Merge branch 'develop' into features/JAL-2295setChimeraAttributes

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 27ff242..7519538 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -35,7 +35,7 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JmolParser;
 import jalview.gui.IProgressIndicator;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
@@ -323,7 +323,7 @@ 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, DataSourceType protocol)
   {
     return setMapping(true, sequence, targetChains, pdbFile, protocol);
   }
@@ -342,13 +342,13 @@ public class StructureSelectionManager
    *          (may be nill, individual elements may be nill)
    * @param pdbFile
    *          - structure data resource
-   * @param protocol
+   * @param sourceType
    *          - 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, String protocol)
+          String pdbFile, DataSourceType sourceType)
   {
     /*
      * There will be better ways of doing this in the future, for now we'll use
@@ -384,10 +384,10 @@ public class StructureSelectionManager
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
     try
     {
-      pdb = new JmolParser(pdbFile, protocol);
+      pdb = new JmolParser(pdbFile, sourceType);
 
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
-              && AppletFormatAdapter.FILE.equals(protocol))
+              && DataSourceType.FILE == sourceType)
       {
         registerPDBFile(pdb.getId().trim(), pdbFile);
       }
@@ -491,12 +491,12 @@ public class StructureSelectionManager
         continue;
       }
 
-      if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+      if (sourceType == DataSourceType.PASTE)
       {
         pdbFile = "INLINE" + pdb.getId();
       }
 
-      ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
+      List<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
       if (isMapUsingSIFTs && seq.isProtein())
       {
         setProgressBar(null);
@@ -534,7 +534,7 @@ public class StructureSelectionManager
         }
         else
         {
-          ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+          List<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
           for (PDBChain chain : pdb.getChains())
           {
             try