X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=a9c5f5cb74e1d02cfbf98fc88df835c5bdd46479;hb=3ffda7877bae6500636fcccaf1a9eae8bff2f45c;hp=dc3d0eef52d3591a0bcdeafbf858ef2af27ec4ea;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index dc3d0ee..a9c5f5c 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -28,7 +28,6 @@ import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureImportSettings;
 import jalview.util.Format;
 import jalview.util.MessageManager;
 
@@ -46,9 +45,9 @@ import org.jmol.c.STR;
 import org.jmol.modelset.ModelSet;
 import org.jmol.viewer.Viewer;
 
-import MCview.Atom;
-import MCview.PDBChain;
-import MCview.Residue;
+import mc_view.Atom;
+import mc_view.PDBChain;
+import mc_view.Residue;
 
 /**
  * Import and process files with Jmol for file like PDB, mmCIF
@@ -60,7 +59,14 @@ public class JmolParser extends StructureFile implements JmolStatusListener
 {
   Viewer viewer = null;
 
-  public JmolParser(String inFile, DataSourceType sourceType)
+  public JmolParser(boolean immediate, Object inFile,
+          DataSourceType sourceType) throws IOException
+  {
+    // BH 2018 File or String for filename
+    super(immediate, inFile, sourceType);
+  }
+
+  public JmolParser(Object inFile, DataSourceType sourceType)
           throws IOException
   {
     super(inFile, sourceType);
@@ -128,8 +134,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
          * params -o (output to sysout) -n (nodisplay) -x (exit when finished)
          * see http://wiki.jmol.org/index.php/Jmol_Application
          */
-        viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
-                null, "-x -o -n", this);
+        
+        viewer = JalviewJmolBinding.getJmolData(this);
         // ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
         viewer.setBooleanProperty("defaultStructureDSSP", true);
       } catch (ClassCastException x)
@@ -166,16 +172,16 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       List<Atom> significantAtoms = convertSignificantAtoms(ms);
       for (Atom tmpatom : significantAtoms)
       {
-        try
+        if (tmpatom.resNumIns.trim().equals(lastID))
+        {
+          // phosphorylated protein - seen both CA and P..
+          continue;
+        }
+        tmpchain = findChain(tmpatom.chain);
+        if (tmpchain != null)
         {
-          tmpchain = findChain(tmpatom.chain);
-          if (tmpatom.resNumIns.trim().equals(lastID))
-          {
-            // phosphorylated protein - seen both CA and P..
-            continue;
-          }
           tmpchain.atoms.addElement(tmpatom);
-        } catch (Exception e)
+        } else
         {
           tmpchain = new PDBChain(getId(), tmpatom.chain);
           getChains().add(tmpchain);
@@ -183,7 +189,11 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         }
         lastID = tmpatom.resNumIns.trim();
       }
-      xferSettings();
+      if (isParseImmediately())
+      {
+        // configure parsing settings from the static singleton
+        xferSettings();
+      }
 
       makeResidueList();
       makeCaBondList();
@@ -200,7 +210,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           prot.add(chainseq);
         }
 
-        if (StructureImportSettings.isProcessSecondaryStructure())
+        // look at local setting for adding secondary tructure
+        if (predictSecondaryStructure)
         {
           createAnnotation(chainseq, chain, ms.at);
         }