in progress..

[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..bd5a5ae 100644 (file)
--- a/forester/java/src/org/forester/io/writers/SequenceWriter.java
+++ b/forester/java/src/org/forester/io/writers/SequenceWriter.java
@@ -1,11 +1,12 @@
 
 package org.forester.io.writers;
 
+import java.io.File;
 import java.io.IOException;
 import java.io.Writer;
 import java.util.List;
 
-import org.forester.sequence.Sequence;
+import org.forester.sequence.MolecularSequence;
 import org.forester.util.ForesterUtil;
 
 public class SequenceWriter {
@@ -14,34 +15,38 @@ public class SequenceWriter {
         FASTA;
     }
 
-    public static StringBuilder toFasta( final Sequence seq, final int width ) {
+    public static StringBuilder toFasta( final MolecularSequence 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;
     }
 
-    public static void toFasta( final Sequence seq, final Writer w, final int width ) throws IOException {
+    public static void toFasta( final MolecularSequence seq, final Writer w, final int width ) throws IOException {
         w.write( ">" );
-        w.write( seq.getIdentifier().toString() );
+        w.write( seq.getIdentifier() );
         w.write( ForesterUtil.LINE_SEPARATOR );
         if ( ( width < 1 ) || ( width >= seq.getLength() ) ) {
             w.write( seq.getMolecularSequence() );
@@ -62,13 +67,22 @@ public class SequenceWriter {
         }
     }
 
-    public static void writeSeqs( final List<Sequence> seqs,
+    public static void writeSeqs( final List<MolecularSequence> seqs,
+                                  final File file,
+                                  final SEQ_FORMAT format,
+                                  final int width ) throws IOException {
+        final Writer w = ForesterUtil.createBufferedWriter( file );
+        SequenceWriter.writeSeqs( seqs, w, format, width );
+        w.close();
+    }
+
+    public static void writeSeqs( final List<MolecularSequence> seqs,
                                   final Writer writer,
                                   final SEQ_FORMAT format,
                                   final int width ) throws IOException {
         switch ( format ) {
             case FASTA:
-                for( final Sequence s : seqs ) {
+                for( final MolecularSequence s : seqs ) {
                     toFasta( s, writer, width );
                     writer.write( ForesterUtil.LINE_SEPARATOR );
                 }