X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=0b40abd1992115f2fe2faf940511d3f97e3dc7d0;hb=5cb4c1540eaca054c26ff42a8319f0dbffb1f8e6;hp=39ded7f633049aab1db2b626494a44db237815c9;hpb=09b8644607fb5b9debbfe39a7177922b0e66aa9a;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 39ded7f..0b40abd 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -79,7 +79,7 @@ public class AlignViewport extends AlignmentViewport
 
   private Rectangle explodedGeometry;
 
-  String viewName;
+  private String viewName;
 
   /*
    * Flag set true on the view that should 'gather' multiple views of the same
@@ -92,12 +92,6 @@ 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.
    * 
@@ -260,18 +254,13 @@ public class AlignViewport extends AlignmentViewport
 
     setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
 
-    AlignmentI al = getAlignment();
-
-    if (Cache.getDefault("NORMALISE_GAPS", true))
-    {
-      al.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
-    }
+		alignment.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 (consensusProfiles == null && !isDataset)
+		if (hconsensus == null && !isDataset)
     {
-      if (!al.isNucleotide())
+			if (!alignment.isNucleotide())
       {
         showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
         showQuality = Cache.getDefault("SHOW_QUALITY", true);
@@ -295,7 +284,7 @@ public class AlignViewport extends AlignmentViewport
     initAutoAnnotation();
     // initInformation();
 
-    String colourProperty = al.isNucleotide()
+		String colourProperty = alignment.isNucleotide()
             ? Preferences.DEFAULT_COLOUR_NUC
             : Preferences.DEFAULT_COLOUR_PROT;
     String schemeName = Cache.getProperty(colourProperty);
@@ -306,7 +295,7 @@ public class AlignViewport extends AlignmentViewport
               ResidueColourScheme.NONE);
     }
     ColourSchemeI colourScheme = ColourSchemeProperty
-            .getColourScheme(al, schemeName);
+            .getColourScheme(this, alignment, schemeName);
     residueShading = new ResidueShader(colourScheme);
 
     if (colourScheme instanceof UserColourScheme)
@@ -318,9 +307,12 @@ public class AlignViewport extends AlignmentViewport
 
     if (residueShading != null)
     {
-      residueShading.setConsensus(consensusProfiles);
+			residueShading.setConsensus(hconsensus);
     }
+    setColourAppliesToAllGroups(true);
   }
+  
+  boolean validCharWidth;
 
   /**
    * {@inheritDoc}
@@ -404,9 +396,9 @@ public class AlignViewport extends AlignmentViewport
     /*
      * replace mappings on our alignment
      */
-    if (getAlignment() != null && align != null)
+		if (alignment != null && align != null)
     {
-      getAlignment().setCodonFrames(align.getCodonFrames());
+      alignment.setCodonFrames(align.getCodonFrames());
     }
   }
 
@@ -475,11 +467,11 @@ public class AlignViewport extends AlignmentViewport
     }
     else
     {
-      end = getAlignment().getWidth();
+      end = alignment.getWidth();
     }
 
-    return getAlignment().getHiddenColumns().getVisContigsIterator(start,
-            end, false);
+    return (alignment.getHiddenColumns().getVisContigsIterator(start,
+            end, false));
   }
 
   /**
@@ -528,6 +520,8 @@ 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
@@ -592,6 +586,19 @@ public class AlignViewport extends AlignmentViewport
     return StructureSelectionManager
             .getStructureSelectionManager(Desktop.instance);
   }
+  
+  @Override
+  public boolean isNormaliseSequenceLogo()
+  {
+    return normaliseSequenceLogo;
+  }
+
+  @Override
+public void setNormaliseSequenceLogo(boolean state)
+  {
+    normaliseSequenceLogo = state;
+  }
+
 
   /**
    * 
@@ -602,6 +609,8 @@ public class AlignViewport extends AlignmentViewport
   {
     return validCharWidth;
   }
+  
+  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
 
   public AutoCalcSetting getCalcIdSettingsFor(String calcId)
   {
@@ -795,7 +804,7 @@ public class AlignViewport extends AlignmentViewport
     AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
             AlignFrame.DEFAULT_HEIGHT);
     newAlignFrame.setTitle(title);
-    newAlignFrame.statusBar.setText(MessageManager
+    newAlignFrame.setStatus(MessageManager
             .formatMessage("label.successfully_loaded_file", new Object[]
             { title }));
 
@@ -1033,4 +1042,13 @@ public class AlignViewport extends AlignmentViewport
     fr.setTransparency(featureSettings.getTransparency());
   }
 
+  public String getViewName()
+  {
+    return viewName;
+  }
+
+  public void setViewName(String viewName)
+  {
+    this.viewName = viewName;
+  }
 }