diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java
index e62ac259a4c3a97bec4d0a772fc92523fc52bcee..d88ff3093f6768c7d38eed879001326746041113 100644
--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
+++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
@@ -30,7 +30,6 @@ import java.io.IOException;
import java.io.InputStream;
import java.io.Writer;
import java.net.URL;
-import java.util.Comparator;
import java.util.List;
import java.util.Vector;
@@ -38,12 +37,7 @@ import javax.swing.Box;
import javax.swing.JCheckBox;
import javax.swing.JComponent;
import javax.swing.JFileChooser;
-import javax.swing.JFrame;
import javax.swing.JOptionPane;
-import javax.swing.JScrollPane;
-import javax.swing.JTable;
-import javax.swing.table.TableModel;
-import javax.swing.table.TableRowSorter;
import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.EntryGroup;
@@ -59,7 +53,6 @@ import uk.ac.sanger.artemis.components.FileViewer;
import uk.ac.sanger.artemis.components.MessageDialog;
import uk.ac.sanger.artemis.components.SequenceViewer;
import uk.ac.sanger.artemis.components.StickyFileChooser;
-import uk.ac.sanger.artemis.components.variant.BCFReader.BCFReaderIterator;
import uk.ac.sanger.artemis.io.DocumentEntry;
import uk.ac.sanger.artemis.io.EntryInformationException;
import uk.ac.sanger.artemis.io.Key;
@@ -635,6 +628,14 @@ class IOUtils
protected static void countVariants(final VCFview vcfView,
final FeatureVector features) throws IOException
{
+ if(features.size () < 1)
+ {
+ JOptionPane.showMessageDialog(null,
+ "No features selected.",
+ "Warning", JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
String[] columnNames = {
"VCF", "Name", "Variant", "Non-variant", "Deletion", "Insertion", "Synonymous", "Non-synonymous"};
Vector<String> columnData = new Vector<String>();
@@ -704,26 +705,10 @@ class IOUtils
rowData.add(thisRow);
}
}
-
- JTable variantData = new JTable(rowData, columnData);
- TableRowSorter<TableModel> sorter =
- new TableRowSorter<TableModel>(variantData.getModel());
- variantData.setRowSorter(sorter);
-
- Comparator<Integer> comparator = new Comparator<Integer>() {
- public int compare(Integer i1, Integer i2) {
- return i1.compareTo(i2);
- }
- };
-
+
+ TableViewer tab = new TableViewer(rowData, columnData, "Variant Overview");
for(int i=2; i< columnData.size(); i++)
- sorter.setComparator(i, comparator);
-
- JScrollPane jsp = new JScrollPane(variantData);
- JFrame f = new JFrame("Variant Overview");
- f.getContentPane().add(jsp);
- f.pack();
- f.setVisible(true);
+ tab.setIntegerRowSorter(i);
}
private static void count(VCFRecord record, int count[], FeatureVector features, AbstractVCFReader reader)
diff --git a/uk/ac/sanger/artemis/components/variant/TableViewer.java b/uk/ac/sanger/artemis/components/variant/TableViewer.java
new file mode 100644
index 0000000000000000000000000000000000000000..12a6b5918acc7e25ec4af63a0eb6cc553e14e488
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/variant/TableViewer.java
@@ -0,0 +1,153 @@
+/* TableViewer
+ *
+ * created: 2011
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2011 Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or(at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ *
+ */
+package uk.ac.sanger.artemis.components.variant;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.Comparator;
+import java.util.Vector;
+
+import javax.swing.Box;
+import javax.swing.JButton;
+import javax.swing.JFrame;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.table.TableModel;
+import javax.swing.table.TableRowSorter;
+
+import uk.ac.sanger.artemis.components.StickyFileChooser;
+
+
+class TableViewer extends JFrame
+{
+ private static final long serialVersionUID = 1L;
+ private Comparator<Integer> comparator = new Comparator<Integer>()
+ {
+ public int compare(Integer i1, Integer i2)
+ {
+ return i1.compareTo(i2);
+ }
+ };
+
+ private TableRowSorter<TableModel> sorter;
+
+ public TableViewer(final Vector<Vector<Object>> rowData, final Vector<String> columnData, String title)
+ {
+ super(title);
+ final JTable variantData = new JTable(rowData, columnData);
+ sorter = new TableRowSorter<TableModel>(variantData.getModel());
+ variantData.setRowSorter(sorter);
+
+ final JFrame f = new JFrame("Variant Overview");
+ final JScrollPane jsp = new JScrollPane(variantData);
+ final Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
+ jsp.setPreferredSize(new Dimension(screen.width/3, screen.height/3));
+ final JPanel overviewPane = new JPanel(new BorderLayout());
+ overviewPane.add(jsp, BorderLayout.CENTER);
+
+ final Box xBox = Box.createHorizontalBox();
+ xBox.add(Box.createHorizontalGlue());
+
+ final JButton save = new JButton("SAVE");
+ save.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ save(variantData, columnData);
+ }
+ });
+ xBox.add(save);
+
+ final JButton close = new JButton("CLOSE");
+ close.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ f.dispose();
+ }
+ });
+ xBox.add(close);
+ overviewPane.add(xBox, BorderLayout.SOUTH);
+ f.getContentPane().add(overviewPane);
+ f.pack();
+ f.setVisible(true);
+ }
+
+ public void setIntegerRowSorter(int colIndex)
+ {
+ sorter.setComparator(colIndex, comparator);
+ }
+
+ private void save(final JTable table, final Vector<String> columnData)
+ {
+ StickyFileChooser fc = new StickyFileChooser();
+ int status = fc.showSaveDialog(TableViewer.this);
+ if(status != StickyFileChooser.APPROVE_OPTION)
+ return;
+ try
+ {
+ File f = fc.getSelectedFile();
+ if(f.exists())
+ {
+ status = JOptionPane.showConfirmDialog(TableViewer.this,
+ f.getName()+" exists overwrite?", "Overwrite", JOptionPane.YES_NO_OPTION);
+ if(status != JOptionPane.YES_OPTION)
+ return;
+ }
+
+ FileWriter writer = new FileWriter(fc.getSelectedFile());
+ for(String col: columnData)
+ writer.write(col+"\t");
+ writer.write("\n");
+
+ int nrows = table.getRowCount();
+ int ncols = table.getColumnCount();
+ for(int i=0; i<nrows; i++)
+ {
+ for(int j=0; j<ncols; j++)
+ {
+ // use the sorted row index
+ int rowIndex = table.convertRowIndexToModel(i);
+ writer.write(table.getModel().getValueAt(rowIndex, j)+"\t");
+ }
+ writer.write("\n");
+ }
+
+ writer.close();
+ }
+ catch (IOException e1)
+ {
+ JOptionPane.showMessageDialog(TableViewer.this, e1.getMessage(),
+ "Problem Writing", JOptionPane.ERROR_MESSAGE);
+ }
+ }
+}
\ No newline at end of file