X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=84be0ddcc7951c0ad9867ec1e3ccc4115996afa9;hb=4184297a80003fc498e7db3899c35c3ca61cb9d6;hp=478aa09735c33abe4a82082bc8f35904bf2bed5b;hpb=90689c5beb87addc534416a3e61e3d5746171292;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 478aa09..84be0dd 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -26,6 +26,7 @@ import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsControllerI;
 import jalview.api.SequenceStructureBinding;
 import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
@@ -59,7 +60,6 @@ import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.PIDColourScheme;
 import jalview.schemes.PurinePyrimidineColourScheme;
 import jalview.schemes.RNAHelicesColourChooser;
-import jalview.schemes.RNAInteractionColourScheme;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.schemes.TaylorColourScheme;
@@ -105,6 +105,8 @@ import java.util.Map;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
+import org.jmol.viewer.Viewer;
+
 public class AlignFrame extends EmbmenuFrame implements ActionListener,
         ItemListener, KeyListener, AlignViewControllerGuiI
 {
@@ -156,6 +158,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public AlignFrame(AlignmentI al, JalviewLite applet,
           String title, boolean embedded, boolean addToDisplay)
   {
+    this(al, null, null, applet, title, embedded, addToDisplay);
+  }
+
+  public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+          ColumnSelection columnSelection, JalviewLite applet,
+          String title, boolean embedded)
+  {
+    this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
+  }
+
+  public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+          ColumnSelection columnSelection, JalviewLite applet,
+          String title, boolean embedded, boolean addToDisplay)
+  {
     if (applet != null)
     {
       jalviewServletURL = applet.getParameter("APPLICATION_URL");
@@ -191,6 +207,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
     }
     viewport = new AlignViewport(al, applet);
+
+    if (hiddenSeqs != null && hiddenSeqs.length > 0)
+    {
+      viewport.hideSequence(hiddenSeqs);
+    }
+    if (columnSelection != null)
+    {
+      viewport.setColumnSelection(columnSelection);
+    }
+
     alignPanel = new AlignmentPanel(this, viewport);
     avc = new jalview.controller.AlignViewController(this, viewport,
             alignPanel);
@@ -902,7 +928,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               : showForSequences);
         aa.visible = visible;
     }
-    alignPanel.validateAnnotationDimensions(false);
+    alignPanel.validateAnnotationDimensions(true);
+    validate();
+    repaint();
   }
 
   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
@@ -1201,10 +1229,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       changeColour(new PurinePyrimidineColourScheme());
     }
-    else if (source == RNAInteractionColour)
-    {
-      changeColour(new RNAInteractionColourScheme());
-    }
+    // else if (source == RNAInteractionColour)
+    // {
+    // changeColour(new RNAInteractionColourScheme());
+    // }
     else if (source == RNAHelixColour)
     {
       new RNAHelicesColourChooser(viewport, alignPanel);
@@ -1313,7 +1341,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
             "label.alignment_output_command", new Object[]
             { e.getActionCommand() }), 600, 500);
-    cap.setText(new AppletFormatAdapter().formatSequences(
+
+    FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
+    cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
             e.getActionCommand(), viewport.getAlignment(),
             viewport.getShowJVSuffix()));
   }
@@ -3040,7 +3070,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   MenuItem purinePyrimidineColour = new MenuItem();
 
-  MenuItem RNAInteractionColour = new MenuItem();
+  // MenuItem RNAInteractionColour = new MenuItem();
 
   MenuItem RNAHelixColour = new MenuItem();
 
@@ -3410,9 +3440,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     purinePyrimidineColour.setLabel(MessageManager
             .getString("label.purine_pyrimidine"));
     purinePyrimidineColour.addActionListener(this);
-    RNAInteractionColour.setLabel(MessageManager
-            .getString("label.rna_interaction"));
-    RNAInteractionColour.addActionListener(this);
+    // RNAInteractionColour.setLabel(MessageManager
+    // .getString("label.rna_interaction"));
+    // RNAInteractionColour.addActionListener(this);
     RNAHelixColour.setLabel(MessageManager
             .getString("action.by_rna_helixes"));
     RNAHelixColour.addActionListener(this);
@@ -3843,10 +3873,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public SequenceStructureBinding addStructureViewInstance(
           Object jmolviewer, String[] sequenceIds)
   {
-    org.jmol.api.JmolViewer viewer = null;
+    Viewer viewer = null;
     try
     {
-      viewer = (org.jmol.api.JmolViewer) jmolviewer;
+      viewer = (Viewer) jmolviewer;
     } catch (ClassCastException ex)
     {
       System.err.println("Unsupported viewer object :"
@@ -3919,7 +3949,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     boolean needtoadd = false;
     if (toaddpdb != null)
     {
-      Vector pdbe = toaddpdb.getPDBId();
+      Vector pdbe = toaddpdb.getAllPDBEntries();
       PDBEntry pdbentry = null;
       if (pdbe != null && pdbe.size() > 0)
       {
@@ -4179,6 +4209,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     this.splitFrame = sf;
   }
 
+    // may not need this
   @Override
   public void setShowSeqFeatures(boolean b)
   {
@@ -4193,4 +4224,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // setMenusFromViewport(viewport);
 
   }
+  @Override
+  public void refreshFeatureUI(boolean enableIfNecessary)
+  {
+    if (enableIfNecessary)
+    {
+      sequenceFeatures.setState(true);
+      alignPanel.av.setShowSequenceFeatures(true);
+    }
+  }
+
+  @Override
+  public FeatureSettingsControllerI getFeatureSettingsUI()
+  {
+    return alignPanel.av.featureSettings;
+  }
+
 }