X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2FMCview%2FPDBCanvas.java;h=4fd7a35fb2f323f4451018e80237bcb2e9d4d80a;hb=b28bddf12e2791a019fba9c233d46407deb65976;hp=b3148df0ec499b17a792b6fd7e0c4a484c1ea563;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
old mode 100755
new mode 100644
index b3148df..4fd7a35
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package MCview;
 
@@ -107,7 +110,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
   boolean seqColoursReady = false;
 
-  jalview.gui.FeatureRenderer fr;
+  jalview.renderer.seqfeatures.FeatureRenderer fr;
 
   Color backgroundColour = Color.black;
 
@@ -124,7 +127,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     this.pdbentry = pdbentry;
     this.sequence = seq;
 
-    ssm = StructureSelectionManager.getStructureSelectionManager();
+    ssm = ap.av.getStructureSelectionManager();
 
     try
     {
@@ -173,8 +176,8 @@ public class PDBCanvas extends JPanel implements MouseListener,
       // Now lets compare the sequences to get
       // the start and end points.
       // Align the sequence to the pdb
-      AlignSeq as = new AlignSeq(sequence, ((PDBChain) pdb.chains
-              .elementAt(i)).sequence, "pep");
+      AlignSeq as = new AlignSeq(sequence,
+              ((PDBChain) pdb.chains.elementAt(i)).sequence, "pep");
       as.calcScoreMatrix();
       as.traceAlignment();
       PrintStream ps = new PrintStream(System.out)
@@ -517,7 +520,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
 
     boolean showFeatures = false;
-    if (ap.av.getShowSequenceFeatures())
+    if (ap.av.isShowSequenceFeatures())
     {
       if (fr == null)
       {
@@ -1067,9 +1070,10 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
   // ////////////////////////////////
   // /StructureListener
-  public String getPdbFile()
+  public String[] getPdbFile()
   {
-    return pdbentry.getFile();
+    return new String[]
+    { pdbentry.getFile() };
   }
 
   String lastMessage;
@@ -1156,4 +1160,11 @@ public class PDBCanvas extends JPanel implements MouseListener,
     repaint();
   }
 
+  @Override
+  public void releaseReferences(Object svl)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
 }