JAL-1990 suggested revision to separate references to UI components from datamodel...

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index fb96b22..f813411 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -70,12 +70,8 @@ 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.
    */
@@ -321,9 +317,11 @@ public class StructureSelectionManager
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public StructureFile setMapping(SequenceI[] sequence,
-          String[] targetChains, String pdbFile, String protocol)
+          String[] targetChains, String pdbFile, String protocol,
+          IProgressIndicator progress)
   {
-    return setMapping(true, sequence, targetChains, pdbFile, protocol);
+    return computeMapping(true, sequence, targetChains, pdbFile, protocol,
+            progress);
   }
 
 
@@ -338,7 +336,7 @@ 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 protocol
@@ -350,6 +348,16 @@ public class StructureSelectionManager
           String pdbFile,
           String protocol)
   {
+    return computeMapping(forStructureView, sequenceArray, targetChainIds,
+            pdbFile, protocol, null);
+  }
+
+  synchronized public StructureFile computeMapping(
+          boolean forStructureView, SequenceI[] sequenceArray,
+          String[] targetChainIds, String pdbFile, String 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
@@ -496,13 +504,14 @@ public class StructureSelectionManager
       {
         pdbFile = "INLINE" + pdb.getId();
       }
-
       ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
       if (isMapUsingSIFTs)
       {
-        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())
@@ -559,17 +568,23 @@ 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);
+        }
         seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
                 maxChain, pdb, maxAlignseq));
       }
-
       if (forStructureView)
       {
         mappings.addAll(seqToStrucMapping);
       }
+      if (progress != null)
+      {
+        progress.setProgressBar(null, progressSessionId);
+      }
     }
     return pdb;
   }
@@ -1294,35 +1309,6 @@ 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;