return RecentUrlsSet.fromString(sessionsString, UIConstants.NUMBER_OF_RECENT_SESSIONS_TO_LIST);
+    }
+
+
     public String getDataServerURL() {
         String masterResourceFile = get(DATA_SERVER_URL_KEY);
         return masterResourceFile;

src/main/java/org/broad/igv/ui/DynamicMenuItemsAdjustmentListener.java

@@ -0,0 +1,76 @@
+package org.broad.igv.ui;
+
+import javax.swing.*;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
+import java.util.function.Function;
+
+/**
+ * MenuListener which updates the availble menu items based on the contents of a changeable collection.
+ *
+ * Whenever the menu is selected the relevant JMenuItems are regenerated according to the current values in the backing
+ * collection.
+ *
+ * Items are inserted in a row beneath a given separator.
+ *
+ * @param <T> element type of the collection
+ */
+public class DynamicMenuItemsAdjustmentListener<T> implements MenuSelectedListener {
+    private final JMenu menu;
+
+    private final JSeparator insertionPoint;
+    private final Collection<T> values;
+    private final Function<T, JMenuItem> itemConstructor;
+
+    //Store the currently visible components here so they can be removed when necessary
+    private final List<JComponent> activeComponents;
+
+    /**
+     *
+     * @param menu the menu to modify
+     * @param insertionPoint a JSeparator which acts as an anchor to always insert elements below.  This element is hidden
+     *                       when the collection is empty
+     * @param values a collection which is used to generate menu items
+     * @param itemConstructor a function to create a JMenuItem from an element in the collection
+     */
+    public DynamicMenuItemsAdjustmentListener(JMenu menu, JSeparator insertionPoint, Collection<T> values, Function<T, JMenuItem> itemConstructor) {
+        this.menu = menu;
+        this.insertionPoint = insertionPoint;
+        this.values = values;
+        this.itemConstructor = itemConstructor;
+        this.activeComponents = new ArrayList<>();
+    }
+
+    private List<JMenuItem> getCurrentItems() {
+        return values.stream().map(itemConstructor).toList();
+    }
+
+    @Override
+    public void menuSelected(MenuEvent e) {
+        List<JMenuItem> newComponents = getCurrentItems();
+
+        // We definitely don't want to be doing this while other things are also changing the menu
+        // this should at least protect against multiple of these listeners modifying the same menu at once.
+        synchronized (menu) {
+            activeComponents.forEach(menu::remove);
+            if (newComponents.isEmpty()) {
+                insertionPoint.setVisible(false);
+            } else {
+                insertionPoint.setVisible(true);
+
+                final int componentIndex = Arrays.asList(menu.getMenuComponents()).indexOf(insertionPoint);
+                for (int i = 0; i < newComponents.size(); i++) {
+                    menu.insert(newComponents.get(i), componentIndex + i + 1);
+                }
+                activeComponents.addAll(newComponents);
+            }
+        }
+
+        menu.revalidate();
+        menu.repaint();
+    }
+}

src/main/java/org/broad/igv/ui/IGV.java

@@ -134,9 +134,10 @@ public class IGV implements IGVEventObserver {
     private Timer sessionAutosaveTimer = new Timer();
 
     // Misc state
-    private Map<String, List<Track>> overlayTracksMap = new HashMap();
-    private Set<Track> overlaidTracks = new HashSet();
-    private LinkedList<String> recentSessionList = new LinkedList<String>();
+    private Map<String, List<Track>> overlayTracksMap = new HashMap<>();
+    private Set<Track> overlaidTracks = new HashSet<>();
+    private RecentFileSet recentSessionList;
+    private RecentUrlsSet recentUrlsList;
 
     // Vertical line that follows the mouse
     private boolean rulerEnabled;
@@ -514,25 +515,15 @@ final public void doViewPreferences() {
     final public void saveStateForExit() {
 
         // Store recent sessions
-        if (!getRecentSessionList().isEmpty()) {
-
-            int size = getRecentSessionList().size();
-            if (size > UIConstants.NUMBER_OF_RECENT_SESSIONS_TO_LIST) {
-                size = UIConstants.NUMBER_OF_RECENT_SESSIONS_TO_LIST;
-            }
-
-            String recentSessions = "";
-            for (int i = 0; i <
-                    size; i++) {
-                recentSessions += getRecentSessionList().get(i);
-
-                if (i < (size - 1)) {
-                    recentSessions += ";";
-                }
+        RecentFileSet recentSessions = getRecentSessionList();
+        if (!recentSessions.isEmpty()) {
+            PreferencesManager.getPreferences().setRecentSessions(recentSessions.asString());
+        }
 
-            }
-            PreferencesManager.getPreferences().remove(RECENT_SESSIONS);
-            PreferencesManager.getPreferences().setRecentSessions(recentSessions);
+        // Store recent files
+        RecentUrlsSet recentUrls = getRecentUrls();
+        if (!recentUrls.isEmpty()) {
+            PreferencesManager.getPreferences().setRecentUrls(recentUrls.asString());
         }
 
         // Stop the timer that is triggering the timed autosave
@@ -991,9 +982,8 @@ public boolean loadSession(String sessionPath, String locus) {
                 }
 
                 mainFrame.setTitle(UIConstants.APPLICATION_NAME + " - Session: " + sessionPath);
-                if (!recentSessionList.contains(sessionPath)) {
-                    recentSessionList.addFirst(sessionPath);
-                }
+
+                getRecentSessionList().add(sessionPath);
                 this.menuBar.enableReloadSession();
 
                 //If there's a RegionNavigatorDialog, kill it.
@@ -1006,7 +996,7 @@ public boolean loadSession(String sessionPath, String locus) {
         } catch (Exception e) {
             String message = "Error loading session session: " + e.getMessage();
             MessageUtils.showMessage(message);
-            recentSessionList.remove(sessionPath);
+            getRecentSessionList().remove(sessionPath);
             log.error(e);
             return false;
         } finally {
@@ -1068,9 +1058,8 @@ public void saveSession(File targetFile) throws IOException {
         String sessionPath = targetFile.getAbsolutePath();
         session.setPath(sessionPath);
         mainFrame.setTitle(UIConstants.APPLICATION_NAME + " - Session: " + sessionPath);
-        if (!recentSessionList.contains(sessionPath)) {
-            recentSessionList.addFirst(sessionPath);
-        }
+
+        getRecentSessionList().add(sessionPath);
         this.menuBar.enableReloadSession();
 
         // No errors so save last location
@@ -1130,10 +1119,36 @@ public MainPanel getMainPanel() {
         return contentPane.getMainPanel();
     }
 
-    public LinkedList<String> getRecentSessionList() {
+    public RecentFileSet getRecentSessionList() {
+        if(recentSessionList == null){
+            recentSessionList = PreferencesManager.getPreferences().getRecentSessions();
+            //remove sessions that no longer exist
+            recentSessionList.removeIf(file -> !(new File(file)).exists());
+        }
         return recentSessionList;
     }
 
+    public RecentUrlsSet getRecentUrls() {
+        if(recentUrlsList == null){
+            recentUrlsList = PreferencesManager.getPreferences().getRecentUrls();
+        }
+        return recentUrlsList;
+    }
+
+    /**
+     * Add new values to the recent URLS set.  Calling this method rather than adding them directly
+     * allows showing the menu when the first URL is added to the collection.
+     * @param toAdd
+     */
+    public void addToRecentUrls(Collection<ResourceLocator> toAdd){
+        RecentUrlsSet recentFiles = getRecentUrls();
+        recentFiles.addAll(toAdd);
+        if(!recentFiles.isEmpty()){
+            menuBar.showRecentFilesMenu();
+        }
+    }
+
+
     public IGVContentPane getContentPane() {
         return contentPane;
     }
@@ -1173,7 +1188,7 @@ public void loadResources(Collection<ResourceLocator> locators) {
 
         for (final ResourceLocator locator : locators) {
 
-            // If its a local file, check explicitly for existence (rather than rely on exception)
+            // If it's a local file, check explicitly for existence (rather than rely on exception)
             if (locator.isLocal()) {
                 File trackSetFile = new File(locator.getPath());
                 if (!trackSetFile.exists()) {
@@ -1182,9 +1197,11 @@ public void loadResources(Collection<ResourceLocator> locators) {
                 }
             }
 
+
             try {
                 List<Track> tracks = load(locator);
                 addTracks(tracks);
+
             } catch (Exception e) {
                 log.error("Error loading track", e);
                 messages.append("Error loading " + locator + ": " + e.getMessage());