X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=b7c83c686b55ce2446b212369dbd2bb542428c70;hb=51909770452369f94b4a0070482ab0acdd96fada;hp=969d195a9e68e8c6bdfc17c128b88981a15b74a5;hpb=7e3a6674abdd31bf48e7e249a74eff50fd2ce589;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index 969d195..b7c83c6 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -88,6 +88,11 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     super(inFile, sourceType, tempfacType);
   }
 
+  public JmolParser(FileParse fp, boolean doXferSettings) throws IOException
+  {
+    super(fp, doXferSettings);
+  }
+
   public JmolParser(FileParse fp) throws IOException
   {
     super(fp);
@@ -108,6 +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());
@@ -132,7 +143,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
                       ? PDBEntry.Type.MMCIF.toString()
                       : "PDB");
 
-      transformJmolModelToJalview(jmolModel.ms);
+      transformJmolModelToJalview(jmolModel.ms, doXferSettings);
     }
   }
 
@@ -202,7 +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
     {
@@ -230,9 +242,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       {
         setId(pdbId);
         setPDBIdAvailable(true);
-        Console.debug("##### DATASOURCETYPE=" + getDataSourceType());
-        setAlphafoldModel(alphaFold.search(pdbId) && isMMCIF
-                && getDataSourceType() == DataSourceType.URL);
+        setAlphafoldModel(alphaFold.search(pdbId) && isMMCIF);
       }
       List<Atom> significantAtoms = convertSignificantAtoms(ms);
       for (Atom tmpatom : significantAtoms)
@@ -262,7 +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();
@@ -294,7 +304,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       {
         try
         {
-          Console.info("retrieving pAE for " + pdbId);
+          Console.info("Retrieving PAE for " + pdbId);
           File paeFile = EBIAlfaFold.fetchAlphaFoldPAE(pdbId, null);
           this.setPAEMatrix(paeFile.getAbsolutePath());
         } catch (Throwable t)
@@ -303,31 +313,16 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         }
       }
       // add a PAEMatrix if set (either by above or otherwise)
-      Console.debug("##### hasPAEMatrix()=" + hasPAEMatrix());
-      Console.debug("##### isAlphafoldModel()=" + isAlphafoldModel());
-      Console.debug("##### getPAEMatrix()=" + getPAEMatrix());
       if (hasPAEMatrix())
       {
         Alignment al = new Alignment(prot.toArray(new SequenceI[0]));
-        if (isAlphafoldModel())
-        {
-          EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0,
-                  null, false, false);
-        }
-        else
-        {
-          EBIAlfaFold.addPAEToStructure(null, this.getInFile(),
-                  new File(this.getPAEMatrix()));
-        }
+        EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0,
+                null, false, false, null);
 
-        Console.debug("##### al.getAlignmentAnnotation()="
-                + al.getAlignmentAnnotation());
         if (al.getAlignmentAnnotation() != null)
         {
           for (AlignmentAnnotation alann : al.getAlignmentAnnotation())
           {
-            Console.debug("##### Adding to alann" + alann.annotationId + "("
-                    + alann.getCalcId() + ")");
             annotations.add(alann);
           }
         }