JAL-3785 JAL- Merge branch 'bug/JAL-3785autoOverviewTitle' into 2_11_2_develop

[jalview.git] / src / jalview / project / Jalview2XML.java

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index acfeb2a..4145703 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -111,6 +111,7 @@ import jalview.gui.AppVarna;
 import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
 import jalview.gui.OOMWarning;
+import jalview.gui.OverviewPanel;
 import jalview.gui.PCAPanel;
 import jalview.gui.PaintRefresher;
 import jalview.gui.SplitFrame;
@@ -184,6 +185,7 @@ import jalview.xml.binding.jalview.JalviewModel.UserColours;
 import jalview.xml.binding.jalview.JalviewModel.Viewport;
 import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
 import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
+import jalview.xml.binding.jalview.JalviewModel.Viewport.Overview;
 import jalview.xml.binding.jalview.JalviewUserColours;
 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
 import jalview.xml.binding.jalview.MapListType.MapListFrom;
@@ -1447,6 +1449,24 @@ public class Jalview2XML
       view.setStartRes(vpRanges.getStartRes());
       view.setStartSeq(vpRanges.getStartSeq());
 
+      OverviewPanel ov = ap.getOverviewPanel();
+      if (ov != null)
+      {
+        Overview overview = new Overview();
+        JInternalFrame frame = (JInternalFrame) SwingUtilities
+                .getAncestorOfClass(JInternalFrame.class, ov);
+        overview.setTitle(frame.getTitle());
+        Rectangle bounds = frame.getBounds();
+        overview.setXpos(bounds.x);
+        overview.setYpos(bounds.y);
+        overview.setWidth(bounds.width);
+        overview.setHeight(bounds.height);
+        overview.setShowHidden(ov.isShowHiddenRegions());
+        overview.setGapColour(ov.getCanvas().getGapColour().getRGB());
+        overview.setResidueColour(ov.getCanvas().getResidueColour().getRGB());
+        overview.setHiddenColour(ov.getCanvas().getHiddenColour().getRGB());
+        view.setOverview(overview);
+      }
       if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
       {
         view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
@@ -4044,7 +4064,7 @@ public class Jalview2XML
     }
 
     /*
-     * Load any trees, PDB structures and viewers
+     * Load any trees, PDB structures and viewers, Overview
      * 
      * Not done if flag is false (when this method is used for New View)
      */
@@ -4054,12 +4074,39 @@ public class Jalview2XML
       loadPCAViewers(jalviewModel, ap);
       loadPDBStructures(jprovider, jseqs, af, ap);
       loadRnaViewers(jprovider, jseqs, ap);
+      loadOverview(view, af);
     }
     // and finally return.
     return af;
   }
 
   /**
+   * Load Overview window, restoring colours, 'show hidden regions' flag, title
+   * and geometry as saved
+   * 
+   * @param view
+   * @param af
+   */
+  protected void loadOverview(Viewport view, AlignFrame af)
+  {
+    Overview overview = view.getOverview();
+    if (overview != null)
+    {
+      OverviewPanel overviewPanel = af
+              .openOverviewPanel(overview.isShowHidden());
+      JInternalFrame frame = (JInternalFrame) SwingUtilities
+              .getAncestorOfClass(JInternalFrame.class, overviewPanel);
+      frame.setTitle(overview.getTitle());
+      frame.setBounds(overview.getXpos(), overview.getYpos(),
+              overview.getWidth(), overview.getHeight());
+      Color gap = new Color(overview.getGapColour());
+      Color residue = new Color(overview.getResidueColour());
+      Color hidden = new Color(overview.getHiddenColour());
+      overviewPanel.getCanvas().setColours(gap, residue, hidden);
+    }
+  }
+
+  /**
    * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
    * panel is restored from separate jar entries, two (gapped and trimmed) per
    * sequence and secondary structure.
@@ -4981,6 +5028,7 @@ public class Jalview2XML
     {
       splitFrameCandidates.put(view, af);
     }
+
     return af;
   }