JAL-2611 reinstate missed merge - again!

[jalview.git] / src / jalview / appletgui / AlignViewport.java

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index ebfd6f0..1d2c4bc 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -26,7 +26,9 @@ import jalview.api.FeatureSettingsModelI;
 import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
@@ -39,7 +41,6 @@ import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Font;
 import java.awt.FontMetrics;
@@ -72,11 +73,10 @@ public class AlignViewport extends AlignmentViewport implements
 
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
-    super();
+    super(al);
     calculator = new jalview.workers.AlignCalcManager();
     this.applet = applet;
-    alignment = al;
-    ranges = new ViewportRanges(this.alignment);
+
     // we always pad gaps
     this.setPadGaps(true);
 
@@ -230,43 +230,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   }
 
-  /**
-   * get the consensus sequence as displayed under the PID consensus annotation
-   * row.
-   * 
-   * @return consensus sequence as a new sequence object
-   */
-  public SequenceI getConsensusSeq()
-  {
-    if (consensus == null)
-    {
-      updateConsensus(null);
-    }
-    if (consensus == null)
-    {
-      return null;
-    }
-    StringBuilder seqs = new StringBuilder(consensus.annotations.length);
-    for (int i = 0; i < consensus.annotations.length; i++)
-    {
-      if (consensus.annotations[i] != null)
-      {
-        if (consensus.annotations[i].description.charAt(0) == '[')
-        {
-          seqs.append(consensus.annotations[i].description.charAt(1));
-        }
-        else
-        {
-          seqs.append(consensus.annotations[i].displayCharacter);
-        }
-      }
-    }
-    SequenceI sq = new Sequence("Consensus", seqs.toString());
-    sq.setDescription("Percentage Identity Consensus "
-            + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
-    return sq;
-  }
-
   java.awt.Frame nullFrame;
 
   protected FeatureSettings featureSettings = null;
@@ -344,7 +307,8 @@ public class AlignViewport extends AlignmentViewport implements
   {
     getStructureSelectionManager().sendSelection(
             new SequenceGroup(getSelectionGroup()),
-            new ColumnSelection(getColumnSelection()), this);
+            new ColumnSelection(getColumnSelection()),
+            new HiddenColumns(getAlignment().getHiddenColumns()), this);
   }
 
   /**
@@ -449,8 +413,9 @@ public class AlignViewport extends AlignmentViewport implements
     int seqOffset = findComplementScrollTarget(sr);
     if (!sr.isEmpty())
     {
-      complementPanel.setFollowingComplementScroll(true);
+      complementPanel.setToScrollComplementPanel(false);
       complementPanel.scrollToCentre(sr, seqOffset);
+      complementPanel.setToScrollComplementPanel(true);
     }
   }