X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fpacked%2FParsePackedSet.java;h=138fef717606bb6e7af189c2390a9f5457212daf;hb=6e5cc965552fadac700baa9b076777697f66386a;hp=a4ef77e990e1ea6021dfc303bd3d38e37ccdb6da;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/io/packed/ParsePackedSet.java b/src/jalview/io/packed/ParsePackedSet.java
index a4ef77e..138fef7 100644
--- a/src/jalview/io/packed/ParsePackedSet.java
+++ b/src/jalview/io/packed/ParsePackedSet.java
@@ -20,8 +20,10 @@
  */
 package jalview.io.packed;
 
+import jalview.api.FeatureColourI;
 import jalview.datamodel.AlignmentI;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.FileFormatI;
 import jalview.io.FileParse;
 import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
@@ -30,7 +32,7 @@ import jalview.io.packed.DataProvider.JvDataType;
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.Hashtable;
+import java.util.HashMap;
 import java.util.List;
 
 public class ParsePackedSet
@@ -63,10 +65,10 @@ public class ParsePackedSet
       FileParse src = dta.getDataSource();
       if (dta.getType().equals(DataProvider.JvDataType.ALIGNMENT))
       {
-        String fmt = null;
+        FileFormatI fmt = null;
         try
         {
-          fmt = new IdentifyFile().Identify(src, false);
+          fmt = new IdentifyFile().identify(src, false);
         } catch (Exception ex)
         {
           exerror = ex;
@@ -75,32 +77,24 @@ public class ParsePackedSet
 
         if (fmt != null)
         {
-          if (!FormatAdapter.isValidIOFormat(fmt, false))
+          // parse the alignment
+          AlignmentI al = null;
+          try
           {
-            errmsg = fmt;
-            exerror = null;
+            al = new FormatAdapter().readFromFile(src, fmt);
+          } catch (Exception e)
+          {
+            errmsg = "Failed to parse alignment from result set";
+            exerror = e;
           }
-          else
+          if (al != null)
           {
-            // parse the alignment
-            AlignmentI al = null;
-            try
-            {
-              al = new FormatAdapter().readFromFile(src, fmt);
-            } catch (Exception e)
-            {
-              errmsg = "Failed to parse alignment from result set";
-              exerror = e;
-            }
-            if (al != null)
-            {
-              // deuniquify and construct/merge additional dataset entries if
-              // necessary.
-              context.addAlignment(al);
-              context.updateSetModified(true);
-              rslt.add(al);
-              deuniquify = true;
-            }
+            // deuniquify and construct/merge additional dataset entries if
+            // necessary.
+            context.addAlignment(al);
+            context.updateSetModified(true);
+            rslt.add(al);
+            deuniquify = true;
           }
         }
       }
@@ -157,7 +151,7 @@ public class ParsePackedSet
         // if not, create one.
         if (context.featureColours == null)
         {
-          context.featureColours = new Hashtable();
+          context.featureColours = new HashMap<String, FeatureColourI>();
         }
         try
         {