JAL-1953 equals and hashCode now takes node ID in account

[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 4b6ddf5..4fa6e81 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/GeneralMsaParser.java
+++ b/forester/java/src/org/forester/io/parsers/GeneralMsaParser.java
@@ -68,7 +68,12 @@ public final class GeneralMsaParser {
                 .matcher( line ).lookingAt() );
     }
 
-    static public Msa parse( final InputStream is ) throws IOException {
+    static final public Msa parseMsa( final InputStream is ) throws IOException {
+        final Msa msa = BasicMsa.createInstance( parseSeqs( is ));
+        return msa;
+    }
+    
+    static final public List<MolecularSequence> parseSeqs( final InputStream is ) throws IOException {
         int block = -1;
         int current_seq_index_per_block = -1;
         String current_name = null;
@@ -145,7 +150,7 @@ public final class GeneralMsaParser {
                                 name = names_in_order.get( current_seq_index_per_block );
                             }
                             catch ( final IndexOutOfBoundsException e ) {
-                                throw new MsaFormatException( "illegalmsa format (line: " + line_counter + "):\n\""
+                                throw new MsaFormatException( "illegal msa format (line: " + line_counter + "):\n\""
                                         + trim( line ) + "\"" );
                             }
                             if ( temp_msa.containsKey( name ) ) {
@@ -161,7 +166,7 @@ public final class GeneralMsaParser {
                 }
                 else {
                     throw new MsaFormatException( "illegal msa format (line: " + line_counter + "):\n\"" + trim( line )
-                            + "\"" );
+                                                  + "\"" );
                 }
                 if ( is_first ) {
                     is_first = false;
@@ -171,10 +176,10 @@ public final class GeneralMsaParser {
         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;
+      
+        return seqs;
     }
 
     private static String trim( final String line ) {