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diff --git a/test/data/test.vcf.gz b/test/data/test.vcf.gz
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diff --git a/test/uk/ac/sanger/artemis/components/variant/WriteVCFTest.java b/test/uk/ac/sanger/artemis/components/variant/WriteVCFTest.java
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+++ b/test/uk/ac/sanger/artemis/components/variant/WriteVCFTest.java
@@ -0,0 +1,234 @@
+
+package uk.ac.sanger.artemis.components.variant;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.io.InputStream;
+import java.io.StringWriter;
+import java.net.URL;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+
+
+import junit.framework.Assert;
+
+import org.junit.Before;
+import org.junit.Test;
+
+import uk.ac.sanger.artemis.Entry;
+import uk.ac.sanger.artemis.EntryGroup;
+import uk.ac.sanger.artemis.FeatureVector;
+import uk.ac.sanger.artemis.Feature;
+import uk.ac.sanger.artemis.Options;
+import uk.ac.sanger.artemis.Selection;
+import uk.ac.sanger.artemis.SimpleEntryGroup;
+import uk.ac.sanger.artemis.components.EntryFileDialog;
+import uk.ac.sanger.artemis.components.variant.VCFview;
+import uk.ac.sanger.artemis.io.EntryInformation;
+import uk.ac.sanger.artemis.sequence.MarkerRange;
+import uk.ac.sanger.artemis.sequence.Strand;
+import uk.ac.sanger.artemis.util.Document;
+import uk.ac.sanger.artemis.util.DocumentFactory;
+
+/**
+ * Tests for writing out sequences based on VCF data.
+ */
+public class WriteVCFTest
+{
+ private VCFview vcfView;
+
+ /**
+ * Write FASTA, from a range selection on the forward strand.
+ * Variation is a SNP.
+ * VCF line : test 120768 . C T
+ */
+ @Test
+ public void testWriteFwdFastaSNP()
+ {
+ StringWriter writer = getWriter(true, 120768, 120777);
+
+ StringBuffer buff = new StringBuffer("> test.embl.gz 120768:120777\n");
+ buff.append("cttgtcaagg\n");
+ buff.append(">test.vcf.gz test.embl.gz 120768:120777\n");
+ buff.append("tttgtcaagg\n");
+ assertEquals("Export FASTA range ", writer.toString(), buff.toString());
+ }
+
+ /**
+ * Write FASTA, from a range selection on the reverse strand.
+ * Variation is a SNP.
+ * VCF line : test 120768 . C T
+ */
+ @Test
+ public void testWriteRevFastaSNP()
+ {
+ StringWriter writer = getWriter(false, 120768, 120777);
+
+ StringBuffer buff = new StringBuffer("> test.embl.gz 120768:120777 reverse\n");
+ buff.append("ccttgacaag\n");
+ buff.append(">test.vcf.gz test.embl.gz 120768:120777 reverse\n");
+ buff.append("ccttgacaaa\n");
+ assertEquals("Export FASTA range ", writer.toString(), buff.toString());
+ }
+
+ /**
+ * Write FASTA, from a range selection on the forward strand.
+ * Variation is a deletion.
+ * test 396838 . tt t
+ */
+ @Test
+ public void testWriteFwdFastaDeletion()
+ {
+ StringWriter writer = getWriter(true, 396835, 396845);
+
+ StringBuffer buff = new StringBuffer("> test.embl.gz 396835:396845\n");
+ buff.append("tttttaggtat\n");
+ buff.append(">test.vcf.gz test.embl.gz 396835:396845\n");
+ buff.append("tttt-aggtat\n");
+ assertEquals("Export FASTA range ", writer.toString(), buff.toString());
+ }
+
+ /**
+ * Write FASTA, from a range selection on the reverse strand.
+ * Variation is a deletion.
+ * test 396838 . tt t
+ */
+ @Test
+ public void testWriteRevFastaDeletion()
+ {
+ StringWriter writer = getWriter(false, 396835, 396845);
+
+ StringBuffer buff = new StringBuffer("> test.embl.gz 396835:396845 reverse\n");
+ buff.append("atacctaaaaa\n");
+ buff.append(">test.vcf.gz test.embl.gz 396835:396845 reverse\n");
+ buff.append("ataccta-aaa\n");
+ assertEquals("Export FASTA range ", writer.toString(), buff.toString());
+ }
+
+ /**
+ * Write FASTA, from a range selection on the forward strand.
+ * Variation is a insertion.
+ * test 366787 . t tT
+ */
+ @Test
+ public void testWriteFwdFastaInsertion()
+ {
+ StringWriter writer = getWriter(true, 366785, 366795);
+
+ StringBuffer buff = new StringBuffer("> test.embl.gz 366785:366795\n");
+ buff.append("tttcgcttttt\n");
+ buff.append(">test.vcf.gz test.embl.gz 366785:366795\n");
+ buff.append("tttTcgcttttt\n");
+ assertEquals("Export FASTA range ", writer.toString(), buff.toString());
+ }
+
+ /**
+ * Write FASTA, from a range selection on the reverse strand.
+ * Variation is a insertion.
+ * test 366787 . t tT
+ */
+ @Test
+ public void testWriteRevFastaInsertion()
+ {
+ StringWriter writer = getWriter(false, 366785, 366795);
+
+ StringBuffer buff = new StringBuffer("> test.embl.gz 366785:366795 reverse\n");
+ buff.append("aaaaagcgaaa\n");
+ buff.append(">test.vcf.gz test.embl.gz 366785:366795 reverse\n");
+ buff.append("aaaaagcgaaaa\n");
+ assertEquals("Export FASTA range ", writer.toString(), buff.toString());
+ }
+
+
+ /**
+ * Write FASTA, from a range selection on the forward strand.
+ * Variation is a multiple allele, (PL number indicates either G or T):
+ * test 361978 . G T 77.76842 . DP=11;AF1=0.95;CI95=0.5,1;DP4=1,0,10,0;MQ=58;PV4=1,9.6e-06,0.37,1 PL:DP:SP:GT:GQ 106,0,0:11:0:1/1:10
+ */
+ @Test
+ public void testWriteFwdFastaMultipleAllele()
+ {
+ StringWriter writer = getWriter(true, 361975, 361985);
+
+ StringBuffer buff = new StringBuffer("> test.embl.gz 361975:361985\n");
+ buff.append("actgaaaaatt\n");
+ buff.append(">test.vcf.gz test.embl.gz 361975:361985\n");
+ buff.append("actkaaaaatt\n");
+ assertEquals("Export FASTA range ", writer.toString(), buff.toString());
+ }
+
+
+ /**
+ * G
+ * @param isFwd
+ * @param start
+ * @param end
+ * @return
+ */
+ private StringWriter getWriter(boolean isFwd, int start, int end)
+ {
+ StringWriter writer = new StringWriter();
+ Selection selection = new Selection(null);
+
+ FeatureVector features = vcfView.getEntryGroup().getAllFeatures();
+ Feature feature = null;
+ for(int i=0; i<features.size(); i++)
+ {
+ if(features.elementAt(i).isForwardFeature() && isFwd)
+ {
+ feature = features.elementAt(i);
+ break;
+ }
+ else if(!features.elementAt(i).isForwardFeature() && !isFwd)
+ {
+ feature = features.elementAt(i);
+
+ int length = vcfView.getEntryGroup().getSequenceEntry().getBases().getLength();
+ int tmp = start;
+ start = length - end + 1;
+ end = length - tmp + 1;
+
+ break;
+ }
+ }
+
+ try
+ {
+ selection.setMarkerRange(new MarkerRange(feature.getStrand(), start, end));
+ }
+ catch(uk.ac.sanger.artemis.util.OutOfRangeException e)
+ {
+ e.printStackTrace();
+ }
+ IOUtils.exportFastaByRange(vcfView, selection, false, writer);
+ return writer;
+ }
+
+
+ /**
+ * Open a flat file and create the components in the TransferAnnotaionTool
+ * used to control the transfer of annotation.
+ */
+ @Before
+ public void setup()
+ {
+ final URL ref = WriteVCFTest.class.getResource("/data/test.embl.gz");
+ final URL vcf = WriteVCFTest.class.getResource("/data/test.vcf.gz");
+
+ List<String> vcfFileList = new Vector<String>();
+ vcfFileList.add(vcf.getFile());
+ JFrame f = new JFrame();
+ vcfView = new VCFview(f, (JPanel) f.getContentPane(),
+ vcfFileList,
+ 5000, 100000000, null,
+ ref.getFile(), null);
+ f.setVisible(false);
+ }
+
+}
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