JAL-4411 store class of provider in PDBEntry

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

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index d15c5fb..b7747f5 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -27,6 +27,8 @@ import jalview.datamodel.AlignmentExportData;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceCollectionI;
@@ -83,8 +85,12 @@ public interface AlignViewportI extends ViewStyleI
   boolean isValidCharWidth();
 
   boolean isShowConsensusHistogram();
+  
+  boolean isShowSSConsensusHistogram();
 
   boolean isShowSequenceLogo();
+  
+  boolean isShowSequenceSSLogo();
 
   boolean isNormaliseSequenceLogo();
 
@@ -127,6 +133,9 @@ public interface AlignViewportI extends ViewStyleI
    * @return
    */
   AlignmentAnnotation getAlignmentConsensusAnnotation();
+  
+  AlignmentAnnotation getAlignmentSecondaryStructureConsensusAnnotation();
+
 
   /**
    * get the container for alignment gap annotation
@@ -173,6 +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
@@ -476,6 +488,17 @@ 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
+   */
+  ContactListI getContactList(AlignmentAnnotation _aa, int column);
+
+  /**
    * Updates view settings with the given font. You may need to call
    * AlignmentPanel.fontChanged to update the layout geometry.
    * 
@@ -552,4 +575,9 @@ public interface AlignViewportI extends ViewStyleI
    * @return
    */
   Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+
+  ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
+
+  ProfilesI getSequenceSSConsensusHash();
+
 }