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 0477cd2..ddcb378 100644 (file)
--- a/forester/java/src/org/forester/io/writers/SequenceWriter.java
+++ b/forester/java/src/org/forester/io/writers/SequenceWriter.java
@@ -1,6 +1,7 @@
 
 package org.forester.io.writers;
 
+import java.io.File;
 import java.io.IOException;
 import java.io.Writer;
 import java.util.List;
@@ -15,30 +16,9 @@ public class SequenceWriter {
     }
 
     public static StringBuilder toFasta( final Sequence seq, final int width ) {
-        final StringBuilder sb = new StringBuilder();
-        sb.append( ">" );
-        sb.append( seq.getIdentifier().toString() );
-        sb.append( ForesterUtil.LINE_SEPARATOR );
-        if ( ( width < 1 ) || ( width >= seq.getLength() ) ) {
-            sb.append( seq.getMolecularSequence() );
-        }
-        else {
-            final int lines = seq.getLength() / width;
-            final int rest = seq.getLength() - ( lines * width );
-            for( int i = 0; i < lines; ++i ) {
-                sb.append( seq.getMolecularSequence(), i * width, 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 );
-            }
-        }
-        return sb;
+        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( ">" );
@@ -49,16 +29,16 @@ public class SequenceWriter {
         }
         else {
             final int lines = mol_seq.length() / width;
-            final int rest =mol_seq.length() - ( lines * width );
+            final int rest = mol_seq.length() - ( lines * width );
             for( int i = 0; i < lines; ++i ) {
-                sb.append( mol_seq, 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( mol_seq, lines * width, rest );
+                sb.append( mol_seq, lines * width, mol_seq.length() );
             }
         }
         return sb;
@@ -87,6 +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,