JAL-2629 revising hmmer annotation updating (wip)

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index b490a4b..ef95161 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -94,6 +94,12 @@ public class AlignViewport extends AlignmentViewport
 
   private AnnotationColumnChooser annotationColumnSelectionState;
 
+  boolean validCharWidth;
+
+  public boolean followSelection = true;
+
+  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
+
   /**
    * Creates a new AlignViewport object.
    * 
@@ -256,14 +262,14 @@ public class AlignViewport extends AlignmentViewport
 
     setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
 
-    alignment
-            .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+    AlignmentI al = getAlignment();
+    al.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
 
     // We must set conservation and consensus before setting colour,
     // as Blosum and Clustal require this to be done
     if (hconsensus == null && !isDataset)
     {
-      if (!alignment.isNucleotide())
+      if (!al.isNucleotide())
       {
         showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
         showQuality = Cache.getDefault("SHOW_QUALITY", true);
@@ -281,10 +287,9 @@ public class AlignViewport extends AlignmentViewport
       showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
     }
     initAutoAnnotation();
-    initInformation();
+    // initInformation();
 
-
-    String colourProperty = alignment.isNucleotide()
+    String colourProperty = al.isNucleotide()
             ? Preferences.DEFAULT_COLOUR_NUC
             : Preferences.DEFAULT_COLOUR_PROT;
     String schemeName = Cache.getProperty(colourProperty);
@@ -295,7 +300,7 @@ public class AlignViewport extends AlignmentViewport
               ResidueColourScheme.NONE);
     }
     ColourSchemeI colourScheme = ColourSchemeProperty
-            .getColourScheme(alignment, schemeName);
+            .getColourScheme(al, schemeName);
     residueShading = new ResidueShader(colourScheme);
 
     if (colourScheme instanceof UserColourScheme)
@@ -311,8 +316,6 @@ public class AlignViewport extends AlignmentViewport
     }
   }
 
-  boolean validCharWidth;
-
   /**
    * {@inheritDoc}
    */
@@ -395,9 +398,9 @@ public class AlignViewport extends AlignmentViewport
     /*
      * replace mappings on our alignment
      */
-    if (alignment != null && align != null)
+    if (getAlignment() != null && align != null)
     {
-      alignment.setCodonFrames(align.getCodonFrames());
+      getAlignment().setCodonFrames(align.getCodonFrames());
     }
   }
 
@@ -466,9 +469,10 @@ public class AlignViewport extends AlignmentViewport
     }
     else
     {
-      end = alignment.getWidth();
+      end = getAlignment().getWidth();
     }
-    viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end);
+    viscontigs = getAlignment().getHiddenColumns().getVisibleContigs(start,
+            end);
     return viscontigs;
   }
 
@@ -518,8 +522,6 @@ public class AlignViewport extends AlignmentViewport
     return false;
   }
 
-  public boolean followSelection = true;
-
   /**
    * @return true if view selection should always follow the selections
    *         broadcast by other selection sources
@@ -597,7 +599,7 @@ public class AlignViewport extends AlignmentViewport
     for (PDBEntry pdb : pdbEntries)
     {
       List<SequenceI> choosenSeqs = new ArrayList<>();
-      for (SequenceI sq : alignment.getSequences())
+      for (SequenceI sq : getAlignment().getSequences())
       {
         Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
                 .getAllPDBEntries();
@@ -664,8 +666,6 @@ public class AlignViewport extends AlignmentViewport
     return validCharWidth;
   }
 
-  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
-
   public AutoCalcSetting getCalcIdSettingsFor(String calcId)
   {
     return calcIdParams.get(calcId);