X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2Fstructures%2FJalviewStructureDisplayI.java;h=77f2b6d69f74686a1506b507f68bd3c67bb03087;hb=39c97de2f7b8ef87b42f121f37d4f158d1651fe9;hp=abb23f89c22d0c58c8c48c8040ff5472d99fcd69;hpb=61aa0f698c7494efa3e6408ce54fac4e8400053c;p=jalview.git

diff --git a/src/jalview/api/structures/JalviewStructureDisplayI.java b/src/jalview/api/structures/JalviewStructureDisplayI.java
index abb23f8..77f2b6d 100644
--- a/src/jalview/api/structures/JalviewStructureDisplayI.java
+++ b/src/jalview/api/structures/JalviewStructureDisplayI.java
@@ -20,10 +20,15 @@
  */
 package jalview.api.structures;
 
+import java.io.File;
+import java.util.Collections;
+import java.util.List;
+
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.StructureViewer;
 import jalview.structures.models.AAStructureBindingModel;
 
 public interface JalviewStructureDisplayI
@@ -59,11 +64,9 @@ public interface JalviewStructureDisplayI
   void closeViewer(boolean closeExternalViewer);
 
   /**
-   * apply a colourscheme to the structures in the viewer
-   * 
-   * @param colourScheme
+   * Check if the external viewer is still running
    */
-  void setJalviewColourScheme(ColourSchemeI colourScheme);
+  boolean stillRunning();
 
   /**
    * 
@@ -123,6 +126,80 @@ public interface JalviewStructureDisplayI
   /**
    * Raise the panel to the top of the stack...
    */
-  void toFront();
+  void raiseViewer();
+
+  AlignmentViewPanel getAlignmentPanel();
+
+  /**
+   * Answers true if the given alignment view is used to colour structures by
+   * sequence, false if not
+   * 
+   * @param ap
+   * @return
+   */
+  boolean isUsedForColourBy(AlignmentViewPanel ap);
+
+  /**
+   * If implemented, shows a command line console in the structure viewer
+   * 
+   * @param show
+   *          true to show, false to hide
+   */
+  void showConsole(boolean show);
+
+  /**
+   * Remove references to the given alignment view for this structure viewer
+   * 
+   * @param avp
+   */
+  void removeAlignmentPanel(AlignmentViewPanel avp);
+
+  /**
+   * Updates the progress bar if there is one. Call stopProgressBar with the
+   * returned handle to remove the message.
+   * 
+   * @param msg
+   * @return handle
+   */
+  long startProgressBar(String msg);
+
+  /**
+   * Ends the progress bar with the specified handle, leaving a message (if not
+   * null) on the status bar
+   * 
+   * @param msg
+   * @param handle
+   */
+  void stopProgressBar(String msg, long handle);
+
+  /**
+   * 
+   * @return true if the actions menu is shown for this viewer
+   */
+  boolean hasViewerActionsMenu();
+
+  String getViewId();
+
+  StructureViewer.ViewerType getViewerType();
+
+  boolean isUsedforaligment(AlignmentViewPanel ap);
+
+  boolean isColouredByViewer();
+
+  int getHeight();
+
+  int getWidth();
+
+  int getY();
+
+  File saveSession();
+
+  /**
+   * 
+   * @return heteroatoms in a form suitable for display and passing to command generator to display hetatms
+   */
+  default List<String> getHetatms() {
+    return Collections.EMPTY_LIST;
+  }
 
 }