From bb5d9c75833e2d0b9ef8f66b8fcd7d5649a3271f Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Fri, 15 Jul 2022 18:38:33 +0100
Subject: [PATCH] JAL-4034 Use the new non-modal JDialog for 3DBeacons uniprot
 lookup confirmation. Link dialog to GStructureChooser's
 frame so it can moveToFront. Minor improvement to Search
 3DB button appearance

---
 src/jalview/gui/StructureChooser.java    |   42 +++++++++++++++---------------
 src/jalview/jbgui/GStructureChooser.java |   19 +++++++++++---
 2 files changed, 37 insertions(+), 24 deletions(-)

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 246d162..6eb8d10 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -321,6 +321,7 @@ public class StructureChooser extends GStructureChooser
       @Override
       public void run()
       {
+        btn_queryTDB.setEnabled(false);
         populateSeqsWithoutSourceDBRef();
 
         final int y = seqsWithoutSourceDBRef.size();
@@ -333,6 +334,7 @@ public class StructureChooser extends GStructureChooser
                   { new jalview.ws.dbsources.Uniprot() }, null, false);
           dbRefFetcher.addListener(afterDbRefFetch);
           // ideally this would also gracefully run with callbacks
+
           dbRefFetcher.fetchDBRefs(true);
         }
         else
@@ -357,33 +359,31 @@ public class StructureChooser extends GStructureChooser
     int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD",
             THRESHOLD_WARN_UNIPROT_FETCH_NEEDED);
     Console.debug("Using Uniprot fetch threshold of " + threshold);
-    boolean runThread = false;
     if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold)
     {
-      runThread = true;
-    }
-    // need cancel and no to result in the discoverPDB action - mocked is
-    // 'cancel' TODO: mock should be OK
-    if (!runThread)
-    {
-      int answer = JvOptionPane.showConfirmDialog(this,
-              MessageManager.formatMessage(
-                      "label.fetch_references_for_3dbeacons",
-                      seqsWithoutSourceDBRef.size()),
-              MessageManager.getString("label.3dbeacons"),
-              JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE);
-      runThread = (answer == JvOptionPane.OK_OPTION);
-    }
-    if (runThread)
-    {
       Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs)
               .start();
       return;
     }
-    else
-    {
-      revertview.run();
-    }
+    // need cancel and no to result in the discoverPDB action - mocked is
+    // 'cancel' TODO: mock should be OK
+
+    StructureChooser thisSC = this;
+    JvOptionPane.newOptionDialog(thisSC.getFrame())
+            .setResponseHandler(JvOptionPane.OK_OPTION,
+                    discoverCanonicalDBrefs)
+            .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview)
+            .setResponseHandler(JvOptionPane.NO_OPTION, revertview)
+            .showDialog(
+                    MessageManager.formatMessage(
+                            "label.fetch_references_for_3dbeacons",
+                            seqsWithoutSourceDBRef.size()),
+                    MessageManager.getString("label.3dbeacons"),
+                    JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE,
+                    null, new Object[]
+                    { MessageManager.getString("action.ok"),
+                        MessageManager.getString("action.cancel") },
+                    MessageManager.getString("action.ok"), false);
   }
 
   /**
diff --git a/src/jalview/jbgui/GStructureChooser.java b/src/jalview/jbgui/GStructureChooser.java
index d8101e3..08cfa03 100644
--- a/src/jalview/jbgui/GStructureChooser.java
+++ b/src/jalview/jbgui/GStructureChooser.java
@@ -28,6 +28,7 @@ import java.awt.Dimension;
 import java.awt.FlowLayout;
 import java.awt.Font;
 import java.awt.GridLayout;
+import java.awt.Insets;
 import java.awt.Point;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -56,6 +57,7 @@ import javax.swing.JTabbedPane;
 import javax.swing.JTable;
 import javax.swing.JTextField;
 import javax.swing.ListCellRenderer;
+import javax.swing.SwingConstants;
 import javax.swing.Timer;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
@@ -595,10 +597,15 @@ public abstract class GStructureChooser extends JPanel
     chk_invertFilter.addItemListener(this);
     btn_queryTDB = new JButton(
             MessageManager.getString("label.search_3dbeacons"));
+    btn_queryTDB.setIconTextGap(12);
+    btn_queryTDB.setIcon(tdbImage);
+    btn_queryTDB.setVerticalTextPosition(SwingConstants.CENTER);
+    btn_queryTDB.setHorizontalTextPosition(SwingConstants.TRAILING);
     btn_queryTDB.setFont(VERDANA_12);
     btn_queryTDB.setToolTipText(
             MessageManager.getString("label.find_models_from_3dbeacons"));
-    btn_queryTDB.setPreferredSize(new Dimension(300, 24));
+    btn_queryTDB.setMargin(new Insets(2, 16, 2, 20));
+    // btn_queryTDB.setPreferredSize(new Dimension(200, 32));
     btn_queryTDB.setVisible(false);
 
     targetView.setVisible(false);
@@ -612,10 +619,11 @@ public abstract class GStructureChooser extends JPanel
 
     JPanel pnl_main = new JPanel(new BorderLayout());
     JPanel pnl_controls = new JPanel();
-    pnl_queryTDB = new JPanel(new FlowLayout());
+    pnl_queryTDB = new JPanel();
+    pnl_queryTDB.setLayout(new FlowLayout(FlowLayout.CENTER, 4, 4));
     pnl_queryTDB.setBackground(getBackground());
-    pnl_queryTDB.add(new JLabel(tdbImage));
     pnl_queryTDB.add(btn_queryTDB);
+
     pnl_queryTDB.setVisible(false);
     pnl_main.add(pnl_queryTDB, BorderLayout.NORTH);
     pnl_controls.add(cmb_filterOption);
@@ -945,4 +953,9 @@ public abstract class GStructureChooser extends JPanel
   protected abstract void tabRefresh();
 
   protected abstract void validateSelections();
+
+  public JInternalFrame getFrame()
+  {
+    return mainFrame;
+  }
 }
\ No newline at end of file
-- 
1.7.10.2