From d7361eaa08dc9af7d996851f39b7a2007d1b8832 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 28 Oct 2016 17:45:02 +0100
Subject: [PATCH] JAL-966 SearchResultsI now on viewmodels.AlignmentViewport
 rather than on SeqCanvas

---
 src/jalview/api/AlignViewportI.java          |   22 ++++++++++++++++++++++
 src/jalview/appletgui/SeqCanvas.java         |   10 ++++------
 src/jalview/gui/AlignFrame.java              |    3 +--
 src/jalview/gui/SeqCanvas.java               |   10 ++++------
 src/jalview/viewmodel/AlignmentViewport.java |   24 ++++++++++++++++++++++++
 5 files changed, 55 insertions(+), 14 deletions(-)

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index bd7d53d..2bed605 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -26,6 +26,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -422,4 +423,25 @@ public interface AlignViewportI extends ViewStyleI
    * @return true if group is defined on the alignment
    */
   boolean isSelectionDefinedGroup();
+
+  /**
+   * 
+   * @return true if there are search results on the view
+   */
+  boolean hasSearchResults();
+
+  /**
+   * set the search results for the view
+   * 
+   * @param results
+   *          - or null to clear current results
+   */
+  void setSearchResults(SearchResultsI results);
+
+  /**
+   * get search results for this view (if any)
+   * 
+   * @return search results or null
+   */
+  SearchResultsI getSearchResults();
 }
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 477f1d6..5d6bb07 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -50,8 +50,6 @@ public class SeqCanvas extends Panel
 
   AlignViewport av;
 
-  SearchResultsI searchResults = null;
-
   boolean fastPaint = false;
 
   int cursorX = 0;
@@ -632,9 +630,10 @@ public class SeqCanvas extends Panel
 
       // / Highlight search Results once all sequences have been drawn
       // ////////////////////////////////////////////////////////
-      if (searchResults != null)
+      if (av.hasSearchResults())
       {
-        int[] visibleResults = searchResults.getResults(nextSeq, startRes,
+        int[] visibleResults = av.getSearchResults().getResults(nextSeq,
+                startRes,
                 endRes);
         if (visibleResults != null)
         {
@@ -845,8 +844,7 @@ public class SeqCanvas extends Panel
 
   public void highlightSearchResults(SearchResultsI results)
   {
-    searchResults = results;
-
+    av.setSearchResults(results);
     repaint();
   }
 
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 63620e5..7dff2ac 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2907,8 +2907,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.setFollowHighlight(state);
     if (state)
     {
-      alignPanel.scrollToPosition(
-              alignPanel.getSeqPanel().seqCanvas.searchResults, false);
+      alignPanel.scrollToPosition(viewport.getSearchResults(), false);
     }
   }
 
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index a621989..d015292 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -62,8 +62,6 @@ public class SeqCanvas extends JComponent
 
   AlignViewport av;
 
-  SearchResultsI searchResults = null;
-
   boolean fastPaint = false;
 
   int LABEL_WEST;
@@ -740,10 +738,10 @@ public class SeqCanvas extends JComponent
 
       // / Highlight search Results once all sequences have been drawn
       // ////////////////////////////////////////////////////////
-      if (searchResults != null)
+      if (av.hasSearchResults())
       {
-        int[] visibleResults = searchResults.getResults(nextSeq, startRes,
-                endRes);
+        int[] visibleResults = av.getSearchResults().getResults(nextSeq,
+                startRes, endRes);
         if (visibleResults != null)
         {
           for (int r = 0; r < visibleResults.length; r += 2)
@@ -969,7 +967,7 @@ public class SeqCanvas extends JComponent
   {
     img = null;
 
-    searchResults = results;
+    av.setSearchResults(results);
 
     repaint();
   }
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 2f733ed..aa7cd12 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -2822,6 +2822,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   private boolean selectionIsDefinedGroup = false;
 
+
   @Override
   public boolean isSelectionDefinedGroup()
   {
@@ -2845,4 +2846,27 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return selectionGroup.getContext() == alignment
             || selectionIsDefinedGroup;
   }
+
+  /**
+   * null, or currently highlighted results on this view
+   */
+  private SearchResultsI searchResults = null;
+
+  @Override
+  public boolean hasSearchResults()
+  {
+    return searchResults != null;
+  }
+
+  @Override
+  public void setSearchResults(SearchResultsI results)
+  {
+    searchResults = results;
+  }
+
+  @Override
+  public SearchResultsI getSearchResults()
+  {
+    return searchResults;
+  }
 }
-- 
1.7.10.2