X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=ff88bb7305c5cb35763bcbea4b23e43304fdf914;hb=5cb4c1540eaca054c26ff42a8319f0dbffb1f8e6;hp=434d4ff75de1d891d7d9a904d6c91086831fdfa1;hpb=31c213885bdaafe2670313893fc62a5282d84eb9;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 434d4ff..ff88bb7 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;
@@ -74,8 +75,6 @@ public class StructureSelectionManager
 
   private boolean addTempFacAnnot = false;
 
-  private SiftsClient siftsClient = null;
-
   /*
    * Set of any registered mappings between (dataset) sequences.
    */
@@ -287,7 +286,8 @@ 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
@@ -296,7 +296,7 @@ public class StructureSelectionManager
   {
     for (StructureMapping sm : mappings)
     {
-      if (sm.getPdbId().equals(pdbid))
+      if (sm.getPdbId().equalsIgnoreCase(pdbid))
       {
         return sm.pdbfile;
       }
@@ -399,8 +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)
       {
@@ -414,7 +417,10 @@ public class StructureSelectionManager
       ex.printStackTrace();
       return null;
     }
-
+    /*
+     * sifts client - non null if SIFTS mappings are to be used 
+     */
+    SiftsClient siftsClient = null;
     try
     {
       if (isMapUsingSIFTs)
@@ -425,6 +431,7 @@ public class StructureSelectionManager
     {
       isMapUsingSIFTs = false;
       e.printStackTrace();
+      siftsClient = null;
     }
 
     String targetChainId;
@@ -527,7 +534,7 @@ public class StructureSelectionManager
           try
           {
             siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
-                    pdb, maxChain, sqmpping, maxAlignseq);
+                    pdb, maxChain, sqmpping, maxAlignseq, siftsClient);
             seqToStrucMapping.add(siftsMapping);
             maxChain.makeExactMapping(siftsMapping, seq);
             maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
@@ -559,7 +566,8 @@ public class StructureSelectionManager
             try
             {
               siftsMapping = getStructureMapping(seq,
-                      pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
+                      pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq,
+                      siftsClient);
               foundSiftsMappings.add(siftsMapping);
               chain.makeExactMapping(siftsMapping, seq);
               chain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
@@ -569,6 +577,13 @@ 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())
           {
@@ -602,7 +617,10 @@ public class StructureSelectionManager
       }
       if (forStructureView)
       {
-        mappings.addAll(seqToStrucMapping);
+        for (StructureMapping sm : seqToStrucMapping)
+        {
+          addStructureMapping(sm); // not addAll!
+        }
       }
       if (progress != null)
       {
@@ -654,7 +672,10 @@ public class StructureSelectionManager
 
   public void addStructureMapping(StructureMapping sm)
   {
-    mappings.add(sm);
+    if (!mappings.contains(sm))
+    {
+      mappings.add(sm);
+    }
   }
 
   /**
@@ -668,13 +689,15 @@ public class StructureSelectionManager
    * @param maxChain
    * @param sqmpping
    * @param maxAlignseq
+   * @param siftsClient
+   *          client for retrieval of SIFTS mappings for this structure
    * @return
    * @throws SiftsException
    */
   private StructureMapping getStructureMapping(SequenceI seq,
           String pdbFile, String targetChainId, StructureFile pdb,
           PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
-          AlignSeq maxAlignseq) throws SiftsException
+          AlignSeq maxAlignseq, SiftsClient siftsClient) throws SiftsException
   {
     StructureMapping curChainMapping = siftsClient
             .getSiftsStructureMapping(seq, pdbFile, targetChainId);
@@ -1148,7 +1171,8 @@ 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);
@@ -1321,7 +1345,10 @@ 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)
         {
         }