JAL-1588 refactoring to StructureViewerBase and related

[jalview.git] / src / jalview / jbgui / GStructureViewer.java

diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index 4471bbb..24e7ee3 100644 (file)
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -21,13 +21,10 @@
 package jalview.jbgui;
 
 import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.gui.AlignmentPanel;
 import jalview.util.MessageManager;
 
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.util.ArrayList;
-import java.util.Vector;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JInternalFrame;
@@ -80,24 +77,6 @@ public abstract class GStructureViewer extends JInternalFrame implements
   protected JMenuItem helpItem = new JMenuItem();
 
   /**
-   * list of sequenceSet ids associated with the view
-   */
-  protected ArrayList<String> _aps = new ArrayList<String>();
-
-  /**
-   * list of alignment panels to use for superposition
-   */
-  protected Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
-
-  /**
-   * list of alignment panels that are used for colouring structures by aligned
-   * sequences
-   */
-  protected Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
-
-  private String viewId = null;
-
-  /**
    * Constructor
    */
   public GStructureViewer()
@@ -464,52 +443,4 @@ public abstract class GStructureViewer extends JInternalFrame implements
   // this.bindingModel = bindingModel;
   // }
 
-  /**
-   * 
-   * @param ap2
-   * @return true if this Jmol instance is linked with the given alignPanel
-   */
-  public boolean isLinkedWith(AlignmentPanel ap2)
-  {
-    return _aps.contains(ap2.av.getSequenceSetId());
-  }
-
-  public boolean isUsedforaligment(AlignmentPanel ap2)
-  {
-  
-    return (_alignwith != null) && _alignwith.contains(ap2);
-  }
-
-  public boolean isUsedforcolourby(AlignmentPanel ap2)
-  {
-    return (_colourwith != null) && _colourwith.contains(ap2);
-  }
-
-  /**
-   * 
-   * @return TRUE if the view is NOT being coloured by the alignment colours.
-   */
-  public boolean isColouredByViewer()
-  {
-    return !getBinding().isColourBySequence();
-  }
-
-  public String getViewId()
-  {
-    if (viewId == null)
-    {
-      viewId = System.currentTimeMillis() + "." + this.hashCode();
-    }
-    return viewId;
-  }
-
-  protected void setViewId(String viewId)
-  {
-    this.viewId = viewId;
-  }
-
-  public String getStateInfo()
-  {
-    return null;
-  }
 }