JAL-1551 format and tidy

[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 009b9e8..159955a 100644 (file)
--- a/src/jalview/ext/jmol/PDBFileWithJmol.java
+++ b/src/jalview/ext/jmol/PDBFileWithJmol.java
@@ -20,6 +20,15 @@
  */
 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.util.MessageManager;
+
 import java.io.IOException;
 import java.util.Hashtable;
 import java.util.Map;
@@ -35,14 +44,6 @@ 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
  * 
@@ -95,10 +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);
       }
     }
@@ -175,6 +173,9 @@ public class PDBFileWithJmol extends AlignFile implements
                   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()))
                   {
@@ -306,11 +307,16 @@ 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);