From c2659617754e9401e7149da678627333b7364a04 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 10 Dec 2020 13:05:25 +0000
Subject: [PATCH 1/1] JAL-1713 save/restore Overview in project (todo: restore
 geometry)

---
 src/jalview/project/Jalview2XML.java |   32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index ccd9ab0..6452644 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -25,6 +25,7 @@ import static jalview.math.RotatableMatrix.Axis.Y;
 import static jalview.math.RotatableMatrix.Axis.Z;
 
 import java.awt.Color;
+import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.Rectangle;
 import java.io.BufferedReader;
@@ -110,6 +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;
@@ -182,6 +184,7 @@ 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 +1450,21 @@ public class Jalview2XML
       view.setStartRes(vpRanges.getStartRes());
       view.setStartSeq(vpRanges.getStartSeq());
 
+      OverviewPanel ov = ap.getOverviewPanel();
+      if (ov != null)
+      {
+        Overview overview = new Overview();
+        Rectangle bounds = ov.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(),
@@ -4966,6 +4984,20 @@ public class Jalview2XML
     {
       splitFrameCandidates.put(view, af);
     }
+    
+    Overview overview = view.getOverview();
+    if (overview != null)
+    {
+      OverviewPanel overviewPanel = af.openOverviewPanel(overview.isShowHidden());
+      overviewPanel.setBounds(overview.getXpos(), overview.getYpos(),
+              overview.getWidth(), overview.getHeight());
+      overviewPanel.setPreferredSize(new Dimension(
+              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);
+    }
     return af;
   }
 
-- 
1.7.10.2