JAL-1683 replace year/version strings with tokens in source

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

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
old mode 100755 (executable)
new mode 100644 (file)
index 6be8dd5..69a958e
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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;
 
@@ -29,6 +32,7 @@ import jalview.datamodel.*;
 
 import jalview.appletgui.*;
 import jalview.structure.*;
+import jalview.util.MessageManager;
 
 public class AppletPDBCanvas extends Panel implements MouseListener,
         MouseMotionListener, StructureListener
@@ -132,7 +136,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     this.pdbentry = pdbentry;
     this.sequence = seq;
 
-    ssm = StructureSelectionManager.getStructureSelectionManager();
+    ssm = StructureSelectionManager
+            .getStructureSelectionManager(ap.av.applet);
 
     try
     {
@@ -176,8 +181,11 @@ public class AppletPDBCanvas extends Panel 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");
+      // TODO: DNa/Pep switch
+      AlignSeq as = new AlignSeq(sequence,
+              ((PDBChain) pdb.chains.elementAt(i)).sequence,
+              ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA
+                      : AlignSeq.PEP);
       as.calcScoreMatrix();
       as.traceAlignment();
       PrintStream ps = new PrintStream(System.out)
@@ -464,7 +472,9 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
       g.fillRect(0, 0, getSize().width, getSize().height);
       g.setColor(Color.black);
       g.setFont(new Font("Verdana", Font.BOLD, 14));
-      g.drawString("Error loading PDB data!!", 50, getSize().height / 2);
+      g.drawString(
+              MessageManager.getString("label.error_loading_pdb_data"), 50,
+              getSize().height / 2);
       return;
     }
 
@@ -472,7 +482,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     {
       g.setColor(Color.black);
       g.setFont(new Font("Verdana", Font.BOLD, 14));
-      g.drawString("Fetching PDB data...", 50, getSize().height / 2);
+      g.drawString(MessageManager.getString("label.fetching_pdb_data"), 50,
+              getSize().height / 2);
       return;
     }
 
@@ -539,7 +550,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
 
     boolean showFeatures = false;
-    if (ap.av.getShowSequenceFeatures())
+    if (ap.av.isShowSequenceFeatures())
     {
       if (fr == null)
       {
@@ -1099,9 +1110,10 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
 
   // ////////////////////////////////
   // /StructureListener
-  public String getPdbFile()
+  public String[] getPdbFile()
   {
-    return pdbentry.getFile();
+    return new String[]
+    { pdbentry.getFile() };
   }
 
   String lastMessage;
@@ -1188,4 +1200,11 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     repaint();
   }
 
+  @Override
+  public void releaseReferences(Object svl)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
 }