JAL-2668 fix broken factory method for colour scheme

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 90271c8..b490a4b 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -22,7 +22,6 @@ package jalview.gui;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureColourI;
@@ -282,6 +281,9 @@ public class AlignViewport extends AlignmentViewport
       showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
     }
     initAutoAnnotation();
+    initInformation();
+
+
     String colourProperty = alignment.isNucleotide()
             ? Preferences.DEFAULT_COLOUR_NUC
             : Preferences.DEFAULT_COLOUR_PROT;
@@ -591,10 +593,10 @@ public class AlignViewport extends AlignmentViewport
    */
   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()
@@ -641,11 +643,17 @@ public class AlignViewport extends AlignmentViewport
     return normaliseSequenceLogo;
   }
 
+
   public void setNormaliseSequenceLogo(boolean state)
   {
     normaliseSequenceLogo = state;
   }
 
+  public void setNormaliseHMMSequenceLogo(boolean state)
+  {
+    normaliseHMMSequenceLogo = state;
+  }
+
   /**
    * 
    * @return true if alignment characters should be displayed
@@ -656,7 +664,7 @@ public class AlignViewport extends AlignmentViewport
     return validCharWidth;
   }
 
-  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
 
   public AutoCalcSetting getCalcIdSettingsFor(String calcId)
   {
@@ -1087,4 +1095,11 @@ public class AlignViewport extends AlignmentViewport
     }
     fr.setTransparency(featureSettings.getTransparency());
   }
+
+  @Override
+  public boolean isNormaliseHMMSequenceLogo()
+  {
+    return normaliseHMMSequenceLogo;
+  }
+
 }