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=86e114426479e03f22c0db2bb279fa56dae483b9;hpb=96356075a122b745936738f478a8ee33ac7e0f0a;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 86e1144..2005b91 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -652,10 +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()
@@ -708,6 +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
@@ -718,7 +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)
   {
@@ -1149,4 +1154,11 @@ public class AlignViewport extends AlignmentViewport implements
     fr.setTransparency(featureSettings.getTransparency());
   }
 
+  @Override
+  public boolean isNormaliseHMMSequenceLogo()
+  {
+    // TODO Auto-generated method stub
+    return normaliseHMMSequenceLogo;
+  }
+
 }