X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=2005b91757de11968e32e4cff50d0280d8f63a5f;hb=refs%2Fheads%2Ffeatures%2Fhmmer_statistics;hp=ad6731ada9a19777d9e8f3c5bf31cd5196c436d2;hpb=4d890895e6aabfc36d45d3b53781ee2cf5cfafdc;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index ad6731a..2005b91 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -57,6 +57,7 @@ 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;
@@ -351,23 +352,19 @@ public class AlignViewport extends AlignmentViewport implements
   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);
     }
@@ -655,10 +652,10 @@ public class AlignViewport extends AlignmentViewport implements
    */
   public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
   {
-    List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
+    List<SequenceI[]> seqvectors = new ArrayList<>();
     for (PDBEntry pdb : pdbEntries)
     {
-      List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
+      List<SequenceI> choosenSeqs = new ArrayList<>();
       for (SequenceI sq : alignment.getSequences())
       {
         Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
@@ -711,6 +708,11 @@ public class AlignViewport extends AlignmentViewport implements
     normaliseSequenceLogo = state;
   }
 
+  public void setNormaliseHMMSequenceLogo(boolean state)
+  {
+    normaliseHMMSequenceLogo = state;
+  }
+
   /**
    * 
    * @return true if alignment characters should be displayed
@@ -721,7 +723,7 @@ public class AlignViewport extends AlignmentViewport implements
     return validCharWidth;
   }
 
-  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
 
   public AutoCalcSetting getCalcIdSettingsFor(String calcId)
   {
@@ -1052,8 +1054,9 @@ 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);
     }
   }
 
@@ -1151,4 +1154,11 @@ public class AlignViewport extends AlignmentViewport implements
     fr.setTransparency(featureSettings.getTransparency());
   }
 
+  @Override
+  public boolean isNormaliseHMMSequenceLogo()
+  {
+    // TODO Auto-generated method stub
+    return normaliseHMMSequenceLogo;
+  }
+
 }