X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=53644e94fb3e0150e73fe0528be6dfd3ca7d11f3;hb=c38d37887ae51d63942ac4321f6769308188ed6b;hp=ad259fd88d0e957830b429597a4c1209cad3f5f2;hpb=083fb85bfa1be57c30db0ac1cb9f5f8ad08d1060;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index ad259fd..53644e9 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -20,8 +20,20 @@
  */
 package jalview.structure;
 
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.IdentityHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
+
 import jalview.analysis.AlignSeq;
 import jalview.api.StructureSelectionManagerProvider;
+import jalview.bin.Cache;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
 import jalview.commands.OrderCommand;
@@ -41,24 +53,13 @@ import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.ws.sifts.SiftsClient;
 import jalview.ws.sifts.SiftsException;
 import jalview.ws.sifts.SiftsSettings;
-
-import java.io.PrintStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.IdentityHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Vector;
-
-import MCview.Atom;
-import MCview.PDBChain;
-import MCview.PDBfile;
+import mc_view.Atom;
+import mc_view.PDBChain;
+import mc_view.PDBfile;
 
 public class StructureSelectionManager
 {
@@ -398,8 +399,11 @@ 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)
       {
@@ -426,7 +430,8 @@ public class StructureSelectionManager
     } catch (SiftsException e)
     {
       isMapUsingSIFTs = false;
-      e.printStackTrace();
+      Cache.log.error("SIFTS mapping failed", e);
+      Cache.log.error("Falling back on Needleman & Wunsch alignment");
       siftsClient = null;
     }
 
@@ -533,15 +538,14 @@ public class StructureSelectionManager
                     pdb, maxChain, sqmpping, maxAlignseq, siftsClient);
             seqToStrucMapping.add(siftsMapping);
             maxChain.makeExactMapping(siftsMapping, seq);
-            maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
-                                                       // "IEA:SIFTS" ?
+            maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS");
             maxChain.transferResidueAnnotation(siftsMapping, null);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
 
           } catch (SiftsException e)
           {
             // fall back to NW alignment
-            System.err.println(e.getMessage());
+            Cache.log.error(e.getMessage());
             StructureMapping nwMapping = getNWMappings(seq, pdbFile,
                     targetChainId, maxChain, pdb, maxAlignseq);
             seqToStrucMapping.add(nwMapping);
@@ -855,13 +859,14 @@ public class StructureSelectionManager
    * @param pdbResNum
    * @param chain
    * @param pdbfile
+   * @return
    */
-  public void mouseOverStructure(int pdbResNum, String chain,
+  public String mouseOverStructure(int pdbResNum, String chain,
           String pdbfile)
   {
     AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0);
     List<AtomSpec> atoms = Collections.singletonList(atomSpec);
-    mouseOverStructure(atoms);
+    return mouseOverStructure(atoms);
   }
 
   /**
@@ -869,12 +874,12 @@ public class StructureSelectionManager
    * 
    * @param atoms
    */
-  public void mouseOverStructure(List<AtomSpec> atoms)
+  public String mouseOverStructure(List<AtomSpec> atoms)
   {
     if (listeners == null)
     {
       // old or prematurely sent event
-      return;
+      return null;
     }
     boolean hasSequenceListener = false;
     for (int i = 0; i < listeners.size(); i++)
@@ -886,18 +891,24 @@ public class StructureSelectionManager
     }
     if (!hasSequenceListener)
     {
-      return;
+      return null;
     }
 
     SearchResultsI results = findAlignmentPositionsForStructurePositions(
             atoms);
+    String result = null;
     for (Object li : listeners)
     {
       if (li instanceof SequenceListener)
       {
-        ((SequenceListener) li).highlightSequence(results);
+        String s = ((SequenceListener) li).highlightSequence(results);
+        if (s != null)
+        {
+          result = s;
+        }
       }
     }
+    return result;
   }
 
   /**
@@ -1167,7 +1178,8 @@ public class StructureSelectionManager
     StringBuilder sb = new StringBuilder(64);
     for (StructureMapping sm : mappings)
     {
-      if (sm.pdbfile.equals(pdbfile) && seqs.contains(sm.sequence))
+      if (Platform.pathEquals(sm.pdbfile, pdbfile)
+              && seqs.contains(sm.sequence))
       {
         sb.append(sm.mappingDetails);
         sb.append(NEWLINE);
@@ -1340,7 +1352,10 @@ public class StructureSelectionManager
         instances.remove(jalviewLite);
         try
         {
-          mnger.finalize();
+          /* bsoares 2019-03-20 finalize deprecated, no apparent external
+           * resources to close
+           */
+          // mnger.finalize();
         } catch (Throwable x)
         {
         }