JAL-3551 save structure viewer session refactorings, PyMol added

[jalview.git] / src / jalview / gui / PymolViewer.java

diff --git a/src/jalview/gui/PymolViewer.java b/src/jalview/gui/PymolViewer.java
index 8f7f2c1..d0c9ea2 100644 (file)
--- a/src/jalview/gui/PymolViewer.java
+++ b/src/jalview/gui/PymolViewer.java
@@ -1,5 +1,13 @@
 package jalview.gui;
 
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JInternalFrame;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.bin.Cache;
@@ -11,14 +19,6 @@ import jalview.io.StructureFile;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
 
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.JInternalFrame;
-import javax.swing.event.InternalFrameAdapter;
-import javax.swing.event.InternalFrameEvent;
-
 public class PymolViewer extends StructureViewerBase
 {
   private static final int myWidth = 500;
@@ -57,6 +57,40 @@ public class PymolViewer extends StructureViewerBase
     openNewPymol(ap, pe, seqs);
   }
 
+  /**
+   * Constructor given a session file to be restored
+   * 
+   * @param sessionFile
+   * @param alignPanel
+   * @param pdbArray
+   * @param seqsArray
+   * @param colourByPymol
+   * @param colourBySequence
+   * @param newViewId
+   */
+  public PymolViewer(String sessionFile, AlignmentPanel alignPanel,
+          PDBEntry[] pdbArray, SequenceI[][] seqsArray,
+          boolean colourByPymol, boolean colourBySequence, String newViewId)
+  {
+    // TODO convert to base/factory class method
+    this();
+    setViewId(newViewId);
+    this.pymolSessionFile = sessionFile;
+    openNewPymol(alignPanel, pdbArray, seqsArray);
+    if (colourByPymol)
+    {
+      binding.setColourBySequence(false);
+      seqColour.setSelected(false);
+      viewerColour.setSelected(true);
+    }
+    else if (colourBySequence)
+    {
+      binding.setColourBySequence(true);
+      seqColour.setSelected(true);
+      viewerColour.setSelected(false);
+    }
+  }
+
   private void openNewPymol(AlignmentPanel ap, PDBEntry[] pe,
           SequenceI[][] seqs)
   {
@@ -320,12 +354,6 @@ public class PymolViewer extends StructureViewerBase
   }
 
   @Override
-  public String getStateInfo()
-  {
-    return null;
-  }
-
-  @Override
   public ViewerType getViewerType()
   {
     return ViewerType.PYMOL;