Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

diff --cc src/jalview/api/AlignViewportI.java
index 5715a95,03efec5..3c266e5
--- 1/src/jalview/api/AlignViewportI.java
--- 2/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@@ -554,5 -557,5 +558,7 @@@ public interface AlignViewportI extend
     */
    Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
  
 +  IdColumns getIdColumns();
++
+   ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
  }

diff --cc src/jalview/gui/PopupMenu.java
Simple merge

diff --cc src/jalview/viewmodel/AlignmentViewport.java
index 0820bcf,36b0851..d41a5be
--- 1/src/jalview/viewmodel/AlignmentViewport.java
--- 2/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@@ -3098,26 -3123,23 +3124,45 @@@ public abstract class AlignmentViewpor
              false));
    }
  
 +  /**
 +   * ordered list of annotation values displayed per sequence in ID panel
 +   */
 +  private IdColumns id_columns = null;
 +
 +  /**
 +   * available and currently visible columns for this view
 +   */
 +  @Override
 +  public IdColumns getIdColumns()
 +  {
 +    if (alignment == null)
 +    {
 +      return null;
 +    }
 +    if (id_columns == null)
 +    {
 +      id_columns = new IdColumns(alignment);
 +    }
 +    return id_columns;
 +  }
 +
+   public void setSavedUpToDate(boolean s)
+   {
+     setSavedUpToDate(s, QuitHandler.Message.UNSAVED_CHANGES);
+   }
+ 
+   public void setSavedUpToDate(boolean s, QuitHandler.Message m)
+   {
+     Console.debug(
+             "Setting " + this.getViewId() + " setSavedUpToDate to " + s);
+     savedUpToDate = s;
+     QuitHandler.setMessage(m);
+   }
+ 
+   public boolean savedUpToDate()
+   {
+     Console.debug("Returning " + this.getViewId() + " savedUpToDate value: "
+             + savedUpToDate);
+     return savedUpToDate;
+   }
  }