X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=6912836683b796e6e3b5b38ff63658b82fead7a9;hb=457deb581a5614633f1c4dd15fee5eeaea5c9758;hp=c27289c468bdc1a396b6b78e9cd92cf410c38b3d;hpb=9e9c7a6358edca8b749b6f760f7faabe364feadf;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index c27289c..6912836 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -31,7 +31,9 @@ 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.StructureFile;
@@ -326,7 +328,6 @@ public class StructureSelectionManager
     return setMapping(true, sequence, targetChains, pdbFile, protocol);
   }
 
-
   /**
    * create sequence structure mappings between each sequence and the given
    * pdbFile (retrieved via the given protocol).
@@ -347,8 +348,7 @@ public class StructureSelectionManager
    */
   synchronized public StructureFile setMapping(boolean forStructureView,
           SequenceI[] sequenceArray, String[] targetChainIds,
-          String pdbFile,
-          String protocol)
+          String pdbFile, String protocol)
   {
     /*
      * There will be better ways of doing this in the future, for now we'll use
@@ -384,27 +384,16 @@ public class StructureSelectionManager
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
     try
     {
-
-      boolean isParseWithJMOL = StructureImportSettings
-              .getDefaultPDBFileParser().equalsIgnoreCase(
-                      StructureImportSettings.StructureParser.JMOL_PARSER
-                              .toString());
-      if (isParseWithJMOL || (pdbFile != null && isCIFFile(pdbFile)))
-      {
-        pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
-                secStructServices, pdbFile, protocol);
-      }
-      else
-      {
-        pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
-                pdbFile, protocol);
-      }
+      pdb = new JmolParser(pdbFile, protocol);
 
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
               && AppletFormatAdapter.FILE.equals(protocol))
       {
         registerPDBFile(pdb.getId().trim(), pdbFile);
       }
+      // if PDBId is unavailable then skip SIFTS mapping execution path
+      isMapUsingSIFTs = pdb.isPPDBIdAvailable();
+
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -551,8 +540,7 @@ public class StructureSelectionManager
             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)
             {
@@ -627,24 +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)
   {
@@ -819,7 +806,7 @@ public class StructureSelectionManager
       return;
     }
 
-    SearchResults results = new SearchResults();
+    SearchResultsI results = new SearchResults();
     for (AtomSpec atom : atoms)
     {
       SequenceI lastseq = null;
@@ -869,7 +856,7 @@ public class StructureSelectionManager
   {
     boolean hasSequenceListeners = handlingVamsasMo
             || !seqmappings.isEmpty();
-    SearchResults results = null;
+    SearchResultsI results = null;
     if (seqPos == -1)
     {
       seqPos = seq.findPosition(indexpos);