Merge branch 'develop' into features/filetypeEnum

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

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index ba57329..858aac7 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -22,10 +22,9 @@ package jalview.ext.jmol;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
-import jalview.io.FileParse;
 import jalview.io.DataSourceType;
+import jalview.io.FileParse;
 import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureImportSettings;
@@ -33,6 +32,7 @@ import jalview.util.MessageManager;
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Vector;
@@ -88,15 +88,6 @@ public class JmolParser extends StructureFile implements JmolStatusListener
   @Override
   public void parse() throws IOException
   {
-    String dataName = getDataName();
-    if (dataName.endsWith(".cif"))
-    {
-      setDbRefType(DBRefSource.MMCIF);
-    }
-    else
-    {
-      setDbRefType(DBRefSource.PDB);
-    }
     setChains(new Vector<PDBChain>());
     Viewer jmolModel = getJmolData();
     jmolModel.openReader(getDataName(), getDataName(), getReader());
@@ -173,7 +164,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
 
       if (getId() == null)
       {
-        setId(inFile.getName());
+        setId(safeName(getDataName()));
       }
       for (PDBChain chain : getChains())
       {
@@ -187,7 +178,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           prot.add(chainseq);
         }
 
-        if (StructureImportSettings.isPredictSecondaryStructure())
+        if (StructureImportSettings.isProcessSecondaryStructure())
         {
           createAnnotation(chainseq, chain, ms.at);
         }
@@ -205,36 +196,91 @@ public class JmolParser extends StructureFile implements JmolStatusListener
   private List<Atom> convertSignificantAtoms(ModelSet ms)
   {
     List<Atom> significantAtoms = new ArrayList<Atom>();
+    HashMap<String, org.jmol.modelset.Atom> chainTerMap = new HashMap<String, org.jmol.modelset.Atom>();
+    org.jmol.modelset.Atom prevAtom = null;
     for (org.jmol.modelset.Atom atom : ms.at)
     {
-      // System.out.println("Seq Id : " + atom.getSeqID());
-      // System.out.println("To String : " + atom.toString());
-      if (!StructureImportSettings.isProcessHETATMs() && atom.isHetero())
-      {
-        continue;
-      }
       if (atom.getAtomName().equalsIgnoreCase("CA")
               || atom.getAtomName().equalsIgnoreCase("P"))
       {
+        if (!atomValidated(atom, prevAtom, chainTerMap))
+        {
+          continue;
+        }
         Atom curAtom = new Atom(atom.x, atom.y, atom.z);
         curAtom.atomIndex = atom.getIndex();
         curAtom.chain = atom.getChainIDStr();
-        curAtom.insCode = atom.group.getInsertionCode();
+        curAtom.insCode = atom.group.getInsertionCode() == '\000' ? ' '
+                : atom.group.getInsertionCode();
         curAtom.name = atom.getAtomName();
         curAtom.number = atom.getAtomNumber();
         curAtom.resName = atom.getGroup3(true);
         curAtom.resNumber = atom.getResno();
         curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
                 .getIndex()] : Float.valueOf(atom.getOccupancy100());
-        curAtom.resNumIns = "" + curAtom.resNumber + curAtom.insCode;
+        curAtom.resNumIns = ("" + curAtom.resNumber + curAtom.insCode)
+                .trim();
         curAtom.tfactor = atom.getBfactor100() / 100f;
         curAtom.type = 0;
-        significantAtoms.add(curAtom);
+        // significantAtoms.add(curAtom);
+        // ignore atoms from subsequent models
+        if (!significantAtoms.contains(curAtom))
+        {
+          significantAtoms.add(curAtom);
+        }
+        prevAtom = atom;
       }
     }
     return significantAtoms;
   }
 
+  private boolean atomValidated(org.jmol.modelset.Atom curAtom,
+          org.jmol.modelset.Atom prevAtom,
+          HashMap<String, org.jmol.modelset.Atom> chainTerMap)
+  {
+    // System.out.println("Atom: " + curAtom.getAtomNumber()
+    // + "   Last atom index " + curAtom.group.lastAtomIndex);
+    if (chainTerMap == null || prevAtom == null)
+    {
+      return true;
+    }
+    String curAtomChId = curAtom.getChainIDStr();
+    String prevAtomChId = prevAtom.getChainIDStr();
+    // new chain encoutered
+    if (!prevAtomChId.equals(curAtomChId))
+    {
+      // On chain switch add previous chain termination to xTerMap if not exists
+      if (!chainTerMap.containsKey(prevAtomChId))
+      {
+        chainTerMap.put(prevAtomChId, prevAtom);
+      }
+      // if current atom belongs to an already terminated chain and the resNum
+      // diff < 5 then mark as valid and update termination Atom
+      if (chainTerMap.containsKey(curAtomChId))
+      {
+        if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
+        {
+          chainTerMap.put(curAtomChId, curAtom);
+          return true;
+        }
+        return false;
+      }
+    }
+    // atom with previously terminated chain encountered
+    else if (chainTerMap.containsKey(curAtomChId))
+    {
+      if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
+      {
+        chainTerMap.put(curAtomChId, curAtom);
+        return true;
+      }
+      return false;
+    }
+    // HETATM with resNum jump > 2
+    return !(curAtom.isHetero() && ((curAtom.getResno() - prevAtom
+            .getResno()) > 2));
+  }
+
   private void createAnnotation(SequenceI sequence, PDBChain chain,
           org.jmol.modelset.Atom[] jmolAtoms)
   {
@@ -398,7 +444,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
    * Not implemented - returns null
    */
   @Override
-  public String print()
+  public String print(SequenceI[] seqs, boolean jvSuffix)
   {
     return null;
   }