setVisible replaces show

[jalview.git] / src / MCview / AppletPDBCanvas.java

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index b2646bc..47aa94b 100755 (executable)
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -95,8 +95,10 @@ public class AppletPDBCanvas
 
     try{
       pdb = ssm.setMapping(seq, pdbentry.getFile(), protocol);
-      if (fr!=null)
-        fr.featuresAdded();
+
+      if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+       pdbentry.setFile("INLINE"+pdb.id);
+
     }catch(Exception ex)
     {
       ex.printStackTrace();
@@ -107,9 +109,7 @@ public class AppletPDBCanvas
 
     ssm.addStructureViewerListener(this);
 
-    colourBySequence(ap.getSequenceRenderer(),
-                     ap.av.getShowSequenceFeatures() ?
-                     ap.getFeatureRenderer() : null);
+    colourBySequence();
 
     int max = -10;
     int maxchain = -1;
@@ -240,9 +240,7 @@ public class AppletPDBCanvas
       }
     }
     seqColoursReady = true;
-    colourBySequence(ap.getSequenceRenderer(),
-                               ap.av.getShowSequenceFeatures() ?
-                               ap.getFeatureRenderer() : null);
+    colourBySequence();
     redrawneeded = true;
     repaint();
   }
@@ -497,18 +495,22 @@ public class AppletPDBCanvas
 
   // This method has been taken out of PDBChain to allow
   // Applet and Application specific sequence renderers to be used
-  void colourBySequence(SequenceRenderer sr, FeatureRenderer fr)
+  void colourBySequence()
   {
+    SequenceRenderer sr = ap.getSequenceRenderer();
+
     StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
 
     boolean showFeatures = false;
-    if (fr!=null)
+    if (ap.av.getShowSequenceFeatures())
     {
       if (fr == null)
       {
         fr = new jalview.appletgui.FeatureRenderer(ap.av);
       }
-      fr.transferSettings(fr);
+
+      fr.transferSettings(ap.getFeatureRenderer());
+
       showFeatures = true;
     }
 
@@ -1144,12 +1146,20 @@ public class AppletPDBCanvas
     repaint();
   }
 
+
+  public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
+  {
+    return Color.white;
+   // if (!pdbfile.equals(pdbentry.getFile()))
+   //   return null;
+
+    //return new Color(viewer.getAtomArgb(atomIndex));
+  }
+
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
-    colourBySequence(ap.getSequenceRenderer(),
-                     ap.av.getShowSequenceFeatures() ?
-                     ap.getFeatureRenderer() : null);
+    colourBySequence();
     redrawneeded = true;
     repaint();
   }