diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java
index dace8e28bdbd2be77471e10c96245223f1892b12..aba86072966c2d5117a00c264cee6a95fb884d56 100644
--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
+++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
@@ -213,24 +213,14 @@ class IOUtils
else
buffSeq = new StringBuffer();
+ String basesStr = entryGroup.getBases().getSubSequence(marker.getRange(), direction);
+ writeOrView(null, name, sbeg, send, marker, writer, basesStr, buffSeq);
for (int i = 0; i < vcfReaders.length; i++)
{
- String basesStr = entryGroup.getBases().getSubSequence(marker.getRange(), direction);
+ basesStr = entryGroup.getBases().getSubSequence(marker.getRange(), direction);
basesStr = getAllBasesInRegion(vcfReaders[i], sbeg, send, basesStr,
features, vcfView, marker.isForwardMarker());
-
- StringBuffer header = new StringBuffer(name+" ");
- header.append(sbeg+":"+send+ (marker.isForwardMarker() ? "" : " reverse"));
- header.append(" (").append(vcfReaders[i].getName()).append(")");
-
- if(view) // sequence viewer
- {
- buffSeq.append(">").append(header.toString()).append("\n");
- wrapString(basesStr, buffSeq);
- buffSeq.append("\n");
- }
- else // write to file
- writeSequence(writer, header.toString(), basesStr);
+ writeOrView(vcfReaders[i], name, sbeg, send, marker, writer, basesStr, buffSeq);
}
if(writer != null)
@@ -260,7 +250,8 @@ class IOUtils
*/
protected static void exportFasta(final VCFview vcfView,
final FeatureVector features,
- final boolean view)
+ final boolean view,
+ final EntryGroup entryGroup)
{
if(features.size () < 1)
{
@@ -285,17 +276,20 @@ class IOUtils
AbstractVCFReader vcfReaders[] = vcfView.getVcfReaders();
JCheckBox single = new JCheckBox("Single FASTA", true);
- JCheckBox combine = new JCheckBox("Combine feature sequences", true);
+ JCheckBox combineFeats = new JCheckBox("Combine feature sequences", true);
Box yBox = Box.createVerticalBox();
if(!view && vcfReaders.length > 1)
yBox.add(single);
- yBox.add(combine);
-
+ yBox.add(combineFeats);
+ String name = entryGroup.getActiveEntries().elementAt(0).getName();
try
{
if(!view)
{
- File f = getFile(vcfReaders[0].getFileName(), 1, suffix, yBox);
+ File newfile = new File(
+ getBaseDirectoryFromEntry(entryGroup.getActiveEntries().elementAt(0)),
+ name);
+ File f = getFile(newfile.getAbsolutePath(), 1, suffix, yBox);
if(f == null)
return;
writer = new FileWriter(f);
@@ -304,16 +298,34 @@ class IOUtils
else
JOptionPane.showMessageDialog(null, yBox, "View Option(s)", JOptionPane.INFORMATION_MESSAGE);
+ // reference sequence
+ StringBuffer buff = new StringBuffer();
+ for (int j = 0; j < features.size() && (!view || j < MAXIMUM_SELECTED_FEATURES); j++)
+ {
+ Feature f = features.elementAt(j);
+ buff.append( f.getBases() );
+ if(!combineFeats.isSelected())
+ {
+ writeOrView(null, f, writer, buff, "");
+ buff = new StringBuffer();
+ }
+ }
+ if(combineFeats.isSelected())
+ writeOrView(null, null, writer, buff, name);
+ if(writer != null && !single.isSelected())
+ writer.close();
+
+ //
for (int i = 0; i < vcfReaders.length; i++)
{
- if(!view && i > 0 && !single.isSelected())
+ if(!view && !single.isSelected())
{
File f = getFile(vcfReaders[i].getFileName(), vcfReaders.length, suffix, null);
writer = new FileWriter(f);
fastaFiles += f.getAbsolutePath()+"\n";
}
-
- StringBuffer buff = new StringBuffer();
+ buff = new StringBuffer();
+
for (int j = 0; j < features.size() && (!view || j < MAXIMUM_SELECTED_FEATURES); j++)
{
Feature f = features.elementAt(j);
@@ -328,15 +340,15 @@ class IOUtils
features, vcfView, f.isForwardFeature()) );
}
- if(!combine.isSelected())
+ if(!combineFeats.isSelected())
{
- writeOrView(vcfReaders[i], f, writer, buff);
+ writeOrView(vcfReaders[i], f, writer, buff, "");
buff = new StringBuffer();
}
}
- if(combine.isSelected())
- writeOrView(vcfReaders[i], null, writer, buff);
+ if(combineFeats.isSelected())
+ writeOrView(vcfReaders[i], null, writer, buff, "");
if(writer != null && !single.isSelected())
writer.close();
@@ -354,6 +366,26 @@ class IOUtils
new MessageDialog (null, "Saved Files", fastaFiles, false);
}
+ private static void writeOrView(AbstractVCFReader reader,
+ String seqName, int sbeg, int send, MarkerRange marker,
+ FileWriter writer, String basesStr, StringBuffer buff) throws IOException
+ {
+ StringBuffer header = new StringBuffer();
+ if(reader != null)
+ header.append(reader.getName());
+ header.append(" ").append(seqName).append(" ");
+ header.append(sbeg).append(":").append(send);
+ header.append((marker.isForwardMarker() ? "" : " reverse"));
+
+ if(writer == null) // sequence viewer
+ {
+ buff.append(">").append(header.toString()).append("\n");
+ wrapString(basesStr, buff);
+ }
+ else // write to file
+ writeSequence(writer, header.toString(), basesStr);
+ }
+
/**
* Construct a header and write or view the sequence.
* @param reader
@@ -363,11 +395,12 @@ class IOUtils
* @throws IOException
*/
private static void writeOrView(AbstractVCFReader reader, Feature f,
- FileWriter writer, StringBuffer buff)
+ FileWriter writer, StringBuffer buff, String hdr)
throws IOException
{
- StringBuffer header = new StringBuffer();
- header.append(reader.getName()).append(" ");
+ StringBuffer header = new StringBuffer(hdr);
+ if(reader != null)
+ header.append(reader.getName()).append(" ");
if(f != null)
{
header.append(f.getSystematicName()).append(" ");
@@ -381,7 +414,7 @@ class IOUtils
{
SequenceViewer viewer =
new SequenceViewer ("Feature base viewer for feature(s)", false);
- viewer.setSequence(header.toString(), buff.toString());
+ viewer.setSequence(">"+header.toString(), buff.toString());
}
else // write to file
writeSequence(writer, header.toString(), buff.toString());
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index 8c1c03d94c10e3a7aebb4e8be0657096c675064c..ea811ab7b49157fb0b05b74d2a7c27de87e02270 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -537,7 +537,7 @@ public class VCFview extends JPanel
public void actionPerformed(ActionEvent e)
{
VCFview.this.setCursor(new Cursor(Cursor.WAIT_CURSOR));
- IOUtils.exportFasta(VCFview.this, selection.getAllFeatures(), false);
+ IOUtils.exportFasta(VCFview.this, selection.getAllFeatures(), false, entryGroup);
VCFview.this.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
}
});
@@ -561,7 +561,7 @@ public class VCFview extends JPanel
public void actionPerformed(ActionEvent e)
{
VCFview.this.setCursor(new Cursor(Cursor.WAIT_CURSOR));
- IOUtils.exportFasta(VCFview.this, selection.getAllFeatures(), true);
+ IOUtils.exportFasta(VCFview.this, selection.getAllFeatures(), true, entryGroup);
VCFview.this.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
}
});