X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=92c762bb861bb38ca1d5e712587aa278eb4e8ce9;hb=eb3e681d6e82ccdd5d312d1981dfb306e7f479f0;hp=a7e30bf57259c3db28eee18ea8f73bd9ba338fcc;hpb=2260a3ddeaf260a591ba32ad6b3f162583a6d3c6;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index a7e30bf..92c762b 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -20,6 +20,7 @@
  */
 package jalview.ext.jmol;
 
+import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -37,6 +38,8 @@ import org.jmol.viewer.Viewer;
 
 import com.stevesoft.pat.Regex;
 
+import jalview.bin.Console;
+import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
@@ -47,8 +50,10 @@ 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;
+import jalview.ws.dbsources.EBIAlfaFold;
 import mc_view.Atom;
 import mc_view.PDBChain;
 import mc_view.Residue;
@@ -63,19 +68,29 @@ public class JmolParser extends StructureFile implements JmolStatusListener
 {
   Viewer viewer = null;
 
-  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);
+    this(inFile, sourceType, null);
+  }
+
+  public JmolParser(Object inFile, DataSourceType sourceType,
+          StructureImportSettings.TFType tempfacType) throws IOException
+  {
+    super(inFile, sourceType, tempfacType);
+  }
+
+  public JmolParser(FileParse fp, boolean doXferSettings) throws IOException
+  {
+    super(fp, doXferSettings);
   }
 
   public JmolParser(FileParse fp) throws IOException
@@ -98,6 +113,12 @@ public class JmolParser extends StructureFile implements JmolStatusListener
   @Override
   public void parse() throws IOException
   {
+    parse(true);
+  }
+
+  @Override
+  public void parse(boolean doXferSettings) throws IOException
+  {
     setChains(new Vector<PDBChain>());
     Viewer jmolModel = getJmolData();
     jmolModel.openReader(getDataName(), getDataName(), getReader());
@@ -122,7 +143,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
                       ? PDBEntry.Type.MMCIF.toString()
                       : "PDB");
 
-      transformJmolModelToJalview(jmolModel.ms);
+      transformJmolModelToJalview(jmolModel.ms, doXferSettings);
     }
   }
 
@@ -192,7 +213,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     return false;
   }
 
-  public void transformJmolModelToJalview(ModelSet ms) throws IOException
+  public void transformJmolModelToJalview(ModelSet ms,
+          boolean localDoXferSettings) throws IOException
   {
     try
     {
@@ -220,8 +242,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       {
         setId(pdbId);
         setPDBIdAvailable(true);
-        alphaFoldModel = alphaFold.search(pdbId) && isMMCIF;
-
+        setAlphafoldModel(alphaFold.search(pdbId) && isMMCIF);
       }
       List<Atom> significantAtoms = convertSignificantAtoms(ms);
       for (Atom tmpatom : significantAtoms)
@@ -239,8 +260,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         else
         {
           AnnotationRowBuilder builder = null;
-          String tempFString = null;
-          if (isAlphafoldModel())
+          if (isAlphafoldModel()
+                  || getTemperatureFactorType() == StructureImportSettings.TFType.PLDDT)
           {
             builder = new AlphaFoldAnnotationRowBuilder();
           }
@@ -251,7 +272,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         }
         lastID = tmpatom.resNumIns.trim();
       }
-      if (isParseImmediately())
+      if (isParseImmediately() && localDoXferSettings)
       {
         // configure parsing settings from the static singleton
         xferSettings();
@@ -278,20 +299,53 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           createAnnotation(chainseq, chain, ms.at);
         }
       }
+      // if Alphafold, fetch the PAE matrix if doesn't already have one
+      if (isAlphafoldModel() && !hasPAEMatrix())
+      {
+        try
+        {
+          Console.info("Retrieving PAE for " + pdbId);
+          File paeFile = EBIAlfaFold.fetchAlphaFoldPAE(pdbId, null);
+          this.setPAEMatrix(paeFile.getAbsolutePath());
+        } catch (Throwable t)
+        {
+          Console.error("Couldn't get the pAE for " + pdbId, t);
+        }
+      }
+      // add a PAEMatrix if set (either by above or otherwise)
+      if (hasPAEMatrix())
+      {
+        try
+        {
+          Alignment al = new Alignment(prot.toArray(new SequenceI[0]));
+          EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0,
+                  null, false, false, null);
+
+          if (al.getAlignmentAnnotation() != null)
+          {
+            for (AlignmentAnnotation alann : al.getAlignmentAnnotation())
+            {
+              annotations.add(alann);
+            }
+          }
+        } catch (Throwable ff)
+        {
+          Console.error("Couldn't import PAE Matrix from " + getPAEMatrix(),
+                  ff);
+          warningMessage += "Couldn't import PAE Matrix"
+                  + getNewlineString() + ff.getLocalizedMessage()
+                  + getNewlineString();
+        }
+      }
     } catch (OutOfMemoryError er)
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
       throw new IOException(MessageManager
               .getString("exception.outofmemory_loading_mmcif_file"));
     }
   }
 
-  private boolean isAlphafoldModel()
-  {
-    return alphaFoldModel;
-  }
-
   private List<Atom> convertSignificantAtoms(ModelSet ms)
   {
     List<Atom> significantAtoms = new ArrayList<Atom>();
@@ -338,7 +392,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           org.jmol.modelset.Atom prevAtom,
           HashMap<String, org.jmol.modelset.Atom> chainTerMap)
   {
-    // System.out.println("Atom: " + curAtom.getAtomNumber()
+    // jalview.bin.Console.outPrintln("Atom: " + curAtom.getAtomNumber()
     // + " Last atom index " + curAtom.group.lastAtomIndex);
     if (chainTerMap == null || prevAtom == null)
     {
@@ -435,15 +489,15 @@ public class JmolParser extends StructureFile implements JmolStatusListener
   {
     int length = sq.getLength();
     boolean ssFound = false;
-    Annotation asecstr[] = new Annotation[length + firstResNum - 1];
+    Annotation asecstr[] = new Annotation[length
+            + (firstResNum - sq.getStart())];
     for (int p = 0; p < length; p++)
     {
       if (secstr[p] >= 'A' && secstr[p] <= 'z')
       {
         try
         {
-          asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
-                  secstrcode[p], Float.NaN);
+          asecstr[p] = new Annotation(null, null, secstrcode[p], Float.NaN);
           ssFound = true;
         } catch (Exception e)
         {