X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=5189e7021aa8467fbc6a4bedb5c00e8099b37a85;hb=b65330720abd1329eac5fddbed9516b8302abe52;hp=11fa6152d5b26f294b282d9c2ee5c816278f6d96;hpb=0ff82a5d931e19c572695992cd0f59346819db56;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 11fa615..5189e70 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -48,4 +48,25 @@ public interface AlignViewportI
   boolean getCentreColumnLabels();
 
   boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
+
+  AlignmentAnnotation getAlignmentQualityAnnot();
+
+  AlignmentAnnotation getAlignmentConservationAnnotation();
+
+  /**
+   * Test to see if viewport is still open and active
+   * @return true indicates that all references to viewport should be dropped 
+   */
+  boolean isClosed();
+  /**
+   * get the associated calculation thread manager for the view
+   * @return
+   */
+  AlignCalcManagerI getCalcManager();
+  
+  /**
+   * get the percentage gaps allowed in a conservation calculation
+   * 
+   */
+  public int getConsPercGaps();
 }