X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=1d2c4bce29fffec9899f3d44410fbf4089b89434;hb=67affee2e65ca942447570c35526c04d64f41fe1;hp=c156c36ad8b6599003debfcc179a9426b93bf2af;hpb=3c75c089a56859ec8e7f674d7054e82af41e4b77;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index c156c36..1d2c4bc 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -26,6 +26,7 @@ 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;
@@ -40,9 +41,9 @@ 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;
 
 public class AlignViewport extends AlignmentViewport implements
         SelectionSource
@@ -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);
 
@@ -130,7 +130,7 @@ public class AlignViewport extends AlignmentViewport implements
         }
       }
     }
-    setFont(font);
+    setFont(font, true);
 
     MAC = new jalview.util.Platform().isAMac();
 
@@ -230,50 +230,17 @@ 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;
 
   private float heightScale = 1, widthScale = 1;
 
-  public void setFont(Font f)
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public void setFont(Font f, boolean setGrid)
   {
     font = f;
     if (nullFrame == null)
@@ -282,14 +249,17 @@ public class AlignViewport extends AlignmentViewport implements
       nullFrame.addNotify();
     }
 
-    java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
-    setCharHeight((int) (heightScale * fm.getHeight()));
-    setCharWidth((int) (widthScale * fm.charWidth('M')));
+    if (setGrid)
+    {
+      FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
+      setCharHeight((int) (heightScale * fm.getHeight()));
+      setCharWidth((int) (widthScale * fm.charWidth('M')));
+    }
 
     if (isUpperCasebold())
     {
       Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
-      fm = nullFrame.getGraphics().getFontMetrics(f2);
+      FontMetrics fm = nullFrame.getGraphics().getFontMetrics(f2);
       setCharWidth((int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)));
     }
   }
@@ -443,8 +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);
     }
   }