From f36d4cc8219864448dd2a058573badc9afd0c45c Mon Sep 17 00:00:00 2001
From: jrobinso <933148+jrobinso@users.noreply.github.com>
Date: Sun, 13 Oct 2024 22:57:47 -0700
Subject: [PATCH] Rename ENCODE items

---
 .../java/org/broad/igv/ui/IGVMenuBar.java     | 32 ++++++++++++++++++-
 1 file changed, 31 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/broad/igv/ui/IGVMenuBar.java b/src/main/java/org/broad/igv/ui/IGVMenuBar.java
index a0427907d..fda2e3510 100644
--- a/src/main/java/org/broad/igv/ui/IGVMenuBar.java
+++ b/src/main/java/org/broad/igv/ui/IGVMenuBar.java
@@ -303,7 +303,37 @@ JMenu createFileMenu() {
             menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
         }
 
-        addEncodeItems(menuItems, genomeId);
+        // ENCODE items.  These will be hidden / shown depending on genome chosen
+        JSeparator separator = new JSeparator();
+        menuItems.add(separator);
+
+        JLabel encodeLabel = new JLabel("   ENCODE");
+        encodeLabel.setFont(encodeLabel.getFont().deriveFont(Font.BOLD));
+        menuItems.add(encodeLabel);
+
+        // Post 2012 ENCODE menu
+        JMenuItem chipItem = new JMenuItem();
+        chipItem.setAction(new BrowseEncodeAction("Signals ChIP ...", 0, BrowseEncodeAction.Type.SIGNALS_CHIP, igv));
+        encodeMenuItems.add(chipItem);
+
+        JMenuItem otherSignalsItem = new JMenuItem();
+        otherSignalsItem.setAction(new BrowseEncodeAction("Signals Other ...", 0, BrowseEncodeAction.Type.SIGNALS_OTHER, igv));
+        encodeMenuItems.add(otherSignalsItem);
+
+        JMenuItem otherItem = new JMenuItem();
+        otherItem.setAction(new BrowseEncodeAction("Other ...", 0, BrowseEncodeAction.Type.OTHER, igv));
+        encodeMenuItems.add(otherItem);
+
+        for(JComponent item : encodeMenuItems) {
+            menuItems.add(item);
+            item.setVisible(EncodeTrackChooser.genomeSupported(genomeId));
+        }
+
+        // UCSC hosted ENCODE menu.
+        encodeUCSCMenuItem = MenuAndToolbarUtils.createMenuItem(
+                new BrowseEncodeAction("UCSC Repository (2012) ...", KeyEvent.VK_E, BrowseEncodeAction.Type.UCSC, igv));
+        encodeUCSCMenuItem.setVisible(EncodeTrackChooser.genomeSupportedUCSC(genomeId));
+        menuItems.add(encodeUCSCMenuItem);
 
         menuItems.add(new JSeparator());
         menuAction = new ReloadTracksMenuAction("Reload Tracks", -1, igv);