From 47d7a627f0bb59aaa87b158ce3572658a9861a08 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 17 Oct 2017 14:42:56 +0100
Subject: [PATCH] JAL-2773 renamed flags for clarity

---
 src/jalview/gui/FeatureColourChooser.java |    6 +++---
 src/jalview/gui/SeqPanel.java             |   25 +++++++++++++------------
 2 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/src/jalview/gui/FeatureColourChooser.java b/src/jalview/gui/FeatureColourChooser.java
index 2e9f0ed..d8db546 100644
--- a/src/jalview/gui/FeatureColourChooser.java
+++ b/src/jalview/gui/FeatureColourChooser.java
@@ -396,9 +396,9 @@ public class FeatureColourChooser extends JalviewDialog
    * feature type, and repaints the alignment, and optionally the Overview
    * and/or structure viewer if open
    * 
-   * @param updateOverview
+   * @param updateStructsAndOverview
    */
-  void changeColour(boolean updateOverview)
+  void changeColour(boolean updateStructsAndOverview)
   {
     // Check if combobox is still adjusting
     if (adjusting)
@@ -507,7 +507,7 @@ public class FeatureColourChooser extends JalviewDialog
     }
     fr.setColour(type, acg);
     cs = acg;
-    ap.paintAlignment(updateOverview, updateOverview);
+    ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
   }
 
   @Override
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 531eca6..516652b 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -852,11 +852,12 @@ public class SeqPanel extends JPanel
 
   /**
    * set when the current UI interaction has resulted in a change that requires
-   * overview shading to be recalculated. this could be changed to something
-   * more expressive that indicates what actually has changed, so selective
-   * redraws can be applied
+   * shading in overviews and structures to be recalculated. this could be
+   * changed to a something more expressive that indicates what actually has
+   * changed, so selective redraws can be applied (ie. only structures, only
+   * overview, etc)
    */
-  private boolean needOverviewUpdate = false; // TODO: refactor to avcontroller
+  private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
 
   /**
    * set if av.getSelectionGroup() refers to a group that is defined on the
@@ -1656,7 +1657,7 @@ public class SeqPanel extends JPanel
     final int res = findColumn(evt);
     final int seq = findSeq(evt);
     oldSeq = seq;
-    needOverviewUpdate = false;
+    updateOverviewAndStructs = false;
 
     startWrapBlock = wrappedBlock;
 
@@ -1821,7 +1822,7 @@ public class SeqPanel extends JPanel
     // always do this - annotation has own state
     // but defer colourscheme update until hidden sequences are passed in
     boolean vischange = stretchGroup.recalcConservation(true);
-    needOverviewUpdate |= vischange && av.isSelectionDefinedGroup()
+    updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
             && afterDrag;
     if (stretchGroup.cs != null)
     {
@@ -1843,8 +1844,8 @@ public class SeqPanel extends JPanel
     PaintRefresher.Refresh(this, av.getSequenceSetId());
     // TODO: structure colours only need updating if stretchGroup used to or now
     // does contain sequences with structure views
-    ap.paintAlignment(needOverviewUpdate, needOverviewUpdate);
-    needOverviewUpdate = false;
+    ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs);
+    updateOverviewAndStructs = false;
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
@@ -1898,7 +1899,7 @@ public class SeqPanel extends JPanel
       if (res > (stretchGroup.getStartRes() - 1))
       {
         stretchGroup.setEndRes(res);
-        needOverviewUpdate |= av.isSelectionDefinedGroup();
+        updateOverviewAndStructs |= av.isSelectionDefinedGroup();
       }
     }
     else if (changeStartRes)
@@ -1906,7 +1907,7 @@ public class SeqPanel extends JPanel
       if (res < (stretchGroup.getEndRes() + 1))
       {
         stretchGroup.setStartRes(res);
-        needOverviewUpdate |= av.isSelectionDefinedGroup();
+        updateOverviewAndStructs |= av.isSelectionDefinedGroup();
       }
     }
 
@@ -1940,7 +1941,7 @@ public class SeqPanel extends JPanel
       if (stretchGroup.getSequences(null).contains(nextSeq))
       {
         stretchGroup.deleteSequence(seq, false);
-        needOverviewUpdate |= av.isSelectionDefinedGroup();
+        updateOverviewAndStructs |= av.isSelectionDefinedGroup();
       }
       else
       {
@@ -1950,7 +1951,7 @@ public class SeqPanel extends JPanel
         }
 
         stretchGroup.addSequence(nextSeq, false);
-        needOverviewUpdate |= av.isSelectionDefinedGroup();
+        updateOverviewAndStructs |= av.isSelectionDefinedGroup();
       }
     }
 
-- 
1.7.10.2