X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=2a43244cb6d6e3cff86e622900f930330205aec2;hb=e69f7ec847b9dbbf88350521ccd3fd773c6aeaa8;hp=dc3d0eef52d3591a0bcdeafbf858ef2af27ec4ea;hpb=be762d8d9c71a7aa3121e845c45911c7192b7827;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index dc3d0ee..2a43244 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;
@@ -28,7 +30,6 @@ 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 +47,11 @@ 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 com.stevesoft.pat.Regex;
+
+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 +63,16 @@ public class JmolParser extends StructureFile implements JmolStatusListener
 {
   Viewer viewer = null;
 
-  public JmolParser(String inFile, DataSourceType sourceType)
+  private boolean alphaFoldModel;
+
+  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);
@@ -105,7 +117,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       // }
       // ;
       // instead, we distinguish .cif from non-.cif by filename
-      setStructureFileType(getDataName().toLowerCase().endsWith(".cif")
+      setStructureFileType(getDataName().toLowerCase(Locale.ROOT).endsWith(".cif")
               ? PDBEntry.Type.MMCIF.toString()
               : "PDB");
 
@@ -128,8 +140,8 @@ 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)
@@ -142,17 +154,58 @@ 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)
       {
         setId(safeName(getDataName()));
@@ -162,28 +215,40 @@ 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);
         }
         lastID = tmpatom.resNumIns.trim();
       }
-      xferSettings();
+      if (isParseImmediately())
+      {
+        // configure parsing settings from the static singleton
+        xferSettings();
+      }
 
       makeResidueList();
       makeCaBondList();
@@ -200,7 +265,8 @@ 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);
         }
@@ -214,6 +280,11 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     }
   }
 
+  private boolean isAlphafoldModel()
+  {
+    return alphaFoldModel;
+  }
+
   private List<Atom> convertSignificantAtoms(ModelSet ms)
   {
     List<Atom> significantAtoms = new ArrayList<Atom>();
@@ -340,7 +411,7 @@ 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