JAL-4199 Fix cancel button not appearing on progress bar

[jalview.git] / src / jalview / structure / StructureSelectionManager.java

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index bb1bb94..7d936ef 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -20,11 +20,12 @@
  */
 package jalview.structure;
 
+
 import jalview.analysis.AlignSeq;
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.bin.ApplicationSingletonProvider;
 import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
 import jalview.commands.OrderCommand;
@@ -57,6 +58,7 @@ 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;
 
@@ -68,6 +70,7 @@ public class StructureSelectionManager implements ApplicationSingletonI
 {
   public final static String NEWLINE = System.lineSeparator();
 
+
   private List<StructureMapping> mappings = new ArrayList<>();
 
   private boolean processSecondaryStructure = false;
@@ -84,7 +87,6 @@ public class StructureSelectionManager implements ApplicationSingletonI
   private List<CommandListener> commandListeners = new ArrayList<>();
 
   private List<SelectionListener> sel_listeners = new ArrayList<>();
-
   /*
    * instances of this class scoped by some context class
    */
@@ -98,7 +100,7 @@ public class StructureSelectionManager implements ApplicationSingletonI
    */
   private static StructureSelectionManager getInstance()
   {
-    return (StructureSelectionManager) ApplicationSingletonProvider
+    return ApplicationSingletonProvider
             .getInstance(StructureSelectionManager.class);
   }
 
@@ -144,7 +146,52 @@ public class StructureSelectionManager implements ApplicationSingletonI
     }
     return instance;
   }
+/** Null provider in 2.11.2
+
+
+  private static StructureSelectionManager nullProvider = null;
 
+  public static StructureSelectionManager getStructureSelectionManager(
+          StructureSelectionManagerProvider context)
+  {
+    if (context == null)
+    {
+      if (nullProvider == null)
+      {
+        if (instances != null)
+        {
+          throw new Error(MessageManager.getString(
+                  "error.implementation_error_structure_selection_manager_null"),
+                  new NullPointerException(MessageManager
+                          .getString("exception.ssm_context_is_null")));
+        }
+        else
+        {
+          nullProvider = new StructureSelectionManager();
+        }
+        return nullProvider;
+      }
+    }
+    if (instances == null)
+    {
+      instances = new java.util.IdentityHashMap<>();
+    }
+    StructureSelectionManager instance = instances.get(context);
+    if (instance == null)
+    {
+      if (nullProvider != null)
+      {
+        instance = nullProvider;
+      }
+      else
+      {
+        instance = new StructureSelectionManager();
+      }
+      instances.put(context, instance);
+    }
+    return instance;
+  }
+*/
 
   /**
    * @return true if will try to use external services for processing secondary
@@ -434,7 +481,17 @@ public class StructureSelectionManager implements ApplicationSingletonI
         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)
     {
@@ -454,8 +511,8 @@ public class StructureSelectionManager implements ApplicationSingletonI
     } catch (SiftsException e)
     {
       isMapUsingSIFTs = false;
-      Cache.log.error("SIFTS mapping failed", e);
-      Cache.log.error("Falling back on Needleman & Wunsch alignment");
+      Console.error("SIFTS mapping failed", e);
+      Console.error("Falling back on Needleman & Wunsch alignment");
       siftsClient = null;
     }
 
@@ -562,22 +619,23 @@ public class StructureSelectionManager implements ApplicationSingletonI
                     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
-                                                                 // this
-                                                        // "IEA:Jalview" ?
+            maxChain.transferRESNUMFeatures(seq, "IEA:Jalview",
+                    pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is
+            // this
+            // "IEA:Jalview" ?
             maxChain.transferResidueAnnotation(nwMapping, sqmpping);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
           }
@@ -595,7 +653,8 @@ public class StructureSelectionManager implements ApplicationSingletonI
                       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)
@@ -620,8 +679,9 @@ public class StructureSelectionManager implements ApplicationSingletonI
             StructureMapping nwMapping = getNWMappings(seq, pdbFile,
                     maxChainId, maxChain, pdb, maxAlignseq);
             seqToStrucMapping.add(nwMapping);
-            maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
-                                                        // "IEA:Jalview" ?
+            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));
           }
@@ -676,6 +736,7 @@ public class StructureSelectionManager implements ApplicationSingletonI
         {
           ds = ds.getDatasetSequence();
         }
+        ;
         if (ds.getAnnotation() != null)
         {
           for (AlignmentAnnotation ala : ds.getAnnotation())
@@ -787,7 +848,8 @@ public class StructureSelectionManager implements ApplicationSingletonI
     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;
@@ -929,9 +991,9 @@ public class StructureSelectionManager implements ApplicationSingletonI
         if (s != null)
         {
           result = s;
+        }
       }
     }
-  }
     return result;
   }
 
@@ -1275,39 +1337,43 @@ public class StructureSelectionManager implements ApplicationSingletonI
   {
     if (mappings != null)
     {
-    mappings.clear();
+      mappings.clear();
     }
     if (seqmappings != null)
     {
-    seqmappings.clear();
+      seqmappings.clear();
     }
     if (sel_listeners != null)
     {
-    sel_listeners.clear();
+      sel_listeners.clear();
     }
     if (listeners != null)
     {
-    listeners.clear();
+      listeners.clear();
     }
     if (commandListeners != null)
     {
-    commandListeners.clear();
+      commandListeners.clear();
     }
     if (view_listeners != null)
     {
-    view_listeners.clear();
+      view_listeners.clear();
     }
     if (pdbFileNameId != null)
     {
-    pdbFileNameId.clear();
+      pdbFileNameId.clear();
     }
     if (pdbIdFileName != null)
     {
-    pdbIdFileName.clear();
+      pdbIdFileName.clear();
     }
   }
 
-  public void addSelectionListener(SelectionListener selecter)
+  public List<SelectionListener> getListeners() {
+    return sel_listeners;
+  }
+  
+   public void addSelectionListener(SelectionListener selecter)
   {
     if (!sel_listeners.contains(selecter))
     {
@@ -1355,7 +1421,7 @@ public class StructureSelectionManager implements ApplicationSingletonI
         {
           slis.viewPosition(startRes, endRes, startSeq, endSeq, source);
         }
-        
+        ;
       }
     }
   }
@@ -1366,12 +1432,11 @@ public class StructureSelectionManager implements ApplicationSingletonI
    * 
    * @param provider
    */
-
   public static void release(StructureSelectionManagerProvider provider)
   {
     getInstance().selectionManagers.remove(provider);
   }
-  
+
   public void registerPDBEntry(PDBEntry pdbentry)
   {
     if (pdbentry.getFile() != null