JAL-3141 Reworked a lot of BackupFiles to allow the Customise Checkbox

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 0e93da9..bc668fd 100644 (file)
--- 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
@@ -290,7 +290,7 @@ public class AlignViewport extends AlignmentViewport
               ResidueColourScheme.NONE);
     }
     ColourSchemeI colourScheme = ColourSchemeProperty
-            .getColourScheme(alignment, schemeName);
+            .getColourScheme(this, alignment, schemeName);
     residueShading = new ResidueShader(colourScheme);
 
     if (colourScheme instanceof UserColourScheme)
@@ -304,6 +304,7 @@ public class AlignViewport extends AlignmentViewport
     {
       residueShading.setConsensus(hconsensus);
     }
+    setColourAppliesToAllGroups(true);
   }
 
   boolean validCharWidth;
@@ -463,7 +464,8 @@ public class AlignViewport extends AlignmentViewport
     {
       end = alignment.getWidth();
     }
-    return (alignment.getHiddenColumns().getVisContigsIterator(start, end));
+    return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+            false));
   }
 
   /**
@@ -794,7 +796,7 @@ 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 }));
 
@@ -1031,4 +1033,14 @@ public class AlignViewport extends AlignmentViewport
     }
     fr.setTransparency(featureSettings.getTransparency());
   }
+
+  public String getViewName()
+  {
+    return viewName;
+  }
+
+  public void setViewName(String viewName)
+  {
+    this.viewName = viewName;
+  }
 }