From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 22 Mar 2017 14:12:50 +0000 (+0000)
Subject: JAL-2388 Reinstated original overview checks for annotation display
X-Git-Tag: Release_2_10_2~3^2~148
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=550949340ef5ccd5757dd50b11b9613d61571046

JAL-2388 Reinstated original overview checks for annotation display
---

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 2fc5716..3ef2936 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -77,7 +77,8 @@ public class OverviewPanel extends Panel implements Runnable,
     sr.forOverview = true;
     fr = new FeatureRenderer(av);
 
-    od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation());
+    od = new OverviewDimensions(av.getRanges(),
+            (av.isShowAnnotation() && av.getSequenceConsensusHash() != null));
 
     setSize(new Dimension(od.getWidth(), od.getHeight()));
     addComponentListener(new ComponentAdapter()
@@ -209,7 +210,9 @@ public class OverviewPanel extends Panel implements Runnable,
 
     buildImage(sampleRow, sampleCol, mg);
 
-    if (av.isShowAnnotation())
+    // check for conservation annotation to make sure overview works for DNA too
+    if (av.isShowAnnotation()
+            && (av.getAlignmentConservationAnnotation() != null))
     {
       for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
       {
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index ac2138f..c530fdc 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -90,7 +90,9 @@ public class OverviewPanel extends JPanel implements Runnable
     sr.forOverview = true;
     fr = new FeatureRenderer(ap);
 
-    od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation());
+    od = new OverviewDimensions(av.getRanges(),
+            (av.isShowAnnotation() && av
+                    .getAlignmentConservationAnnotation() != null));
 
     addComponentListener(new ComponentAdapter()
     {
@@ -201,7 +203,9 @@ public class OverviewPanel extends JPanel implements Runnable
 
     buildImage(sampleRow, sampleCol);
 
-    if (av.isShowAnnotation())
+    // check for conservation annotation to make sure overview works for DNA too
+    if (av.isShowAnnotation()
+            && (av.getAlignmentConservationAnnotation() != null))
     {
       renderer.updateFromAlignViewport(av);
       for (int col = 0; col < od.getWidth() && !resizeAgain; col++)