JAL-2074 corrected classpathentry for Groovy 2.4.6

[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 c9243ed..0cbd620 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -64,14 +64,12 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           throws IOException
   {
     super(inFile, type);
-    // addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
   }
 
   public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
           boolean externalSecStr, FileParse fp) throws IOException
   {
     super(fp);
-    // addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
   }
 
   public JmolParser()
@@ -167,6 +165,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         }
         lastID = tmpatom.resNumIns.trim();
       }
+      xferSettings();
+
       makeResidueList();
       makeCaBondList();
 
@@ -220,7 +220,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
                 .getIndex()] : Float.valueOf(atom.getOccupancy100());
         curAtom.resNumIns = "" + curAtom.resNumber + curAtom.insCode;
-        // curAtom.tfactor = atom.group.;
+        curAtom.tfactor = atom.getBfactor100() / 100f;
         curAtom.type = 0;
         significantAtoms.add(curAtom);
       }
@@ -277,9 +277,15 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     {
       if (secstr[p] >= 'A' && secstr[p] <= 'z')
       {
+        try
+        {
         asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
                 secstrcode[p], Float.NaN);
         ssFound = true;
+        } catch (Exception e)
+        {
+          // e.printStackTrace();
+        }
       }
     }
 
@@ -560,4 +566,14 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     this.predictSecondaryStructure = predictSecondaryStructure;
   }
 
+  public boolean isVisibleChainAnnotation()
+  {
+    return visibleChainAnnotation;
+  }
+
+  public void setVisibleChainAnnotation(boolean visibleChainAnnotation)
+  {
+    this.visibleChainAnnotation = visibleChainAnnotation;
+  }
+
 }