X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=ab6bbcc1a54b9e6e36afb04a18fca2e12da04caf;hb=7190c3c673890ea5d282b36ac89a7b15be522206;hp=e94da73a687c655ee81a5b4a645fb9c21c8ca321;hpb=b879c4a2d32d3489e63ac06917e81637e6bb4068;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index e94da73..ab6bbcc 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -20,6 +20,8 @@
  */
 package jalview.ext.jmol;
 
+import java.util.Locale;
+
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
@@ -45,6 +47,8 @@ import org.jmol.c.STR;
 import org.jmol.modelset.ModelSet;
 import org.jmol.viewer.Viewer;
 
+import com.stevesoft.pat.Regex;
+
 import mc_view.Atom;
 import mc_view.PDBChain;
 import mc_view.Residue;
@@ -59,6 +63,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
 {
   Viewer viewer = null;
 
+  private boolean alphaFoldModel;
+
   public JmolParser(boolean immediate, Object inFile,
           DataSourceType sourceType) throws IOException
   {
@@ -111,9 +117,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       // }
       // ;
       // instead, we distinguish .cif from non-.cif by filename
-      setStructureFileType(getDataName().toLowerCase().endsWith(".cif")
-              ? PDBEntry.Type.MMCIF.toString()
-              : "PDB");
+      setStructureFileType(
+              getDataName().toLowerCase(Locale.ROOT).endsWith(".cif")
+                      ? PDBEntry.Type.MMCIF.toString()
+                      : "PDB");
 
       transformJmolModelToJalview(jmolModel.ms);
     }
@@ -134,9 +141,8 @@ 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)
@@ -150,15 +156,60 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     return viewer;
   }
 
+  public static Regex getNewAlphafoldValidator()
+  {
+    Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
+    validator.setIgnoreCase(true);
+    return validator;
+  }
+
+  PDBEntry.Type jmolFiletype = null;
+
+  /**
+   * resolve a jmol filetype string and update the jmolFiletype field
+   * accordingly
+   * 
+   * @param jmolIdentifiedFileType
+   * @return true if filetype was identified as MMCIF, PDB
+   */
+  public boolean updateFileType(String jmolIdentifiedFileType)
+  {
+    if (jmolIdentifiedFileType == null
+            || jmolIdentifiedFileType.trim().equals(""))
+    {
+      return false;
+    }
+    if ("mmcif".equalsIgnoreCase(jmolIdentifiedFileType))
+    {
+      jmolFiletype = PDBEntry.Type.MMCIF;
+      return true;
+    }
+    if ("pdb".equalsIgnoreCase(jmolIdentifiedFileType))
+    {
+      jmolFiletype = PDBEntry.Type.PDB;
+      return true;
+    }
+    return false;
+  }
+
   public void transformJmolModelToJalview(ModelSet ms) throws IOException
   {
     try
     {
+      Regex alphaFold = getNewAlphafoldValidator();
       String lastID = "";
       List<SequenceI> rna = new ArrayList<SequenceI>();
       List<SequenceI> prot = new ArrayList<SequenceI>();
       PDBChain tmpchain;
       String pdbId = (String) ms.getInfo(0, "title");
+      boolean isMMCIF = false;
+      String jmolFileType_String = (String) ms.getInfo(0, "fileType");
+      if (updateFileType(jmolFileType_String))
+      {
+        setStructureFileType(jmolFiletype.toString());
+      }
+
+      isMMCIF = PDBEntry.Type.MMCIF.equals(jmolFiletype);
 
       if (pdbId == null)
       {
@@ -169,22 +220,31 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       {
         setId(pdbId);
         setPDBIdAvailable(true);
+        alphaFoldModel = alphaFold.search(pdbId) && isMMCIF;
+
       }
       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);
+          String tempFString = null;
+          if (isAlphafoldModel())
+          {
+            tempFString = "Alphafold Reliability";
+          }
+
+          tmpchain = new PDBChain(getId(), tmpatom.chain, tempFString);
           getChains().add(tmpchain);
           tmpchain.atoms.addElement(tmpatom);
         }
@@ -226,6 +286,11 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     }
   }
 
+  private boolean isAlphafoldModel()
+  {
+    return alphaFoldModel;
+  }
+
   private List<Atom> convertSignificantAtoms(ModelSet ms)
   {
     List<Atom> significantAtoms = new ArrayList<Atom>();
@@ -352,7 +417,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
 
   /**
    * Helper method that adds an AlignmentAnnotation for secondary structure to
-   * the sequence, provided at least one secondary structure prediction has been
+   * the sequence, provided at least one secondary structure assignment has been
    * made
    * 
    * @param modelTitle