Merge branch 'bug/JAL-2634' into develop

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 0acb786..db0b47e 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -36,6 +36,7 @@ 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;
@@ -385,6 +386,7 @@ public class StructureSelectionManager
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
     try
     {
+      sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
       pdb = new JmolParser(pdbFile, sourceType);
 
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
@@ -455,7 +457,7 @@ public class StructureSelectionManager
        * Attempt pairwise alignment of the sequence with each chain in the PDB,
        * and remember the highest scoring chain
        */
-      int max = -10;
+      float max = -10;
       AlignSeq maxAlignseq = null;
       String maxChainId = " ";
       PDBChain maxChain = null;
@@ -740,7 +742,7 @@ public class StructureSelectionManager
       if (listeners.elementAt(i) instanceof StructureListener)
       {
         sl = (StructureListener) listeners.elementAt(i);
-        for (String pdbfile : sl.getPdbFile())
+        for (String pdbfile : sl.getStructureFiles())
         {
           pdbs.remove(pdbfile);
         }