(JAL-958) - normalised sequence logo for applet

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 5ac946a..1c6a94e 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -40,7 +40,7 @@ import java.util.*;
 import java.awt.*;
 
 import jalview.analysis.*;
-import jalview.api.StructureSelectionManagerProvider;
+import jalview.api.AlignViewportI;
 
 import jalview.bin.*;
 
@@ -57,7 +57,7 @@ import jalview.structure.VamsasSource;
  * @author $author$
  * @version $Revision: 1.141 $
  */
-public class AlignViewport implements SelectionSource, VamsasSource
+public class AlignViewport implements SelectionSource, VamsasSource, AlignViewportI
 {
   private static final int RIGHT_JUSTIFY = 1;
 
@@ -2481,4 +2481,46 @@ public class AlignViewport implements SelectionSource, VamsasSource
   {
     normaliseSequenceLogo = state;
   }
+
+  public boolean isCalcInProgress()
+  {
+    // TODO generalise to iterate over all calculators associated with av
+    return updatingConsensus || updatingConservation || updatingStrucConsensus;
+  }
+
+  public boolean isCalculationInProgress(
+          AlignmentAnnotation alignmentAnnotation)
+  {
+    if (!alignmentAnnotation.autoCalculated)
+      return false;
+    if ((updatingConsensus && consensus==alignmentAnnotation)
+            || (updatingConservation && (conservation==alignmentAnnotation || quality==alignmentAnnotation))
+            || (updatingStrucConsensus && strucConsensus==alignmentAnnotation)
+            )
+    {
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * 
+   * @return true if alignment characters should be displayed 
+   */
+  public boolean isValidCharWidth()
+  {
+    return validCharWidth;
+  }
+
+  @Override
+  public Hashtable[] getSequenceConsensusHash()
+  {
+    return hconsensus;
+  }
+
+  @Override
+  public Hashtable[] getRnaStructureConsensusHash()
+  {
+    return hStrucConsensus;
+  }
 }