JAL-2668 add tests for HMMER commands, annotation and io

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 6409b56..3be48d6 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -285,6 +285,8 @@ public class AlignViewport extends AlignmentViewport implements
       showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
     }
     initAutoAnnotation();
+    initInformation();
+
     String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
             : Preferences.DEFAULT_COLOUR_PROT;
     String schemeName = Cache.getProperty(colourProperty);
@@ -652,10 +654,10 @@ 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()
@@ -703,11 +705,17 @@ public class AlignViewport extends AlignmentViewport implements
     return normaliseSequenceLogo;
   }
 
+
   public void setNormaliseSequenceLogo(boolean state)
   {
     normaliseSequenceLogo = state;
   }
 
+  public void setNormaliseHMMSequenceLogo(boolean state)
+  {
+    normaliseHMMSequenceLogo = state;
+  }
+
   /**
    * 
    * @return true if alignment characters should be displayed
@@ -718,7 +726,7 @@ 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)
   {
@@ -1049,8 +1057,9 @@ 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);
     }
   }
 
@@ -1148,4 +1157,12 @@ public class AlignViewport extends AlignmentViewport implements
     fr.setTransparency(featureSettings.getTransparency());
   }
 
+  @Override
+  public boolean isNormaliseHMMSequenceLogo()
+  {
+    return normaliseHMMSequenceLogo;
+  }
+
+
+
 }