X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FPDBFileWithJmol.java;h=3df8957d9c01a47f566ce4f72b2abca926ec3853;hb=93d63f3c608771bb48b5ac18f761194a1ea28554;hp=5702558cd9a4c63fb7373064d64360519c9b5cf8;hpb=d49248578538f9d06141ac17c55ab9b93a5e48d4;p=jalview.git

diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java
index 5702558..3df8957 100644
--- a/src/jalview/ext/jmol/PDBFileWithJmol.java
+++ b/src/jalview/ext/jmol/PDBFileWithJmol.java
@@ -1,22 +1,35 @@
 /*
- * 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 ($$Version-Rel$$)
+ * 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 jalview.ext.jmol;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.AlignFile;
+import jalview.io.FileParse;
+import jalview.schemes.ResidueProperties;
+import jalview.util.MessageManager;
+
 import java.io.IOException;
 import java.util.Hashtable;
 import java.util.Map;
@@ -32,14 +45,6 @@ import org.jmol.modelsetbio.BioPolymer;
 import org.jmol.viewer.Viewer;
 import org.openscience.jmol.app.JmolApp;
 
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-import jalview.io.AlignFile;
-import jalview.io.FileParse;
-
 /**
  * Import and process PDB files with Jmol
  * 
@@ -54,12 +59,10 @@ 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
   {
@@ -94,10 +97,7 @@ 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);
       }
     }
@@ -154,11 +154,17 @@ public class PDBFileWithJmol extends AlignFile implements
               {
                 if (len > 0)
                 {
+                  boolean isNa = (biopoly.isDna() || biopoly.isRna());
+                  // normalise sequence from Jmol to jalview 
+                  int[] cinds = isNa ? ResidueProperties.nucleotideIndex : ResidueProperties.aaIndex;
+                  int nonGap = isNa ? ResidueProperties.maxNucleotideIndex
+                          : ResidueProperties.maxProteinIndex;
+                  char ngc = 'X';
                   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++)
                   {
+                    newseq[p] = cinds[seq[p]] == nonGap ? ngc : seq[p];
                     if (secstr[p] >= 'A' && secstr[p] <= 'z')
                     {
                       asecstr[p] = new Annotation("" + secstr[p], null,
@@ -171,17 +177,32 @@ public class PDBFileWithJmol extends AlignFile implements
                   PDBEntry pdbe = new PDBEntry();
                   pdbe.setFile(getDataName());
                   pdbe.setId(getDataName());
-                  sq.addPDBId(pdbe);
                   pdbe.setProperty(new Hashtable());
-                  pdbe.getProperty().put("CHAIN",""+_lastChainId);
+                  // pdbe.getProperty().put("CHAIN", "" + _lastChainId);
+                  pdbe.setChainCode(String.valueOf(_lastChainId));
+                  sq.addPDBId(pdbe);
+                  // 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()))
+                  if (!isNa)
                   {
+                    String mt = model.getModelTitle() == null ? getDataName()
+                            : model.getModelTitle();
+                    if (_lastChainId >= ' ')
+                    {
+                      mt += _lastChainId;
+                    }
                     AlignmentAnnotation ann = new AlignmentAnnotation(
                             "Secondary Structure",
-                            "Secondary Structure from PDB File", asecstr);
+                            "Secondary Structure for " + mt, asecstr);
+                    ann.belowAlignment=true;
+                    ann.visible=true;
+                    ann.autoCalculated=false;
                     ann.setCalcId(getClass().getName());
                     sq.addAlignmentAnnotation(ann);
+                    ann.adjustForAlignment();
+                    ann.validateRangeAndDisplay();
                     annotations.add(ann);
                   }
                 }
@@ -300,11 +321,16 @@ public class PDBFileWithJmol extends AlignFile implements
     case MEASURE:
       String mystatus = (String) data[3];
       if (mystatus.indexOf("Picked") >= 0
-              || mystatus.indexOf("Sequence") >= 0) // picking mode
+              || mystatus.indexOf("Sequence") >= 0)
+      {
+        // Picking mode
         sendConsoleMessage(strInfo);
+      }
       else if (mystatus.indexOf("Completed") >= 0)
+      {
         sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2,
                 strInfo.length() - 1));
+      }
       break;
     case MESSAGE:
       sendConsoleMessage(data == null ? null : strInfo);