X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=7eb910746e18f8025039b110bafe7c0e68bef6df;hb=75db7abd6c89a9465861dc7604faca4893c52101;hp=b973f45f869a381d6e052ea355a51482c77977a4;hpb=461fa736a460f28d57cb0fe1f3a1cd05c32f0f7c;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index b973f45..7eb9107 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -66,7 +66,7 @@ public class StructureSelectionManager
 
   static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
 
-  private List<StructureMapping> mappings = new ArrayList<StructureMapping>();
+  private List<StructureMapping> mappings = new ArrayList<>();
 
   private boolean processSecondaryStructure = false;
 
@@ -74,20 +74,16 @@ public class StructureSelectionManager
 
   private boolean addTempFacAnnot = false;
 
-  private IProgressIndicator progressIndicator;
-
   private SiftsClient siftsClient = null;
 
-  private long progressSessionId;
-
   /*
    * Set of any registered mappings between (dataset) sequences.
    */
-  private List<AlignedCodonFrame> seqmappings = new ArrayList<AlignedCodonFrame>();
+  private List<AlignedCodonFrame> seqmappings = new ArrayList<>();
 
-  private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
+  private List<CommandListener> commandListeners = new ArrayList<>();
 
-  private List<SelectionListener> sel_listeners = new ArrayList<SelectionListener>();
+  private List<SelectionListener> sel_listeners = new ArrayList<>();
 
   /**
    * @return true if will try to use external services for processing secondary
@@ -175,9 +171,9 @@ public class StructureSelectionManager
    * map between the PDB IDs (or structure identifiers) used by Jalview and the
    * absolute filenames for PDB data that corresponds to it
    */
-  Map<String, String> pdbIdFileName = new HashMap<String, String>();
+  Map<String, String> pdbIdFileName = new HashMap<>();
 
-  Map<String, String> pdbFileNameId = new HashMap<String, String>();
+  Map<String, String> pdbFileNameId = new HashMap<>();
 
   public void registerPDBFile(String idForFile, String absoluteFile)
   {
@@ -228,7 +224,7 @@ public class StructureSelectionManager
     }
     if (instances == null)
     {
-      instances = new java.util.IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager>();
+      instances = new java.util.IdentityHashMap<>();
     }
     StructureSelectionManager instance = instances.get(context);
     if (instance == null)
@@ -324,9 +320,11 @@ public class StructureSelectionManager
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public StructureFile setMapping(SequenceI[] sequence,
-          String[] targetChains, String pdbFile, DataSourceType protocol)
+          String[] targetChains, String pdbFile, DataSourceType protocol, 
+          IProgressIndicator progress)
   {
-    return setMapping(true, sequence, targetChains, pdbFile, protocol);
+    return computeMapping(true, sequence, targetChains, pdbFile, protocol,
+            progress);
   }
 
   /**
@@ -353,6 +351,16 @@ public class StructureSelectionManager
           SequenceI[] sequenceArray, String[] targetChainIds,
           String pdbFile, DataSourceType sourceType)
   {
+    return computeMapping(forStructureView, sequenceArray, targetChainIds,
+            pdbFile, sourceType, null);
+  }
+
+  synchronized public StructureFile computeMapping(
+          boolean forStructureView, SequenceI[] sequenceArray,
+          String[] targetChainIds, String pdbFile, DataSourceType sourceType,
+          IProgressIndicator progress)
+  {
+    long progressSessionId = System.currentTimeMillis() * 3;
     /*
      * There will be better ways of doing this in the future, for now we'll use
      * the tried and tested MCview pdb mapping
@@ -500,12 +508,14 @@ public class StructureSelectionManager
         pdbFile = "INLINE" + pdb.getId();
       }
 
-      List<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
+      List<StructureMapping> seqToStrucMapping = new ArrayList<>();
       if (isMapUsingSIFTs && seq.isProtein())
       {
-        setProgressBar(null);
-        setProgressBar(MessageManager
-                .getString("status.obtaining_mapping_with_sifts"));
+        if (progress!=null) {
+          progress.setProgressBar(MessageManager
+                .getString("status.obtaining_mapping_with_sifts"),
+                  progressSessionId);
+        }
         jalview.datamodel.Mapping sqmpping = maxAlignseq
                 .getMappingFromS1(false);
         if (targetChainId != null && !targetChainId.trim().isEmpty())
@@ -538,7 +548,7 @@ public class StructureSelectionManager
         }
         else
         {
-          List<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+          List<StructureMapping> foundSiftsMappings = new ArrayList<>();
           for (PDBChain chain : pdb.getChains())
           {
             try
@@ -575,20 +585,25 @@ public class StructureSelectionManager
       }
       else
       {
-        setProgressBar(null);
-        setProgressBar(MessageManager
-                .getString("status.obtaining_mapping_with_nw_alignment"));
+        if (progress != null)
+        {
+          progress.setProgressBar(MessageManager
+				  .getString("status.obtaining_mapping_with_nw_alignment"),
+                  progressSessionId);
+        }
         StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId,
                 maxChain, pdb, maxAlignseq);
         seqToStrucMapping.add(nwMapping);
         ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
-
       }
-
       if (forStructureView)
       {
         mappings.addAll(seqToStrucMapping);
       }
+      if (progress != null)
+      {
+        progress.setProgressBar(null, progressSessionId);
+      }
     }
     return pdb;
   }
@@ -683,7 +698,7 @@ public class StructureSelectionManager
             .getMappingFromS1(false);
     maxChain.transferRESNUMFeatures(seq, null);
 
-    HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
+    HashMap<Integer, int[]> mapping = new HashMap<>();
     int resNum = -10000;
     int index = 0;
     char insCode = ' ';
@@ -737,7 +752,7 @@ public class StructureSelectionManager
      * Remove mappings to the closed listener's PDB files, but first check if
      * another listener is still interested
      */
-    List<String> pdbs = new ArrayList<String>(Arrays.asList(pdbfiles));
+    List<String> pdbs = new ArrayList<>(Arrays.asList(pdbfiles));
 
     StructureListener sl;
     for (int i = 0; i < listeners.size(); i++)
@@ -758,7 +773,7 @@ public class StructureSelectionManager
      */
     if (pdbs.size() > 0)
     {
-      List<StructureMapping> tmp = new ArrayList<StructureMapping>();
+      List<StructureMapping> tmp = new ArrayList<>();
       for (StructureMapping sm : mappings)
       {
         if (!pdbs.contains(sm.pdbfile))
@@ -952,7 +967,7 @@ public class StructureSelectionManager
       return;
     }
     int atomNo;
-    List<AtomSpec> atoms = new ArrayList<AtomSpec>();
+    List<AtomSpec> atoms = new ArrayList<>();
     for (StructureMapping sm : mappings)
     {
       if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence()
@@ -1060,7 +1075,7 @@ public class StructureSelectionManager
 
   public StructureMapping[] getMapping(String pdbfile)
   {
-    List<StructureMapping> tmp = new ArrayList<StructureMapping>();
+    List<StructureMapping> tmp = new ArrayList<>();
     for (StructureMapping sm : mappings)
     {
       if (sm.pdbfile.equals(pdbfile))
@@ -1220,7 +1235,7 @@ public class StructureSelectionManager
     }
   }
 
-  Vector<AlignmentViewPanelListener> view_listeners = new Vector<AlignmentViewPanelListener>();
+  Vector<AlignmentViewPanelListener> view_listeners = new Vector<>();
 
   public synchronized void sendViewPosition(
           jalview.api.AlignmentViewPanel source, int startRes, int endRes,
@@ -1343,35 +1358,6 @@ public class StructureSelectionManager
     return null;
   }
 
-  public IProgressIndicator getProgressIndicator()
-  {
-    return progressIndicator;
-  }
-
-  public void setProgressIndicator(IProgressIndicator progressIndicator)
-  {
-    this.progressIndicator = progressIndicator;
-  }
-
-  public long getProgressSessionId()
-  {
-    return progressSessionId;
-  }
-
-  public void setProgressSessionId(long progressSessionId)
-  {
-    this.progressSessionId = progressSessionId;
-  }
-
-  public void setProgressBar(String message)
-  {
-    if (progressIndicator == null)
-    {
-      return;
-    }
-    progressIndicator.setProgressBar(message, progressSessionId);
-  }
-
   public List<AlignedCodonFrame> getSequenceMappings()
   {
     return seqmappings;