Merge branch 'features/JAL-1333' into Release_2_8_2_Branch

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index c075bf5..cadb205 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -35,6 +35,7 @@ import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.SequenceStructureBindingModel;
 
 import java.awt.Color;
 import java.awt.Container;
@@ -56,26 +57,13 @@ import org.jmol.api.JmolViewer;
 import org.jmol.constant.EnumCallback;
 import org.jmol.popup.JmolPopup;
 
-public abstract class JalviewJmolBinding implements StructureListener,
+public abstract class JalviewJmolBinding extends SequenceStructureBindingModel implements StructureListener,
         JmolStatusListener, SequenceStructureBinding,
         JmolSelectionListener, ComponentListener,
         StructureSelectionManagerProvider
 
 {
   /**
-   * set if Jmol state is being restored from some source - instructs binding
-   * not to apply default display style when structure set is updated for first
-   * time.
-   */
-  private boolean loadingFromArchive = false;
-
-  /**
-   * second flag to indicate if the jmol viewer should ignore sequence colouring
-   * events from the structure manager because the GUI is still setting up
-   */
-  private boolean loadingFinished = true;
-
-  /**
    * state flag used to check if the Jmol viewer's paint method can be called
    */
   private boolean finishedInit = false;
@@ -641,7 +629,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
   public void colourBySequence(boolean showFeatures,
           jalview.api.AlignmentViewPanel alignmentv)
   {
-    if (!colourBySequence || !loadingFinished)
+    if (!colourBySequence || !isLoadingFinished())
       return;
     if (ssm == null)
     {
@@ -1509,32 +1497,6 @@ public abstract class JalviewJmolBinding implements StructureListener,
     showConsole(false);
   }
 
-  public void setLoadingFromArchive(boolean loadingFromArchive)
-  {
-    this.loadingFromArchive = loadingFromArchive;
-  }
-
-  /**
-   * 
-   * @return true if Jmol is still restoring state or loading is still going on
-   *         (see setFinsihedLoadingFromArchive)
-   */
-  public boolean isLoadingFromArchive()
-  {
-    return loadingFromArchive && !loadingFinished;
-  }
-
-  /**
-   * modify flag which controls if sequence colouring events are honoured by the
-   * binding. Should be true for normal operation
-   * 
-   * @param finishedLoading
-   */
-  public void setFinishedLoadingFromArchive(boolean finishedLoading)
-  {
-    loadingFinished = finishedLoading;
-  }
-
   public void setBackgroundColour(java.awt.Color col)
   {
     jmolHistory(false);