JAL-3390 Chimera showStructures() respects visible/chain selections

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

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 840dbae..cc431ac 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
@@ -90,13 +91,13 @@ public abstract class StructureViewerBase extends GStructureViewer
   /**
    * list of alignment panels to use for superposition
    */
-  protected Vector<AlignmentPanel> _alignwith = new Vector<>();
+  protected Vector<AlignmentViewPanel> _alignwith = new Vector<>();
 
   /**
    * list of alignment panels that are used for colouring structures by aligned
    * sequences
    */
-  protected Vector<AlignmentPanel> _colourwith = new Vector<>();
+  protected Vector<AlignmentViewPanel> _colourwith = new Vector<>();
 
   private String viewId = null;
 
@@ -165,9 +166,10 @@ public abstract class StructureViewerBase extends GStructureViewer
     return (_alignwith != null) && _alignwith.contains(ap2);
   }
 
-  public boolean isUsedforcolourby(AlignmentPanel ap2)
+  @Override
+  public boolean isUsedforcolourby(AlignmentViewPanel avp)
   {
-    return (_colourwith != null) && _colourwith.contains(ap2);
+    return (_colourwith != null) && _colourwith.contains(avp);
   }
 
   /**
@@ -564,7 +566,8 @@ public abstract class StructureViewerBase extends GStructureViewer
   {
     AlignmentI al = getAlignmentPanel().av.getAlignment();
     ColourSchemeI cs = ColourSchemes.getInstance()
-            .getColourScheme(colourSchemeName, al, null);
+            .getColourScheme(colourSchemeName, getAlignmentPanel().av, al,
+                    null);
     getBinding().setJalviewColourScheme(cs);
   }
 
@@ -708,6 +711,19 @@ public abstract class StructureViewerBase extends GStructureViewer
             });
     viewMenu.add(seqColourBy);
 
+    showAlignmentOnly = new JCheckBoxMenuItem("Visible alignment only");
+    showAlignmentOnly.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        getBinding().setShowAlignmentOnly(showAlignmentOnly.isSelected());
+        getBinding().showStructures(getAlignmentPanel().getAlignViewport(),
+                true);
+      }
+    });
+    viewMenu.add(showAlignmentOnly);
+
     final ItemListener handler = new ItemListener()
     {
       @Override
@@ -783,11 +799,12 @@ public abstract class StructureViewerBase extends GStructureViewer
       int[] alm = new int[_alignwith.size()];
       int a = 0;
 
-      for (AlignmentPanel alignPanel : _alignwith)
+      for (AlignmentViewPanel alignPanel : _alignwith)
       {
-        als[a] = alignPanel.av.getAlignment();
+        AlignViewportI av = alignPanel.getAlignViewport();
+        als[a] = av.getAlignment();
         alm[a] = -1;
-        alc[a++] = alignPanel.av.getAlignment().getHiddenColumns();
+        alc[a++] = av.getAlignment().getHiddenColumns();
       }
       reply = getBinding().superposeStructures(als, alm, alc);
       if (reply != null)
@@ -799,9 +816,10 @@ public abstract class StructureViewerBase extends GStructureViewer
     } catch (Exception e)
     {
       StringBuffer sp = new StringBuffer();
-      for (AlignmentPanel alignPanel : _alignwith)
+      for (AlignmentViewPanel avp : _alignwith)
       {
-        sp.append("'" + alignPanel.alignFrame.getTitle() + "' ");
+        sp.append(
+                "'" + ((AlignmentPanel) avp).alignFrame.getTitle() + "' ");
       }
       Cache.log.info("Couldn't align structures with the " + sp.toString()
               + "associated alignment panels.", e);
@@ -865,9 +883,9 @@ public abstract class StructureViewerBase extends GStructureViewer
         }
       }
       // Set the colour using the current view for the associated alignframe
-      for (AlignmentPanel alignPanel : _colourwith)
+      for (AlignmentViewPanel avp : _colourwith)
       {
-        binding.colourBySequence(alignPanel);
+        binding.colourBySequence(avp);
       }
       seqColoursApplied = true;
     }
@@ -1034,4 +1052,10 @@ public abstract class StructureViewerBase extends GStructureViewer
     return seqColoursApplied;
   }
 
+  @Override
+  public void raiseViewer()
+  {
+    toFront();
+  }
+
 }