X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=0209e200bbfb66c32a969eee0479ce6343321da0;hb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;hp=65df67937b3a2268f01e6d4191030320af059963;hpb=c6d5255c09855fc1b0d03a085da9988a75cd3898;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 65df679..0209e20 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -20,8 +20,21 @@
  */
 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.Locale;
+import java.util.Map;
+import java.util.Vector;
+
 import jalview.analysis.AlignSeq;
 import jalview.api.StructureSelectionManagerProvider;
+import jalview.bin.Console;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
 import jalview.commands.OrderCommand;
@@ -41,24 +54,13 @@ 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
 {
@@ -409,7 +411,17 @@ public class StructureSelectionManager
         registerPDBFile(pdb.getId().trim(), pdbFile);
       }
       // if PDBId is unavailable then skip SIFTS mapping execution path
-      isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable();
+      // TODO: JAL-3868 need to know if structure is actually from 
+      // PDB (has valid PDB ID and has provenance suggesting it 
+      // actually came from PDB)
+      boolean isProtein = false;
+      for (SequenceI s:sequenceArray) {
+        if (s.isProtein()) {
+          isProtein = true;
+          break;
+        }
+      }
+      isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable() && !pdb.getId().startsWith("AF-") && isProtein;
 
     } catch (Exception ex)
     {
@@ -429,7 +441,8 @@ public class StructureSelectionManager
     } catch (SiftsException e)
     {
       isMapUsingSIFTs = false;
-      e.printStackTrace();
+      Console.error("SIFTS mapping failed", e);
+      Console.error("Falling back on Needleman & Wunsch alignment");
       siftsClient = null;
     }
 
@@ -536,20 +549,19 @@ 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",pdb.getId().toLowerCase(Locale.ROOT));
             maxChain.transferResidueAnnotation(siftsMapping, null);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
 
           } catch (SiftsException e)
           {
             // fall back to NW alignment
-            System.err.println(e.getMessage());
+            Console.error(e.getMessage());
             StructureMapping nwMapping = getNWMappings(seq, pdbFile,
                     targetChainId, maxChain, pdb, maxAlignseq);
             seqToStrucMapping.add(nwMapping);
             maxChain.makeExactMapping(maxAlignseq, seq);
-            maxChain.transferRESNUMFeatures(seq, "IEA:Jalview"); // FIXME: is
+            maxChain.transferRESNUMFeatures(seq, "IEA:Jalview",pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is
                                                                  // this
                                                         // "IEA:Jalview" ?
             maxChain.transferResidueAnnotation(nwMapping, sqmpping);
@@ -569,7 +581,7 @@ public class StructureSelectionManager
                       siftsClient);
               foundSiftsMappings.add(siftsMapping);
               chain.makeExactMapping(siftsMapping, seq);
-              chain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
+              chain.transferRESNUMFeatures(seq, "IEA: SIFTS",pdb.getId().toLowerCase(Locale.ROOT));// FIXME: is this
               // "IEA:SIFTS" ?
               chain.transferResidueAnnotation(siftsMapping, null);
             } catch (SiftsException e)
@@ -594,7 +606,7 @@ public class StructureSelectionManager
             StructureMapping nwMapping = getNWMappings(seq, pdbFile,
                     maxChainId, maxChain, pdb, maxAlignseq);
             seqToStrucMapping.add(nwMapping);
-            maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+            maxChain.transferRESNUMFeatures(seq, null,pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is this
                                                         // "IEA:Jalview" ?
             maxChain.transferResidueAnnotation(nwMapping, sqmpping);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
@@ -762,7 +774,7 @@ public class StructureSelectionManager
     maxChain.makeExactMapping(maxAlignseq, seq);
     jalview.datamodel.Mapping sqmpping = maxAlignseq
             .getMappingFromS1(false);
-    maxChain.transferRESNUMFeatures(seq, null);
+    maxChain.transferRESNUMFeatures(seq, null, pdb.getId().toLowerCase(Locale.ROOT));
 
     HashMap<Integer, int[]> mapping = new HashMap<>();
     int resNum = -10000;
@@ -1177,7 +1189,8 @@ 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);
@@ -1350,7 +1363,10 @@ 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)
         {
         }