X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=cd986c0550cecca569f19e213f22cd26e3aacbbc;hb=32d1b850ae63a01a6b3fae305d9577ac16552515;hp=0e4384164ecf18f494510a886eec5121bee80e85;hpb=1719c61073682fdfe66a63408bab498b6ca4234c;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 0e43841..cd986c0 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -285,7 +285,8 @@ public class StructureSelectionManager
   }
 
   /**
-   * Returns the file name for a mapped PDB id (or null if not mapped).
+   * Returns the filename the PDB id is already mapped to if known, or null if
+   * it is not mapped
    * 
    * @param pdbid
    * @return
@@ -294,7 +295,7 @@ public class StructureSelectionManager
   {
     for (StructureMapping sm : mappings)
     {
-      if (sm.getPdbId().equals(pdbid))
+      if (sm.getPdbId().equalsIgnoreCase(pdbid))
       {
         return sm.pdbfile;
       }
@@ -397,8 +398,11 @@ public class StructureSelectionManager
     {
       // FIXME if sourceType is not null, we've lost data here
       sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
-      pdb = new JmolParser(pdbFile, sourceType);
-
+      pdb = new JmolParser(false, pdbFile, sourceType);
+      pdb.addSettings(parseSecStr && processSecondaryStructure,
+              parseSecStr && addTempFacAnnot,
+              parseSecStr && secStructServices);
+      pdb.doParse();
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
               && DataSourceType.FILE == sourceType)
       {
@@ -426,6 +430,7 @@ public class StructureSelectionManager
     {
       isMapUsingSIFTs = false;
       e.printStackTrace();
+      siftsClient = null;
     }
 
     String targetChainId;
@@ -571,6 +576,13 @@ public class StructureSelectionManager
             {
               System.err.println(e.getMessage());
             }
+            catch (Exception e)
+            {
+              System.err
+                      .println(
+                              "Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair");
+              System.err.println(e.getMessage());
+            }
           }
           if (!foundSiftsMappings.isEmpty())
           {
@@ -604,7 +616,10 @@ public class StructureSelectionManager
       }
       if (forStructureView)
       {
-        mappings.addAll(seqToStrucMapping);
+        for (StructureMapping sm : seqToStrucMapping)
+        {
+          addStructureMapping(sm); // not addAll!
+        }
       }
       if (progress != null)
       {
@@ -656,7 +671,10 @@ public class StructureSelectionManager
 
   public void addStructureMapping(StructureMapping sm)
   {
-    mappings.add(sm);
+    if (!mappings.contains(sm))
+    {
+      mappings.add(sm);
+    }
   }
 
   /**