Merge branch 'features/JAL-1738_JAL-345_selectionfromhighlight' into develop

[jalview.git] / src / jalview / gui / AlignmentPanel.java

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index b551ad0..235c81f 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -25,7 +25,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -297,7 +297,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * Highlight the given results on the alignment.
    * 
    */
-  public void highlightSearchResults(SearchResults results)
+  public void highlightSearchResults(SearchResultsI results)
   {
     scrollToPosition(results);
     getSeqPanel().seqCanvas.highlightSearchResults(results);
@@ -309,7 +309,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * 
    * @param results
    */
-  public boolean scrollToPosition(SearchResults results)
+  public boolean scrollToPosition(SearchResultsI results)
   {
     return scrollToPosition(results, 0, true, false);
   }
@@ -322,7 +322,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param redrawOverview
    * @return
    */
-  public boolean scrollToPosition(SearchResults searchResults,
+  public boolean scrollToPosition(SearchResultsI searchResults,
           boolean redrawOverview)
   {
     return scrollToPosition(searchResults, 0, redrawOverview, false);
@@ -342,7 +342,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    *          if true, try to centre the search results horizontally in the view
    * @return false if results were not found
    */
-  public boolean scrollToPosition(SearchResults results,
+  public boolean scrollToPosition(SearchResultsI results,
           int verticalOffset, boolean redrawOverview, boolean centre)
   {
     int startv, endv, starts, ends;
@@ -1840,14 +1840,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param verticalOffset
    *          the number of visible sequences to show above the mapped region
    */
-  public void scrollToCentre(SearchResults sr, int verticalOffset)
+  public void scrollToCentre(SearchResultsI sr, int verticalOffset)
   {
     /*
      * To avoid jumpy vertical scrolling (if some sequences are gapped or not
      * mapped), we can make the scroll-to location a sequence above the one
      * actually mapped.
      */
-    SequenceI mappedTo = sr.getResultSequence(0);
+    SequenceI mappedTo = sr.getResults().get(0).getSequence();
     List<SequenceI> seqs = av.getAlignment().getSequences();
 
     /*