Merge branch 'develop' into features/JAL-4134_use_annotation_row_for_colours_and_groups

[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 a276fb6..c64dac1 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -88,6 +88,10 @@ 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 +112,12 @@ 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 +142,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
                       ? PDBEntry.Type.MMCIF.toString()
                       : "PDB");
 
-      transformJmolModelToJalview(jmolModel.ms);
+      transformJmolModelToJalview(jmolModel.ms, doXferSettings);
     }
   }
 
@@ -202,7 +212,8 @@ 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
     {
@@ -260,7 +271,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         }
         lastID = tmpatom.resNumIns.trim();
       }
-      if (isParseImmediately())
+      if (isParseImmediately() && localDoXferSettings)
       {
         // configure parsing settings from the static singleton
         xferSettings();
@@ -292,7 +303,7 @@ 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)
@@ -303,16 +314,26 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       // add a PAEMatrix if set (either by above or otherwise)
       if (hasPAEMatrix())
       {
-        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)
+        try
         {
-          for (AlignmentAnnotation alann : al.getAlignmentAnnotation())
+          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)
           {
-            annotations.add(alann);
+            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)