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 6e79477..f4db6cb 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/GeneralMsaParser.java
+++ b/forester/java/src/org/forester/io/parsers/GeneralMsaParser.java
@@ -22,7 +22,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.io.parsers;
 
@@ -41,14 +41,14 @@ 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 {
 
     private static final Pattern NAME_SEQ_PATTERN          = Pattern.compile( "(\\S+)\\s+(\\S+)\\s*" );
     private static final Pattern INDENTED_SEQ_PATTERN      = Pattern.compile( "\\s+(\\S+)\\s*" );
     private static final Pattern NON_INDENTED_SEQ_PATTERN  = Pattern.compile( "(\\S+).*" );
-    private static final Pattern PROBCONS_REGEX            = Pattern.compile( "^CLUSTAL\\s" );
+    private static final Pattern PROBCONS_REGEX            = Pattern.compile( "^CLUSTAL" );
     private static final Pattern MUSCLE_REGEX              = Pattern.compile( "^MUSCLE\\s\\(" );
     private static final Pattern CLUSTAL_REGEX             = Pattern.compile( "^PROBCONS\\s" );
     private static final Pattern ANYTHING_REGEX            = Pattern.compile( "[\\d\\s]+" );
@@ -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;