JAL-2602 pulled up identical methods to base class

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 1c53b61..835371f 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -39,7 +39,6 @@ import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShader;
@@ -52,12 +51,12 @@ import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.ViewportRanges;
 import jalview.ws.params.AutoCalcSetting;
 
 import java.awt.Container;
 import java.awt.Dimension;
 import java.awt.Font;
+import java.awt.FontMetrics;
 import java.awt.Rectangle;
 import java.util.ArrayList;
 import java.util.Hashtable;
@@ -106,7 +105,7 @@ public class AlignViewport extends AlignmentViewport implements
    */
   public AlignViewport(AlignmentI al)
   {
-    setAlignment(al);
+    super(al);
     init();
   }
 
@@ -124,6 +123,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   public AlignViewport(AlignmentI al, String seqsetid, String viewid)
   {
+    super(al);
     sequenceSetID = seqsetid;
     viewId = viewid;
     // TODO remove these once 2.4.VAMSAS release finished
@@ -136,8 +136,8 @@ public class AlignViewport extends AlignmentViewport implements
     {
       Cache.log.debug("Setting viewport's view id : " + viewId);
     }
-    setAlignment(al);
     init();
+
   }
 
   /**
@@ -150,7 +150,7 @@ public class AlignViewport extends AlignmentViewport implements
    */
   public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns)
   {
-    setAlignment(al);
+    super(al);
     if (hiddenColumns != null)
     {
       al.setHiddenColumns(hiddenColumns);
@@ -185,6 +185,7 @@ public class AlignViewport extends AlignmentViewport implements
   public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
           String seqsetid, String viewid)
   {
+    super(al);
     sequenceSetID = seqsetid;
     viewId = viewid;
     // TODO remove these once 2.4.VAMSAS release finished
@@ -197,7 +198,7 @@ public class AlignViewport extends AlignmentViewport implements
     {
       Cache.log.debug("Setting viewport's view id : " + viewId);
     }
-    setAlignment(al);
+
     if (hiddenColumns != null)
     {
       al.setHiddenColumns(hiddenColumns);
@@ -239,7 +240,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   void init()
   {
-    ranges = new ViewportRanges(this.alignment);
     applyViewProperties();
 
     String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
@@ -310,64 +310,22 @@ 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;
-    }
-    StringBuffer seqs = new StringBuffer();
-    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;
-  }
-
   boolean validCharWidth;
 
   /**
-   * update view settings with the given font. You may need to call
-   * alignPanel.fontChanged to update the layout geometry
-   * 
-   * @param setGrid
-   *          when true, charWidth/height is set according to font mentrics
+   * {@inheritDoc}
    */
+  @Override
   public void setFont(Font f, boolean setGrid)
   {
     font = f;
 
     Container c = new Container();
 
-    java.awt.FontMetrics fm = c.getFontMetrics(font);
-    int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle
-            .getCharHeight();
     if (setGrid)
     {
+      FontMetrics fm = c.getFontMetrics(font);
+      int ww = fm.charWidth('M');
       setCharHeight(fm.getHeight());
       setCharWidth(ww);
     }
@@ -1052,8 +1010,9 @@ public class AlignViewport extends AlignmentViewport implements
       // TODO would like next line without cast but needs more refactoring...
       final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
               .getAlignPanel();
-      complementPanel.setDontScrollComplement(true);
+      complementPanel.setToScrollComplementPanel(false);
       complementPanel.scrollToCentre(sr, verticalOffset);
+      complementPanel.setToScrollComplementPanel(true);
     }
   }