fixed various null pointer exceptions that occur when PDB files imported into Jmol...

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 936f139..0fb8428 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -97,12 +97,18 @@ public class StructureSelectionManager
   }
 
   /**
-   * create sequence structure mappings between each sequence and the given pdbFile (retrieved via the given protocol).
+   * create sequence structure mappings between each sequence and the given
+   * pdbFile (retrieved via the given protocol).
    * 
-   * @param sequence  - one or more sequences to be mapped to pdbFile
-   * @param targetChains - optional chain specification for mapping each sequence to pdb (may be nill, individual elements may be nill)  
-   * @param pdbFile - structure data resource
-   * @param protocol - how to resolve data from resource
+   * @param sequence
+   *          - one or more sequences to be mapped to pdbFile
+   * @param targetChains
+   *          - optional chain specification for mapping each sequence to pdb
+   *          (may be nill, individual elements may be nill)
+   * @param pdbFile
+   *          - structure data resource
+   * @param protocol
+   *          - how to resolve data from resource
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public MCview.PDBfile setMapping(SequenceI[] sequence,
@@ -139,35 +145,37 @@ public class StructureSelectionManager
       AlignSeq maxAlignseq = null;
       String maxChainId = " ";
       PDBChain maxChain = null;
-      boolean first=true;
+      boolean first = true;
       for (int i = 0; i < pdb.chains.size(); i++)
       {
-        // TODO: re http://issues.jalview.org/browse/JAL-583 : this patch may need to be revoked 
+        // TODO: re http://issues.jalview.org/browse/JAL-583 : this patch may
+        // need to be revoked
         PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));
-        if (targetChain.length()>0 && !targetChain.equals(chain.id))
+        if (targetChain.length() > 0 && !targetChain.equals(chain.id))
         {
           continue; // don't try to map chains don't match.
         }
         // end of patch for limiting computed mappings
         // TODO: correctly determine sequence type for mixed na/peptide
         // structures
-        AlignSeq as = new AlignSeq(sequence[s], ((PDBChain) pdb.chains
-                .elementAt(i)).sequence, ((PDBChain) pdb.chains
-                .elementAt(i)).isNa ? AlignSeq.DNA : AlignSeq.PEP);
+        AlignSeq as = new AlignSeq(sequence[s],
+                ((PDBChain) pdb.chains.elementAt(i)).sequence,
+                ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA
+                        : AlignSeq.PEP);
         as.calcScoreMatrix();
         as.traceAlignment();
 
         if (first || as.maxscore > max
                 || (as.maxscore == max && chain.id.equals(targetChain)))
         {
-          first=false;
+          first = false;
           maxChain = chain;
           max = as.maxscore;
           maxAlignseq = as;
           maxChainId = chain.id;
         }
       }
-      if (maxChain==null)
+      if (maxChain == null)
       {
         continue;
       }
@@ -233,8 +241,8 @@ public class StructureSelectionManager
         pdbFile = "INLINE" + pdb.id;
 
       mappings[mappings.length - 1] = new StructureMapping(sequence[s],
-              pdbFile, pdb.id, maxChainId, mapping, mappingDetails
-                      .toString());
+              pdbFile, pdb.id, maxChainId, mapping,
+              mappingDetails.toString());
       maxChain.transferResidueAnnotation(mappings[mappings.length - 1]);
     }
     // ///////
@@ -245,7 +253,7 @@ public class StructureSelectionManager
   public void removeStructureViewerListener(Object svl, String[] pdbfiles)
   {
     listeners.removeElement(svl);
-    if (pdbfiles==null)
+    if (pdbfiles == null)
     {
       return;
     }
@@ -271,8 +279,8 @@ public class StructureSelectionManager
 
       }
     }
-    
-    if (pdbs.size()>0  && mappings != null)
+
+    if (pdbs.size() > 0 && mappings != null)
     {
       Vector tmp = new Vector();
       for (int i = 0; i < mappings.length; i++)
@@ -301,23 +309,26 @@ public class StructureSelectionManager
           results = new SearchResults();
         }
         int indexpos;
-        for (int j = 0; j < mappings.length; j++)
+        if (mappings != null)
         {
-          if (mappings[j].pdbfile.equals(pdbfile)
-                  && mappings[j].pdbchain.equals(chain))
+          for (int j = 0; j < mappings.length; j++)
           {
-            indexpos = mappings[j].getSeqPos(pdbResNum);
-            results.addResult(mappings[j].sequence, indexpos, indexpos);
-            // construct highlighted sequence list
-            if (seqmappings != null)
+            if (mappings[j].pdbfile.equals(pdbfile)
+                    && mappings[j].pdbchain.equals(chain))
             {
+              indexpos = mappings[j].getSeqPos(pdbResNum);
+              results.addResult(mappings[j].sequence, indexpos, indexpos);
+              // construct highlighted sequence list
+              if (seqmappings != null)
+              {
 
-              Enumeration e = seqmappings.elements();
-              while (e.hasMoreElements())
+                Enumeration e = seqmappings.elements();
+                while (e.hasMoreElements())
 
-              {
-                ((AlignedCodonFrame) e.nextElement()).markMappedRegion(
-                        mappings[j].sequence, indexpos, results);
+                {
+                  ((AlignedCodonFrame) e.nextElement()).markMappedRegion(
+                          mappings[j].sequence, indexpos, results);
+                }
               }
             }
           }
@@ -361,7 +372,7 @@ public class StructureSelectionManager
       if (listeners.elementAt(i) instanceof StructureListener)
       {
         sl = (StructureListener) listeners.elementAt(i);
-        if (mappings==null)
+        if (mappings == null)
         {
           continue;
         }
@@ -524,14 +535,16 @@ public class StructureSelectionManager
   public StructureMapping[] getMapping(String pdbfile)
   {
     Vector tmp = new Vector();
-    for (int i = 0; i < mappings.length; i++)
+    if (mappings != null)
     {
-      if (mappings[i].pdbfile.equals(pdbfile))
+      for (int i = 0; i < mappings.length; i++)
       {
-        tmp.addElement(mappings[i]);
+        if (mappings[i].pdbfile.equals(pdbfile))
+        {
+          tmp.addElement(mappings[i]);
+        }
       }
     }
-
     StructureMapping[] ret = new StructureMapping[tmp.size()];
     for (int i = 0; i < tmp.size(); i++)
     {