Merge branch 'Release_2_8_2_Branch_i18n' into Release_2_8_2_Branch

[jalview.git] / src / jalview / ext / jmol / PDBFileWithJmol.java

diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java
index 77755f8..847453f 100644 (file)
--- a/src/jalview/ext/jmol/PDBFileWithJmol.java
+++ b/src/jalview/ext/jmol/PDBFileWithJmol.java
@@ -1,23 +1,27 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 jalview.ext.jmol;
 
 import java.io.IOException;
+import java.util.Hashtable;
 import java.util.Map;
 
 import org.jmol.api.JmolStatusListener;
@@ -38,6 +42,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.io.AlignFile;
 import jalview.io.FileParse;
+import jalview.util.MessageManager;
 
 /**
  * Import and process PDB files with Jmol
@@ -53,12 +58,10 @@ public class PDBFileWithJmol extends AlignFile implements
 
   Viewer viewer = null;
 
-  public PDBFileWithJmol(String inFile, String type)
-          throws IOException
+  public PDBFileWithJmol(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
-  
 
   public PDBFileWithJmol(FileParse fp) throws IOException
   {
@@ -93,10 +96,7 @@ public class PDBFileWithJmol extends AlignFile implements
         jmolApp.startViewer(viewer, null);
       } catch (ClassCastException x)
       {
-        throw new Error(
-                "Jmol version "
-                        + JmolViewer.getJmolVersion()
-                        + " is not compatible with this version of Jalview. Report this problem at issues.jalview.org",
+        throw new Error(MessageManager.formatMessage("error.jmol_version_not_compatible_with_jalview_version", new String[]{JmolViewer.getJmolVersion()}),
                 x);
       }
     }
@@ -155,7 +155,7 @@ public class PDBFileWithJmol extends AlignFile implements
                 {
                   char newseq[] = new char[len];
                   System.arraycopy(seq, 0, newseq, 0, len);
-                  Annotation asecstr[] = new Annotation[len];
+                  Annotation asecstr[] = new Annotation[len+firstrnum-1];
                   for (int p = 0; p < len; p++)
                   {
                     if (secstr[p] >= 'A' && secstr[p] <= 'z')
@@ -171,13 +171,24 @@ public class PDBFileWithJmol extends AlignFile implements
                   pdbe.setFile(getDataName());
                   pdbe.setId(getDataName());
                   sq.addPDBId(pdbe);
+                  pdbe.setProperty(new Hashtable());
+                  pdbe.getProperty().put("CHAIN", "" + _lastChainId);
+                  // JAL-1533
+                  // Need to put the number of models for this polymer somewhere for Chimera/others to grab
+                  //                  pdbe.getProperty().put("PDBMODELS", biopoly.)
                   seqs.add(sq);
                   if (!(biopoly.isDna() || biopoly.isRna()))
                   {
                     AlignmentAnnotation ann = new AlignmentAnnotation(
                             "Secondary Structure",
                             "Secondary Structure from PDB File", asecstr);
+                    ann.belowAlignment=true;
+                    ann.visible=true;
+                    ann.autoCalculated=false;
+                    ann.setCalcId(getClass().getName());
                     sq.addAlignmentAnnotation(ann);
+                    ann.adjustForAlignment();
+                    ann.validateRangeAndDisplay();
                     annotations.add(ann);
                   }
                 }