JAL-1588 part work save/restore of Chimera session

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

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 34398fe..13af0e8 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -1,5 +1,8 @@
 package jalview.gui;
 
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.jbgui.GStructureViewer;
+
 import java.awt.Component;
 import java.util.ArrayList;
 import java.util.List;
@@ -7,9 +10,6 @@ import java.util.Vector;
 
 import javax.swing.JMenuItem;
 
-import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.jbgui.GStructureViewer;
-
 /**
  * Base class with common functionality for JMol, Chimera or other structure
  * viewers.
@@ -81,10 +81,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     this.viewId = viewId;
   }
 
-  public String getStateInfo()
-  {
-    return "";
-  }
+  public abstract String getStateInfo();
 
   protected void buildActionMenu()
   {
@@ -115,4 +112,114 @@ public abstract class StructureViewerBase extends GStructureViewer
   {
     this.ap = alp;
   }
+
+  public AlignmentPanel[] getAllAlignmentPanels()
+  {
+    AlignmentPanel[] t, list = new AlignmentPanel[0];
+    for (String setid : _aps)
+    {
+      AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
+      if (panels != null)
+      {
+        t = new AlignmentPanel[list.length + panels.length];
+        System.arraycopy(list, 0, t, 0, list.length);
+        System.arraycopy(panels, 0, t, list.length, panels.length);
+        list = t;
+      }
+    }
+  
+    return list;
+  }
+
+  /**
+   * set the primary alignmentPanel reference and add another alignPanel to the
+   * list of ones to use for colouring and aligning
+   * 
+   * @param nap
+   */
+  public void addAlignmentPanel(AlignmentPanel nap)
+  {
+    if (getAlignmentPanel() == null)
+    {
+      setAlignmentPanel(nap);
+    }
+    if (!_aps.contains(nap.av.getSequenceSetId()))
+    {
+      _aps.add(nap.av.getSequenceSetId());
+    }
+  }
+
+  /**
+   * remove any references held to the given alignment panel
+   * 
+   * @param nap
+   */
+  public void removeAlignmentPanel(AlignmentPanel nap)
+  {
+    try
+    {
+      _alignwith.remove(nap);
+      _colourwith.remove(nap);
+      if (getAlignmentPanel() == nap)
+      {
+        setAlignmentPanel(null);
+        for (AlignmentPanel aps : getAllAlignmentPanels())
+        {
+          if (aps != nap)
+          {
+            setAlignmentPanel(aps);
+            break;
+          }
+        }
+      }
+    } catch (Exception ex)
+    {
+    }
+    if (getAlignmentPanel() != null)
+    {
+      buildActionMenu();
+    }
+  }
+
+  public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
+  {
+    addAlignmentPanel(nap);
+    if (!_alignwith.contains(nap))
+    {
+      _alignwith.add(nap);
+    }
+  }
+
+  public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
+  {
+    if (_alignwith.contains(nap))
+    {
+      _alignwith.remove(nap);
+    }
+  }
+
+  public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, boolean enableColourBySeq)
+  {
+    useAlignmentPanelForColourbyseq(nap);
+    getBinding().setColourBySequence(enableColourBySeq);
+    seqColour.setSelected(enableColourBySeq);
+    viewerColour.setSelected(!enableColourBySeq);
+  }
+
+  public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
+  {
+    addAlignmentPanel(nap);
+    if (!_colourwith.contains(nap))
+    {
+      _colourwith.add(nap);
+    }
+  }
+
+  public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
+  {
+    if (_colourwith.contains(nap))
+    {
+      _colourwith.remove(nap);
+    }
+  }
 }