Merge branch 'develop' into bug/JAL-4289_group_boundary_not_drawn_properly_in_fastpai...

[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 b7c83c6..0ca2ba8 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -92,7 +92,6 @@ public class JmolParser extends StructureFile implements JmolStatusListener
   {
     super(fp, doXferSettings);
   }
-
   public JmolParser(FileParse fp) throws IOException
   {
     super(fp);
@@ -315,21 +314,31 @@ 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)
     {
-      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"));
@@ -382,7 +391,7 @@ 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)
     {
@@ -479,7 +488,7 @@ 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')