X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2Fstructures%2FJalviewStructureDisplayI.java;h=a27cec6ea3502e7c2afc3a20eab800f102e6e5e8;hb=e06ef51ba3dd8cdae7632d71db162ff416b88256;hp=e37f46710329352d7dd0b94c2462ecb73f6b5339;hpb=ecfc49bc5a7e416c0f967677651923993f105dd8;p=jalview.git

diff --git a/src/jalview/api/structures/JalviewStructureDisplayI.java b/src/jalview/api/structures/JalviewStructureDisplayI.java
index e37f467..a27cec6 100644
--- a/src/jalview/api/structures/JalviewStructureDisplayI.java
+++ b/src/jalview/api/structures/JalviewStructureDisplayI.java
@@ -1,39 +1,92 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.api.structures;
 
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.api.SequenceStructureBinding;
-import jalview.datamodel.AlignmentI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
-import jalview.ext.jmol.JalviewJmolBinding;
-import jalview.structure.StructureMappingcommandSet;
-import jalview.structure.StructureSelectionManager;
+import jalview.schemes.ColourSchemeI;
+import jalview.structures.models.AAStructureBindingModel;
 
 public interface JalviewStructureDisplayI
 {
 
-  SequenceStructureBinding getBinding();
+  AAStructureBindingModel getBinding();
 
   /**
-   * @return true if there is an active GUI handling a structure display 
+   * @return true if there is an active GUI handling a structure display
    */
   boolean isVisible();
 
   /**
-   * enable or disable the structure display - note this might just hide or show a GUI element, but not actually reset the display
+   * enable or disable the structure display - note this might just hide or show
+   * a GUI element, but not actually reset the display
+   * 
    * @param b
    */
   void setVisible(boolean b);
 
   /**
-   * free up any external resources that were used by this display and collect garbage
+   * free up any external resources that were used by this display and collect
+   * garbage
    */
   void dispose();
 
   /**
-   * shutdown any structure viewing processes started by this display
+   * Shutdown any Jalview structure viewing processes started by this display
+   * 
+   * @param closeExternalViewer
+   *          if true, force close any linked external viewer process
    */
-  void closeViewer();
+  void closeViewer(boolean closeExternalViewer);
 
+  /**
+   * apply a colourscheme to the structures in the viewer
+   * 
+   * @param colourScheme
+   */
+  void setJalviewColourScheme(ColourSchemeI colourScheme);
+
+  /**
+   * 
+   * @return true if all background sequence/structure binding threads have
+   *         completed for this viewer instance
+   */
+  boolean hasMapping();
+
+  // construction method - move to another interface ?
+  boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
+          AlignmentViewPanel apanel, String pdbId);
+
+  // construction method - move to another interface ?
+  boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
+          String[] chains, AlignmentViewPanel apanel, String pdbId);
+
+  /**
+   * refresh GUI after reconfiguring structure(s) and alignment panels
+   */
+  void updateTitleAndMenus();
+
+  boolean isAlignAddedStructures();
+
+  void setAlignAddedStructures(boolean alignAdded);
 
 }