in progress...

[jalview.git] / forester / java / src / org / forester / io / parsers / GeneralMsaParser.java

diff --git a/forester/java/src/org/forester/io/parsers/GeneralMsaParser.java b/forester/java/src/org/forester/io/parsers/GeneralMsaParser.java
index 507ae1f..f4db6cb 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/GeneralMsaParser.java
+++ b/forester/java/src/org/forester/io/parsers/GeneralMsaParser.java
@@ -41,7 +41,7 @@ import org.forester.msa.BasicMsa;
 import org.forester.msa.Msa;
 import org.forester.msa.MsaFormatException;
 import org.forester.sequence.BasicSequence;
-import org.forester.sequence.Sequence;
+import org.forester.sequence.MolecularSequence;
 
 public final class GeneralMsaParser {
 
@@ -161,17 +161,17 @@ public final class GeneralMsaParser {
                 }
                 else {
                     throw new MsaFormatException( "illegal msa format (line: " + line_counter + "):\n\"" + trim( line )
-                            + "\"" );
+                                                  + "\"" );
                 }
                 if ( is_first ) {
                     is_first = false;
                 }
             }
         } // while ( ( line = reader.readLine() ) != null )
-        final List<Sequence> seqs = new ArrayList<Sequence>();
+        final List<MolecularSequence> seqs = new ArrayList<MolecularSequence>();
         for( int i = 0; i < names_in_order.size(); ++i ) {
             seqs.add( BasicSequence.createAaSequence( names_in_order.get( i ), temp_msa.get( names_in_order.get( i ) )
-                    .toString() ) );
+                                                      .toString() ) );
         }
         final Msa msa = BasicMsa.createInstance( seqs );
         return msa;