inprogress

[jalview.git] / forester / java / src / org / forester / io / writers / SequenceWriter.java

diff --git a/forester/java/src/org/forester/io/writers/SequenceWriter.java b/forester/java/src/org/forester/io/writers/SequenceWriter.java
index 327f955..8e6ef95 100644 (file)
--- a/forester/java/src/org/forester/io/writers/SequenceWriter.java
+++ b/forester/java/src/org/forester/io/writers/SequenceWriter.java
@@ -15,25 +15,29 @@ public class SequenceWriter {
     }
 
     public static StringBuilder toFasta( final Sequence seq, final int width ) {
+        return toFasta( seq.getIdentifier(), seq.getMolecularSequenceAsString(), width );
+    }
+
+    public static StringBuilder toFasta( final String name, final String mol_seq, final int width ) {
         final StringBuilder sb = new StringBuilder();
         sb.append( ">" );
-        sb.append( seq.getIdentifier().toString() );
+        sb.append( name );
         sb.append( ForesterUtil.LINE_SEPARATOR );
-        if ( ( width < 1 ) || ( width >= seq.getLength() ) ) {
-            sb.append( seq.getMolecularSequence() );
+        if ( ( width < 1 ) || ( width >= mol_seq.length() ) ) {
+            sb.append( mol_seq );
         }
         else {
-            final int lines = seq.getLength() / width;
-            final int rest = seq.getLength() - ( lines * width );
+            final int lines = mol_seq.length() / width;
+            final int rest = mol_seq.length() - ( lines * width );
             for( int i = 0; i < lines; ++i ) {
-                sb.append( seq.getMolecularSequence(), i * width, width );
+                sb.append( mol_seq, i * width, ( i + 1 ) * width );
                 if ( i < ( lines - 1 ) ) {
                     sb.append( ForesterUtil.LINE_SEPARATOR );
                 }
             }
             if ( rest > 0 ) {
                 sb.append( ForesterUtil.LINE_SEPARATOR );
-                sb.append( seq.getMolecularSequence(), lines * width, rest );
+                sb.append( mol_seq, lines * width, mol_seq.length() );
             }
         }
         return sb;