From c3fd9c03ee4e09e1b30f9c15ec5cbbf628075611 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 10 Feb 2011 15:39:01 +0000
Subject: [PATCH] add option to show non-variants and provide file selection
when exporting
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15486 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/variant/IOUtils.java | 33 ++++++++++++++++---
.../artemis/components/variant/VCFFilter.java | 11 +++++++
.../artemis/components/variant/VCFview.java | 22 +++++++++++--
3 files changed, 59 insertions(+), 7 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java
index 9b337790d..06843480c 100644
--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
+++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
@@ -23,6 +23,7 @@
*/
package uk.ac.sanger.artemis.components.variant;
+import java.io.File;
import java.io.FileInputStream;
import java.io.FileWriter;
import java.io.IOException;
@@ -30,12 +31,15 @@ import java.io.InputStream;
import java.net.URL;
import java.util.List;
+import javax.swing.JFileChooser;
+
import uk.ac.sanger.artemis.EntryGroup;
import uk.ac.sanger.artemis.Feature;
import uk.ac.sanger.artemis.FeatureEnumeration;
import uk.ac.sanger.artemis.FeatureKeyQualifierPredicate;
import uk.ac.sanger.artemis.FeatureVector;
import uk.ac.sanger.artemis.components.MessageDialog;
+import uk.ac.sanger.artemis.components.StickyFileChooser;
import uk.ac.sanger.artemis.io.Key;
import net.sf.samtools.util.BlockCompressedInputStream;
@@ -49,17 +53,18 @@ class IOUtils
* @param vcfView
* @param features
*/
- protected static void writeVCF(final String vcfFileName,
+ protected static File writeVCF(final String vcfFileName,
final VCFview vcfView,
final FeatureVector features)
{
try
{
- FileWriter writer = new FileWriter(vcfFileName+".filter");
+ File filterFile = getFile(vcfFileName);
+ FileWriter writer = new FileWriter(filterFile);
if(IOUtils.isBCF(vcfFileName))
{
BCFReader.writeVCF(writer, vcfFileName);
- return;
+ return filterFile;
}
TabixReader tr = new TabixReader(vcfFileName);
@@ -79,13 +84,31 @@ class IOUtils
writer.write(line+'\n');
}
writer.close();
+ return filterFile;
}
catch (IOException e)
{
e.printStackTrace();
+ return null;
}
}
+ private static File getFile(final String vcfFileName) throws IOException
+ {
+ final StickyFileChooser file_dialog = new StickyFileChooser();
+
+ file_dialog.setSelectedFile(new File(vcfFileName+".filter"));
+ file_dialog.setDialogTitle("Choose save file ...");
+ file_dialog.setDialogType(JFileChooser.SAVE_DIALOG);
+ final int status = file_dialog.showSaveDialog(null);
+
+ if(status != JFileChooser.APPROVE_OPTION ||
+ file_dialog.getSelectedFile() == null)
+ return null;
+
+ return file_dialog.getSelectedFile();
+ }
+
/**
* Export as a VCF based on the filtering applied in the VCFview.
* @param entryGroup
@@ -113,8 +136,8 @@ class IOUtils
String filterFiles = "";
for(int i=0; i<vcfFiles.size(); i++)
{
- IOUtils.writeVCF(vcfFiles.get(i), vcfView, features);
- filterFiles += vcfFiles.get(i)+".filter\n";
+ File filterFile = IOUtils.writeVCF(vcfFiles.get(i), vcfView, features);
+ filterFiles += filterFile.getAbsolutePath()+"\n";
}
new MessageDialog (null, "Saved Files", filterFiles, false);
diff --git a/uk/ac/sanger/artemis/components/variant/VCFFilter.java b/uk/ac/sanger/artemis/components/variant/VCFFilter.java
index 72e425edd..a418497c5 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFFilter.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFFilter.java
@@ -112,6 +112,17 @@ public class VCFFilter extends JFrame
}
});
+ c.gridy = c.gridy + 1;
+ final JCheckBox showNonVariantMenu = new JCheckBox("Non-Varaints", vcfView.showNonVariants);
+ panel.add(showNonVariantMenu, c);
+ showNonVariantMenu.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent e)
+ {
+ vcfView.showNonVariants = showNonVariantMenu.isSelected();
+ vcfView.repaint();
+ }
+ });
+
if(vcfView.getEntryGroup() == null || vcfView.getEntryGroup().getAllFeaturesCount() == 0)
{
showSyn.setEnabled(false);
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index 19cd88e48..4e4258521 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -144,6 +144,7 @@ public class VCFview extends JPanel
protected boolean showMultiAlleles = true;
// show variants that do not overlap CDS
protected boolean showNonOverlappings = true;
+ protected boolean showNonVariants = false;
private boolean markAsNewStop = false;
private JCheckBoxMenuItem markNewStops =
@@ -498,6 +499,9 @@ public class VCFview extends JPanel
popup.addSeparator();
+ final JMenu export = new JMenu("Export");
+ popup.add(export);
+
final JMenuItem exportVCF = new JMenuItem("Export filtered VCF");
exportVCF.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent e)
@@ -507,7 +511,18 @@ public class VCFview extends JPanel
VCFview.this.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
}
});
- popup.add(exportVCF);
+ export.add(exportVCF);
+
+ final JMenuItem exportFasta = new JMenuItem("Export FASTA");
+ exportFasta.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent e)
+ {
+ VCFview.this.setCursor(new Cursor(Cursor.WAIT_CURSOR));
+ //IOUtils.export(entryGroup, vcfFiles, VCFview.this);
+ VCFview.this.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
+ }
+ });
+
}
private static EntryGroup getReference(String reference)
@@ -954,7 +969,10 @@ public class VCFview extends JPanel
return false;
if(!showNonOverlappings && !isOverlappingFeature(features, basePosition))
- return false;
+ return false;
+
+ if(!showNonVariants && record.getAlt().equals("."))
+ return false;
short isSyn = -1;
markAsNewStop = false;
--
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