JAL-4159 sometimes the progress bar may not be available - null check

[jalview.git] / src / jalview / api / AlignViewportI.java

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index e3478ea..9624f83 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -20,6 +20,13 @@
  */
 package jalview.api;
 
+import java.awt.Color;
+import java.awt.Font;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
 import jalview.analysis.Conservation;
 import jalview.analysis.TreeModel;
 import jalview.datamodel.AlignmentAnnotation;
@@ -38,13 +45,6 @@ import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
 import jalview.viewmodel.ViewportRanges;
 
-import java.awt.Color;
-import java.awt.Font;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
 /**
  * @author jimp
  * 
@@ -85,8 +85,12 @@ public interface AlignViewportI extends ViewStyleI
   boolean isValidCharWidth();
 
   boolean isShowConsensusHistogram();
+  
+  boolean isShowSSConsensusHistogram();
 
   boolean isShowSequenceLogo();
+  
+  boolean isShowSequenceSSLogo();
 
   boolean isNormaliseSequenceLogo();
 
@@ -129,6 +133,9 @@ public interface AlignViewportI extends ViewStyleI
    * @return
    */
   AlignmentAnnotation getAlignmentConsensusAnnotation();
+  
+  AlignmentAnnotation getAlignmentSecondaryStructureConsensusAnnotation();
+
 
   /**
    * get the container for alignment gap annotation
@@ -175,6 +182,9 @@ public interface AlignViewportI extends ViewStyleI
    * @param hconsensus
    */
   void setSequenceConsensusHash(ProfilesI hconsensus);
+  
+  void setSequenceSSConsensusHash(ProfilesI hSSConsensus);
+  
 
   /**
    * Set the cDNA complement consensus for the viewport
@@ -478,9 +488,13 @@ public interface AlignViewportI extends ViewStyleI
   SearchResultsI getSearchResults();
 
   /**
-   * Retrieve a ContactListI corresponding to column in an annotation row in an alignment.
-   * @param _aa - annotation with associated matrix data
-   * @param column - column in alignment where _aa is associated
+   * Retrieve a ContactListI corresponding to column in an annotation row in an
+   * alignment.
+   * 
+   * @param _aa
+   *          - annotation with associated matrix data
+   * @param column
+   *          - column in alignment where _aa is associated
    */
   ContactListI getContactList(AlignmentAnnotation _aa, int column);
 
@@ -561,6 +575,19 @@ public interface AlignViewportI extends ViewStyleI
    * @return
    */
   Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+  /**
+   * notify all concerned that the alignment data has changed and derived data
+   * needs to be recalculated
+   */
+  public void notifyAlignmentChanged();
 
+  /**
+   * retrieve a matrix associated with the view's alignment's annotation 
+   * @param alignmentAnnotation
+   * @return contact matrix or NULL
+   */
   ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
+
+  ProfilesI getSequenceSSConsensusHash();
+
 }