X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fio%2Fparsers%2FFastaParser.java;h=dc4fc469339791a1ac08d2a17ee3b40e701f8146;hb=7ae646b73c00d1458582858319ec62f05e40c71a;hp=348bec419d0f4006655a58fb42b291b8dd953c91;hpb=656be28debec520e0e35a8b311114398a40ea366;p=jalview.git

diff --git a/forester/java/src/org/forester/io/parsers/FastaParser.java b/forester/java/src/org/forester/io/parsers/FastaParser.java
index 348bec4..dc4fc46 100644
--- a/forester/java/src/org/forester/io/parsers/FastaParser.java
+++ b/forester/java/src/org/forester/io/parsers/FastaParser.java
@@ -42,7 +42,7 @@ 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 class FastaParser {
 
@@ -51,7 +51,7 @@ public class FastaParser {
     private static final Pattern ANYTHING_REGEX  = Pattern.compile( "[\\d\\s]+" );
     //>gi|71834668|ref|NP_001025424.1| Bcl2 [Danio rerio]
     public static final Pattern  FASTA_DESC_LINE = Pattern
-                                                         .compile( ">?\\s*([^|]+)\\|([^|]+)\\S*\\s+(.+)\\s+\\[(.+)\\]" );
+            .compile( ">?\\s*([^|]+)\\|([^|]+)\\S*\\s+(.+)\\s+\\[(.+)\\]" );
 
     public static void main( final String[] args ) {
         final String a = ">gi|71834668|ref|NP_001025424.1| Bcl2 [Danio rerio]";
@@ -109,11 +109,11 @@ public class FastaParser {
         return parseMsa( new ByteArrayInputStream( bytes ) );
     }
 
-    static public List<Sequence> parse( final File f ) throws IOException {
+    static public List<MolecularSequence> parse( final File f ) throws IOException {
         return parse( new FileInputStream( f ) );
     }
 
-    static public List<Sequence> parse( final InputStream is ) throws IOException {
+    static public List<MolecularSequence> parse( final InputStream is ) throws IOException {
         final BufferedReader reader = new BufferedReader( new InputStreamReader( is, "UTF-8" ) );
         String line = null;
         int line_counter = 0;
@@ -151,7 +151,7 @@ public class FastaParser {
         }
         addSeq( name, current_seq, temp_msa );
         reader.close();
-        final List<Sequence> seqs = new ArrayList<Sequence>();
+        final List<MolecularSequence> seqs = new ArrayList<MolecularSequence>();
         for( int i = 0; i < temp_msa.size(); ++i ) {
             seqs.add( BasicSequence.createAaSequence( temp_msa.get( i )[ 0 ].toString(),
                                                       temp_msa.get( i )[ 1 ].toString() ) );