From 269257481bdc261d6f99cb43dac33c10c3b4e9e1 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 27 Apr 2007 15:32:12 +0000
Subject: [PATCH] Trouble with featureRenderers fixed

---
 src/MCview/AppletPDBCanvas.java |   17 +++++++++++------
 src/MCview/AppletPDBViewer.java |    5 +++--
 2 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index c3ad10e..a61ecb2 100755
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -95,6 +95,9 @@ public class AppletPDBCanvas
 
     try{
       pdb = ssm.setMapping(seq, pdbentry.getFile(), protocol);
+
+      if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+       pdbentry.setFile("INLINE"+pdb.id);
       //if (fr!=null)
       //  fr.featuresAdded();
     }catch(Exception ex)
@@ -109,7 +112,7 @@ public class AppletPDBCanvas
 
     colourBySequence(ap.getSequenceRenderer(),
                      ap.av.getShowSequenceFeatures() ?
-                     ap.getFeatureRenderer() : null);
+                     fr : null);
 
     int max = -10;
     int maxchain = -1;
@@ -242,7 +245,7 @@ public class AppletPDBCanvas
     seqColoursReady = true;
     colourBySequence(ap.getSequenceRenderer(),
                                ap.av.getShowSequenceFeatures() ?
-                               ap.getFeatureRenderer() : null);
+                               fr : null);
     redrawneeded = true;
     repaint();
   }
@@ -497,18 +500,20 @@ 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, FeatureRenderer seqcanvasfr)
   {
     StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
 
     boolean showFeatures = false;
-    if (fr!=null)
+    if (seqcanvasfr!=null)
     {
       if (fr == null)
       {
         fr = new jalview.appletgui.FeatureRenderer(ap.av);
       }
-      fr.transferSettings(fr);
+
+      fr.transferSettings(seqcanvasfr);
+
       showFeatures = true;
     }
 
@@ -1159,7 +1164,7 @@ public class AppletPDBCanvas
     AlignmentPanel ap = (AlignmentPanel) source;
     colourBySequence(ap.getSequenceRenderer(),
                      ap.av.getShowSequenceFeatures() ?
-                     ap.getFeatureRenderer() : null);
+                     fr : null);
     redrawneeded = true;
     repaint();
   }
diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java
index 916e920..b610122 100755
--- a/src/MCview/AppletPDBViewer.java
+++ b/src/MCview/AppletPDBViewer.java
@@ -24,8 +24,7 @@ import java.awt.event.*;
 import jalview.appletgui.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
-import jalview.structure.StructureListener;
-import jalview.structure.*;
+
 
 public class AppletPDBViewer
     extends Frame implements ActionListener, ItemListener
@@ -51,6 +50,8 @@ public class AppletPDBViewer
 
     add(pdbcanvas, BorderLayout.CENTER);
 
+    System.out.println(seq[0].getName()+" ASFA");
+
     StringBuffer title = new StringBuffer(seq[0].getName()
                                           + ":"
                                           + pdbcanvas.pdbentry.getFile());
-- 
1.7.10.2