X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=054ed2fde6420e173f4d0e4ae77e7c8fd11ac014;hb=5c6564f903f75960af960720a8635ab8709afc37;hp=34ca6ba50c716ee020778855fb8356a725832d04;hpb=a7a69103cb81f7e40803cbed0beb41d05707f641;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 34ca6ba..054ed2f 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -41,6 +41,7 @@ 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;
@@ -399,7 +400,9 @@ public class StructureSelectionManager
       // FIXME if sourceType is not null, we've lost data here
       sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
       pdb = new JmolParser(false, pdbFile, sourceType);
-      pdb.addSettings(parseSecStr, parseSecStr, parseSecStr);
+      pdb.addSettings(parseSecStr && processSecondaryStructure,
+              parseSecStr && addTempFacAnnot,
+              parseSecStr && secStructServices);
       pdb.doParse();
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
               && DataSourceType.FILE == sourceType)
@@ -856,13 +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);
   }
 
   /**
@@ -870,12 +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++)
@@ -887,18 +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;
   }
 
   /**
@@ -1168,7 +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);
@@ -1341,7 +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)
         {
         }