X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fio%2Fwriters%2FSequenceWriter.java;h=ddcb378f16c43f06311ac32deb38b17f2f56ee95;hb=e8890012b315b30af8bf6c90db6e800b7d046147;hp=b4135d1e7e9291b2d14b3614607cbd048da32b3e;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git

diff --git a/forester/java/src/org/forester/io/writers/SequenceWriter.java b/forester/java/src/org/forester/io/writers/SequenceWriter.java
index b4135d1..ddcb378 100644
--- a/forester/java/src/org/forester/io/writers/SequenceWriter.java
+++ b/forester/java/src/org/forester/io/writers/SequenceWriter.java
@@ -1,11 +1,11 @@
 
 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.BasicSequence;
 import org.forester.sequence.Sequence;
 import org.forester.util.ForesterUtil;
 
@@ -15,41 +15,30 @@ public class SequenceWriter {
         FASTA;
     }
 
-    public static void main( final String[] args ) {
-        final Sequence s = BasicSequence.createAaSequence( "name", "abcdefghiiklmnap" );
-        System.out.println( s.toString() );
-        System.out.println( SequenceWriter.toFasta( s, 0 ).toString() );
-        System.out.println( SequenceWriter.toFasta( s, 5 ).toString() );
-        System.out.println( SequenceWriter.toFasta( s, 8 ).toString() );
-        System.out.println( SequenceWriter.toFasta( s, 4 ).toString() );
-        System.out.println( SequenceWriter.toFasta( s, 3 ).toString() );
-        System.out.println( SequenceWriter.toFasta( s, 2 ).toString() );
-        System.out.println( SequenceWriter.toFasta( s, 1 ).toString() );
-        System.out.println( SequenceWriter.toFasta( s, 100 ).toString() );
-        System.out.println( SequenceWriter.toFasta( s, 15 ).toString() );
-        System.out.println( SequenceWriter.toFasta( s, 16 ).toString() );
+    public static StringBuilder toFasta( final Sequence seq, final int width ) {
+        return toFasta( seq.getIdentifier(), seq.getMolecularSequenceAsString(), width );
     }
 
-    public static StringBuilder toFasta( final Sequence seq, final int 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;
@@ -78,6 +67,13 @@ public class SequenceWriter {
         }
     }
 
+    public static void writeSeqs( final List<Sequence> 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<Sequence> seqs,
                                   final Writer writer,
                                   final SEQ_FORMAT format,