JAL-2136 merged and resolved conflicts with 80edaa84d6d9beac9f0d2c71b50b7b56fd393427

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index bda269c..b0c185b 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -326,11 +326,14 @@ 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);
   }
 
+
   /**
    * create sequence structure mappings between each sequence and the given
    * pdbFile (retrieved via the given protocol).
@@ -342,17 +345,27 @@ public class StructureSelectionManager
    *          - one or more sequences to be mapped to pdbFile
    * @param targetChainIds
    *          - optional chain specification for mapping each sequence to pdb
-   *          (may be nill, individual elements may be nill)
+   *          (may be null, individual elements may be null)
    * @param pdbFile
    *          - structure data resource
-   * @param sourceType
+   * @param protocol
    *          - how to resolve data from resource
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public StructureFile setMapping(boolean forStructureView,
           SequenceI[] sequenceArray, String[] targetChainIds,
-          String pdbFile, DataSourceType sourceType)
+          String pdbFile, DataSourceType protocol)
   {
+    return computeMapping(forStructureView, sequenceArray, targetChainIds,
+            pdbFile, protocol, null);
+  }
+
+  synchronized public StructureFile computeMapping(
+          boolean forStructureView, SequenceI[] sequenceArray,
+          String[] targetChainIds, String pdbFile, DataSourceType protocol,
+          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
@@ -387,10 +400,10 @@ public class StructureSelectionManager
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
     try
     {
-      pdb = new JmolParser(pdbFile, sourceType);
+      pdb = new JmolParser(pdbFile, protocol);
 
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
-              && DataSourceType.FILE == sourceType)
+              && DataSourceType.FILE == protocol)
       {
         registerPDBFile(pdb.getId().trim(), pdbFile);
       }
@@ -494,7 +507,7 @@ public class StructureSelectionManager
         continue;
       }
 
-      if (sourceType == DataSourceType.PASTE)
+      if (protocol.equals(DataSourceType.PASTE))
       {
         pdbFile = "INLINE" + pdb.getId();
       }
@@ -502,9 +515,11 @@ public class StructureSelectionManager
       List<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
       if (!isMappingForPhyre2Model() && 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())
@@ -591,9 +606,12 @@ 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);