From 2f5ec5b2d34b61e807dc17bb8421b5e62e853800 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 17 Feb 2011 16:23:15 +0000
Subject: [PATCH] add option to view VCF sequence
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15555 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/variant/VCFview.java | 20 +++++++++++++++----
1 file changed, 16 insertions(+), 4 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index e218b20b5..289ca3e50 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -497,10 +497,10 @@ public class VCFview extends JPanel
popup.addSeparator();
- final JMenu export = new JMenu("Export");
+ final JMenu export = new JMenu("Export / View");
popup.add(export);
- final JMenuItem exportVCF = new JMenuItem("Filtered VCF");
+ final JMenuItem exportVCF = new JMenuItem("Write Filtered VCF");
exportVCF.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent e)
{
@@ -511,18 +511,30 @@ public class VCFview extends JPanel
});
export.add(exportVCF);
- final JMenuItem exportFastaSelected = new JMenuItem("FASTA of selected feature(s)");
+ final JMenuItem exportFastaSelected = new JMenuItem("Write FASTA of selected feature(s)");
exportFastaSelected.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent e)
{
VCFview.this.setCursor(new Cursor(Cursor.WAIT_CURSOR));
IOUtils.exportFasta(entryGroup, vcfReaders, chr, VCFview.this, vcf_v4,
- selection.getAllFeatures());
+ selection.getAllFeatures(), false);
VCFview.this.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
}
});
export.add(exportFastaSelected);
+ final JMenuItem viewFastaSelected = new JMenuItem("View FASTA of selected feature(s)");
+ viewFastaSelected.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent e)
+ {
+ VCFview.this.setCursor(new Cursor(Cursor.WAIT_CURSOR));
+ IOUtils.exportFasta(entryGroup, vcfReaders, chr, VCFview.this, vcf_v4,
+ selection.getAllFeatures(), true);
+ VCFview.this.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
+ }
+ });
+ export.add(viewFastaSelected);
+
final JMenuItem exportFasta = new JMenuItem("FASTA");
exportFasta.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent e)
--
GitLab