X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=1c46ca8db3f2680e0c415fca68ba40022b60136f;hb=c6e8e8ccd10f21698226ae37196cd9680e6804a0;hp=7b103be62fc568b09a7b620afceeec6d7da9ab18;hpb=ce6f02a53c98e51cb96533d40db5f94d1bfea00a;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 7b103be..1c46ca8 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -31,10 +31,11 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JmolParser;
 import jalview.gui.IProgressIndicator;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
@@ -322,12 +323,11 @@ public class StructureSelectionManager
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public StructureFile setMapping(SequenceI[] sequence,
-          String[] targetChains, String pdbFile, String protocol)
+          String[] targetChains, String pdbFile, DataSourceType protocol)
   {
     return setMapping(true, sequence, targetChains, pdbFile, protocol);
   }
 
-
   /**
    * create sequence structure mappings between each sequence and the given
    * pdbFile (retrieved via the given protocol).
@@ -342,14 +342,13 @@ public class StructureSelectionManager
    *          (may be nill, individual elements may be nill)
    * @param pdbFile
    *          - structure data resource
-   * @param protocol
+   * @param sourceType
    *          - how to resolve data from resource
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public StructureFile setMapping(boolean forStructureView,
           SequenceI[] sequenceArray, String[] targetChainIds,
-          String pdbFile,
-          String protocol)
+          String pdbFile, DataSourceType sourceType)
   {
     /*
      * There will be better ways of doing this in the future, for now we'll use
@@ -385,13 +384,16 @@ public class StructureSelectionManager
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
     try
     {
-      pdb = new JmolParser(pdbFile, protocol);
+      pdb = new JmolParser(pdbFile, sourceType);
 
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
-              && AppletFormatAdapter.FILE.equals(protocol))
+              && DataSourceType.FILE == sourceType)
       {
         registerPDBFile(pdb.getId().trim(), pdbFile);
       }
+      // if PDBId is unavailable then skip SIFTS mapping execution path
+      isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable();
+
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -452,7 +454,7 @@ public class StructureSelectionManager
        * Attempt pairwise alignment of the sequence with each chain in the PDB,
        * and remember the highest scoring chain
        */
-      int max = -10;
+      float max = -10;
       AlignSeq maxAlignseq = null;
       String maxChainId = " ";
       PDBChain maxChain = null;
@@ -489,12 +491,12 @@ public class StructureSelectionManager
         continue;
       }
 
-      if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+      if (sourceType == DataSourceType.PASTE)
       {
         pdbFile = "INLINE" + pdb.getId();
       }
 
-      ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
+      List<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
       if (isMapUsingSIFTs && seq.isProtein())
       {
         setProgressBar(null);
@@ -532,14 +534,13 @@ public class StructureSelectionManager
         }
         else
         {
-          ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+          List<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
           for (PDBChain chain : pdb.getChains())
           {
             try
             {
               StructureMapping siftsMapping = getStructureMapping(seq,
-                      pdbFile,
-                      chain.id, pdb, chain, sqmpping, maxAlignseq);
+                      pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
               foundSiftsMappings.add(siftsMapping);
             } catch (SiftsException e)
             {
@@ -614,24 +615,23 @@ public class StructureSelectionManager
           PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
           AlignSeq maxAlignseq) throws SiftsException
   {
-      StructureMapping curChainMapping = siftsClient
-              .getSiftsStructureMapping(seq, pdbFile, targetChainId);
-      try
-      {
+    StructureMapping curChainMapping = siftsClient
+            .getSiftsStructureMapping(seq, pdbFile, targetChainId);
+    try
+    {
       PDBChain chain = pdb.findChain(targetChainId);
       if (chain != null)
       {
         chain.transferResidueAnnotation(curChainMapping, sqmpping);
       }
-      } catch (Exception e)
-      {
-        e.printStackTrace();
-      }
-      return curChainMapping;
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    return curChainMapping;
   }
 
-  private StructureMapping getNWMappings(SequenceI seq,
-          String pdbFile,
+  private StructureMapping getNWMappings(SequenceI seq, String pdbFile,
           String maxChainId, PDBChain maxChain, StructureFile pdb,
           AlignSeq maxAlignseq)
   {
@@ -806,7 +806,7 @@ public class StructureSelectionManager
       return;
     }
 
-    SearchResults results = new SearchResults();
+    SearchResultsI results = new SearchResults();
     for (AtomSpec atom : atoms)
     {
       SequenceI lastseq = null;
@@ -856,7 +856,7 @@ public class StructureSelectionManager
   {
     boolean hasSequenceListeners = handlingVamsasMo
             || !seqmappings.isEmpty();
-    SearchResults results = null;
+    SearchResultsI results = null;
     if (seqPos == -1)
     {
       seqPos = seq.findPosition(indexpos);