diff --git a/uk/ac/sanger/artemis/components/EntryEdit.java b/uk/ac/sanger/artemis/components/EntryEdit.java
index 9ecfae72a5f9876bc50ac18dd9f71f2d59ba2e1f..c22d76a8b5f6ef928f876ba23fba56b9e34a37af 100644
--- a/uk/ac/sanger/artemis/components/EntryEdit.java
+++ b/uk/ac/sanger/artemis/components/EntryEdit.java
@@ -34,6 +34,7 @@ import uk.ac.sanger.artemis.components.alignment.FileSelectionDialog;
import uk.ac.sanger.artemis.components.alignment.LookSeqPanel;
import uk.ac.sanger.artemis.components.filetree.FileList;
import uk.ac.sanger.artemis.components.filetree.FileManager;
+import uk.ac.sanger.artemis.components.variant.VCFview;
import uk.ac.sanger.artemis.editor.BigPane;
import uk.ac.sanger.artemis.editor.FastaTextPane;
import uk.ac.sanger.artemis.editor.HitInfo;
@@ -112,8 +113,10 @@ public class EntryEdit extends JFrame
/** Alignment panel */
private BamView jamView;
- private JPanel jamPanel;
+ private JPanel bamPanel;
+ private JPanel vcfPanel;
private JSplitPane lowerSplitPane;
+ private JSplitPane ngSplitPane;
/**
* The EntrySourceVector reference that is created in the constructor.
@@ -233,20 +236,27 @@ public class EntryEdit extends JFrame
base_plot_group =
new BasePlotGroup(getEntryGroup(), this, getSelection(),
getGotoEventSource());
- //box_panel.add(base_plot_group);
- jamPanel = new JPanel();
+ bamPanel = new JPanel();
+ vcfPanel = new JPanel();
+ ngSplitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT,
+ bamPanel, vcfPanel);
+ ngSplitPane.setBorder(null);
+ ngSplitPane.setResizeWeight(0.5);
+ ngSplitPane.setDividerLocation(1);
+ Dimension minimumSize = new Dimension(0, 0);
+ bamPanel.setMinimumSize(minimumSize);
+ vcfPanel.setMinimumSize(minimumSize);
+
+
lowerSplitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT,
- jamPanel, mainPanel);
+ ngSplitPane, mainPanel);
lowerSplitPane.setResizeWeight(0.);
lowerSplitPane.setDividerSize(0);
lowerSplitPane.setDividerLocation(0);
-
- //lowerSplitPane.setBorder(null);
-
+
final JSplitPane splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT,
base_plot_group, lowerSplitPane);
-
splitPane.setDividerSize(0);
splitPane.setResizeWeight(0.);
splitPane.setBorder(null);
@@ -274,7 +284,7 @@ public class EntryEdit extends JFrame
getGotoEventSource(), base_plot_group);
// read alignment panel
- //main_box_panel.add(jamPanel);
+ //main_box_panel.add(bamPanel);
one_line_per_entry_display.setShowLabels(false);
one_line_per_entry_display.setOneLinePerEntry(true);
@@ -530,15 +540,20 @@ public class EntryEdit extends JFrame
return base_plot_group;
}
- protected JPanel getJamPanel()
+ protected JPanel getBamPanel()
{
- return jamPanel;
+ return bamPanel;
}
protected JPanel getJamView()
{
return jamView;
}
+
+ protected JPanel getVcfPanel()
+ {
+ return vcfPanel;
+ }
/**
@@ -1245,50 +1260,94 @@ public class EntryEdit extends JFrame
file_menu.addSeparator();
- JMenuItem read_bam_file = new JMenuItem("Read BAM ...");
+ JMenuItem read_bam_file = new JMenuItem("Read BAM / VCF ...");
read_bam_file.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
FileSelectionDialog fileChooser = new FileSelectionDialog(
- null, false, "BamView", "BAM");
- List<String> listBams = fileChooser.getBamFiles();
+ null, false, "BAM / VCF View", "BAM / VCF");
- jamPanel.removeAll();
+ List<String> listBams = fileChooser.getFiles(".*\\.bam$");
+ logger4j.debug("No. BAM FILES="+listBams.size());
- try
+ if(listBams.size() > 0)
{
- jamView = new BamView(listBams, null, 2000);
+ bamPanel.removeAll();
+ try
+ {
+ jamView = new BamView(listBams, null, 2000);
+ }
+ catch (Exception ex)
+ {
+ JOptionPane.showMessageDialog(null, ex.getMessage(), "Error",
+ JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+
+ jamView.setShowScale(false);
+ jamView.setBases(getEntryGroup().getBases());
+ jamView.addJamToPanel(bamPanel, null, true, feature_display);
+ jamView.getJspView().setHorizontalScrollBarPolicy(
+ JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+ jamView.removeBorder();
+ jamView.setDisplay(feature_display.getFirstVisibleForwardBase(),
+ feature_display.getLastVisibleForwardBase(), null);
+ bamPanel.revalidate();
+ jamView.getJspView().getVerticalScrollBar().setValue(
+ jamView.getJspView().getVerticalScrollBar().getMaximum());
+ feature_display.addDisplayAdjustmentListener(jamView);
+ feature_display.getSelection().addSelectionChangeListener(jamView);
+
+ lowerSplitPane.setDividerSize(3);
+ lowerSplitPane.setDividerLocation(0.35d);
+
+ if(vcfPanel.getComponents().length > 0)
+ {
+ ngSplitPane.setResizeWeight(0.5);
+ ngSplitPane.setDividerSize(3);
+ ngSplitPane.setDividerLocation(0.5);
+ }
+ else
+ {
+ ngSplitPane.setResizeWeight(1);
+ ngSplitPane.setDividerSize(1);
+ ngSplitPane.setDividerLocation(1.d);
+ }
}
- catch(Exception ex)
+
+ List<String> vcfFiles = fileChooser.getFiles(".*\\.vcf(\\.gz)*$");
+ logger4j.debug("No. VCF FILES="+vcfFiles.size());
+ if (vcfFiles.size() > 0)
{
- JOptionPane.showMessageDialog(null,
- ex.getMessage(),
- "Error",
- JOptionPane.ERROR_MESSAGE);
- return;
+ vcfPanel.removeAll();
+ VCFview vcfView = new VCFview(null, vcfPanel, vcfFiles,
+ feature_display.getMaxVisibleBases(), 1, null, null,
+ feature_display);
+
+ feature_display.addDisplayAdjustmentListener(vcfView);
+
+ lowerSplitPane.setDividerSize(3);
+ lowerSplitPane.setDividerLocation(0.35d);
+
+ if(bamPanel.getComponents().length > 0)
+ {
+ ngSplitPane.setResizeWeight(0.5);
+ ngSplitPane.setDividerSize(3);
+ ngSplitPane.setDividerLocation(0.5);
+ }
+ else
+ {
+ ngSplitPane.setResizeWeight(0);
+ ngSplitPane.setDividerSize(0);
+ ngSplitPane.setDividerLocation(0.);
+ }
}
-
- jamView.setShowScale(false);
- jamView.setBases(getEntryGroup().getBases());
- jamView.addJamToPanel(jamPanel, null, true, feature_display);
- jamView.getJspView().setHorizontalScrollBarPolicy(
- JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
- jamView.removeBorder();
- jamView.setDisplay(feature_display.getFirstVisibleForwardBase(),
- feature_display.getLastVisibleForwardBase(), null);
- jamPanel.revalidate();
- jamView.getJspView().getVerticalScrollBar().setValue(
- jamView.getJspView().getVerticalScrollBar().getMaximum());
- feature_display.addDisplayAdjustmentListener(jamView);
- feature_display.getSelection().addSelectionChangeListener(jamView);
-
- lowerSplitPane.setDividerSize(3);
- lowerSplitPane.setDividerLocation(0.35d);
}
});
file_menu.add(read_bam_file);
-
+
+
file_menu.addSeparator();
final JMenuItem save_default =
diff --git a/uk/ac/sanger/artemis/components/MultiComparator.java b/uk/ac/sanger/artemis/components/MultiComparator.java
index d29924d36dc32a05a3aa31b97952ce61411e17bb..29294c11e6ce2b89c64e69ddc6da8c0e90dde6e9 100644
--- a/uk/ac/sanger/artemis/components/MultiComparator.java
+++ b/uk/ac/sanger/artemis/components/MultiComparator.java
@@ -949,7 +949,7 @@ public class MultiComparator extends JFrame
{
FileSelectionDialog fileChooser = new FileSelectionDialog(
null, false, "BamView", "BAM");
- List<String> listBams = fileChooser.getBamFiles();
+ List<String> listBams = fileChooser.getFiles(".*\\.bam$");
thisBamPanel.removeAll();
thisBamPanel.setVisible(true);
diff --git a/uk/ac/sanger/artemis/components/PrintArtemis.java b/uk/ac/sanger/artemis/components/PrintArtemis.java
index be57b8e3f4feacc3bd5830832b9063c9fc00fa61..80de655eefc4095bea72ca372e50c3d5d92720b8 100644
--- a/uk/ac/sanger/artemis/components/PrintArtemis.java
+++ b/uk/ac/sanger/artemis/components/PrintArtemis.java
@@ -96,8 +96,8 @@ public class PrintArtemis extends ScrollPanel implements Printable
if(jamDisplay.isSelected() && entry.getJamView() != null && entry.getJamView().isVisible())
{
- entry.getJamPanel().paintComponents(g2d);
- g2d.translate(0,entry.getJamPanel().getHeight());
+ entry.getBamPanel().paintComponents(g2d);
+ g2d.translate(0,entry.getBamPanel().getHeight());
}
// one line per entry
@@ -152,7 +152,7 @@ public class PrintArtemis extends ScrollPanel implements Printable
if(jamDisplay.isSelected() &&
entry.getJamView() != null && entry.getJamView().isVisible())
- height += entry.getJamPanel().getHeight();
+ height += entry.getBamPanel().getHeight();
if(plotsDisplay.isSelected())
height += entry.getBasePlotGroup().getHeight();
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 82a69a6806e7de1bec4cb2aaedcfb675f7d15c37..9fe224ea57bb1fc1ad83a19f1c647631de5d6d8d 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -2026,10 +2026,10 @@ public class BamView extends JPanel
{
FileSelectionDialog bamFileSelection = new FileSelectionDialog(
null, false, "BamView", "BAM");
- List<String> bamFiles = bamFileSelection.getBamFiles();
+ List<String> bamFiles = bamFileSelection.getFiles(".*\\.bam$");
int count = bamList.size();
- bamList.addAll(bamFileSelection.getBamFiles());
+ bamList.addAll(bamFileSelection.getFiles(".*\\.bam$"));
for(int i=0; i<bamFiles.size(); i++)
addToViewMenu(i+count);
@@ -2925,13 +2925,16 @@ public class BamView extends JPanel
System.setProperty("default_directory", System.getProperty("user.dir"));
FileSelectionDialog fileSelection = new FileSelectionDialog(
null, true, "BamView", "BAM");
- bam = fileSelection.getBamFiles();
+ bam = fileSelection.getFiles(".*\\.bam$");
reference = fileSelection.getReferenceFile();
if(reference == null || reference.equals(""))
reference = null;
if(bam == null || bam.size() < 1)
+ {
+ System.err.println("No files found.");
System.exit(0);
+ }
}
else if(!args[0].startsWith("-"))
{
diff --git a/uk/ac/sanger/artemis/components/alignment/FileSelectionDialog.java b/uk/ac/sanger/artemis/components/alignment/FileSelectionDialog.java
index ccf7efe7baec57712779928fc1d42cfba680b84c..288039d183f1dfcf4ea867468494d7b04bddd4e7 100644
--- a/uk/ac/sanger/artemis/components/alignment/FileSelectionDialog.java
+++ b/uk/ac/sanger/artemis/components/alignment/FileSelectionDialog.java
@@ -19,6 +19,8 @@ import java.io.Reader;
import java.net.URL;
import java.util.List;
import java.util.Vector;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
import javax.swing.JButton;
import javax.swing.JDialog;
@@ -254,27 +256,38 @@ public class FileSelectionDialog extends JDialog
}
/**
- * Get the BAM files as a <code>List</code> of <code>String</code>'s.
+ * Get the BAM or VCF files as a <code>List</code> of <code>String</code>'s.
* @return
*/
- public List<String> getBamFiles()
+ public List<String> getFiles(String patternStr)
{
- List<String> bamFiles = new Vector<String>();
+ Pattern p = Pattern.compile(patternStr);
+
+ List<String> files = new Vector<String>();
for(int i=0; i<bamFields.size(); i++)
{
String file = bamFields.get(i).getText();
-
if(file != null && !file.equals(""))
{
if(isListOfFiles(file))
{
- bamFiles.addAll(getListOfFiles(file));
+ List<String> filesInList = getListOfFiles(file);
+ for(int j=0; j<filesInList.size(); j++)
+ {
+ Matcher m = p.matcher(filesInList.get(j));
+ if(m.matches())
+ files.add(filesInList.get(j));
+ }
}
else
- bamFiles.add(file);
+ {
+ Matcher m = p.matcher(file);
+ if(m.matches())
+ files.add(file);
+ }
}
}
- return bamFiles;
+ return files;
}
/**
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index 984064f3468f6e8f7d2c73abe84ae1b2f2f11eb8..317a9229cf0038e50eefc32284182bed07988984 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -27,6 +27,7 @@ import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
+import java.awt.FlowLayout;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Insets;
@@ -49,6 +50,7 @@ import java.util.Vector;
import javax.swing.JButton;
import javax.swing.JComboBox;
+import javax.swing.JComponent;
import javax.swing.JFrame;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
@@ -57,6 +59,8 @@ import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JScrollBar;
import javax.swing.JScrollPane;
+import javax.swing.border.Border;
+import javax.swing.border.EmptyBorder;
import net.sf.samtools.util.BlockCompressedInputStream;
@@ -65,8 +69,13 @@ import org.apache.log4j.Level;
import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.EntryGroup;
import uk.ac.sanger.artemis.Options;
+import uk.ac.sanger.artemis.SelectionChangeEvent;
+import uk.ac.sanger.artemis.SelectionChangeListener;
import uk.ac.sanger.artemis.SimpleEntryGroup;
+import uk.ac.sanger.artemis.components.DisplayAdjustmentEvent;
+import uk.ac.sanger.artemis.components.DisplayAdjustmentListener;
import uk.ac.sanger.artemis.components.EntryFileDialog;
+import uk.ac.sanger.artemis.components.FeatureDisplay;
import uk.ac.sanger.artemis.components.FileViewer;
import uk.ac.sanger.artemis.components.MessageDialog;
import uk.ac.sanger.artemis.components.alignment.FileSelectionDialog;
@@ -86,42 +95,50 @@ import uk.ac.sanger.artemis.util.OutOfRangeException;
public class VCFview extends JPanel
+ implements DisplayAdjustmentListener, SelectionChangeListener
{
private static final long serialVersionUID = 1L;
private JScrollBar scrollBar;
+ private JPanel vcfPanel;
private TabixReader tr[];
private String header[];
+ private FeatureDisplay feature_display;
private int nbasesInView;
private int seqLength;
private String chr;
private String mouseOverVCFline;
private int mouseOverIndex = -1;
private JPopupMenu popup;
- private int LINE_HEIGHT = 25;
+ private int LINE_HEIGHT = 20;
- public VCFview(final JFrame frame,
+ public VCFview(final JFrame frame,
+ final JPanel vcfPanel,
final List<String> vcfFiles,
final int nbasesInView,
final int seqLength,
final String chr,
- final String reference)
+ final String reference,
+ final FeatureDisplay feature_display)
{
super();
this.nbasesInView = nbasesInView;
this.seqLength = seqLength;
this.chr = chr;
+ this.feature_display = feature_display;
+ this.vcfPanel = vcfPanel;
setBackground(Color.white);
- setPreferredSize(new Dimension(900, vcfFiles.size()*(LINE_HEIGHT+5)));
MultiLineToolTipUI.initialize();
setToolTipText("");
+ vcfPanel.setPreferredSize(new Dimension(900, vcfFiles.size()*(LINE_HEIGHT+5)));
- if(reference != null)
- {
- EntryGroup entryGroup = getReference(reference);
- this.seqLength = entryGroup.getSequenceEntry().getBases().getLength();
- }
+ if(feature_display != null)
+ this.seqLength = feature_display.getBases().getLength();
+ else if(reference != null)
+ this.seqLength = getReference(reference).getSequenceEntry().getBases().getLength();
+
+
try
{
@@ -136,7 +153,6 @@ public class VCFview extends JPanel
}
catch (IOException e)
{
- // TODO Auto-generated catch block
e.printStackTrace();
}
@@ -144,7 +160,8 @@ public class VCFview extends JPanel
JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
- frame.getContentPane().add(jspView, BorderLayout.CENTER);
+ vcfPanel.setLayout(new BorderLayout());
+ vcfPanel.add(jspView, BorderLayout.CENTER);
if(this.nbasesInView > this.seqLength)
this.nbasesInView = this.seqLength/2;
@@ -177,9 +194,32 @@ public class VCFview extends JPanel
addMouseListener(new PopupListener());
//
- //
- JMenuBar topPanel = new JMenuBar();
- frame.setJMenuBar((JMenuBar)topPanel);
+ createMenus(frame);
+ setDisplay();
+
+ if(feature_display == null)
+ {
+ vcfPanel.add(scrollBar, BorderLayout.SOUTH);
+ frame.pack();
+ frame.setVisible(true);
+ }
+ else
+ {
+ Border empty = new EmptyBorder(0,0,0,0);
+ jspView.setBorder(empty);
+ }
+ }
+
+ private void createMenus(JFrame frame)
+ {
+ JComponent topPanel;
+ if(feature_display != null)
+ topPanel = new JPanel(new FlowLayout(FlowLayout.LEADING, 0, 0));
+ else
+ {
+ topPanel = new JMenuBar();
+ frame.setJMenuBar((JMenuBar)topPanel);
+ }
JMenu fileMenu = new JMenu("File");
topPanel.add(fileMenu);
@@ -223,7 +263,6 @@ public class VCFview extends JPanel
}
});
-
JButton zoomIn = new JButton("-");
Insets ins = new Insets(1,1,1,1);
zoomIn.setMargin(ins);
@@ -248,7 +287,6 @@ public class VCFview extends JPanel
topPanel.add(zoomOut);
final JComboBox combo = new JComboBox(tr[0].getmSeq());
-
if(chr == null)
this.chr = tr[0].getmSeq()[0];
combo.setSelectedItem(this.chr);
@@ -264,10 +302,6 @@ public class VCFview extends JPanel
}
});
topPanel.add(combo);
-
- frame.getContentPane().add(scrollBar, BorderLayout.SOUTH);
- frame.pack();
- frame.setVisible(true);
}
private static EntryGroup getReference(String reference)
@@ -381,17 +415,17 @@ public class VCFview extends JPanel
protected void paintComponent(Graphics g)
{
super.paintComponent(g);
-
mouseOverVCFline = null;
float pixPerBase = getPixPerBaseByWidth();
String s;
- int start = scrollBar.getValue();
+ int start = getBaseAtStartOfView();
int end = start+nbasesInView;
String region = chr+":"+start+"-"+end;
- drawScale((Graphics2D)g, start, end, pixPerBase, getHeight());
+ //if(feature_display == null)
+ drawScale((Graphics2D)g, start, end, pixPerBase, getHeight());
// a region is specified; random access
for (int i = 0; i < tr.length; i++)
{
@@ -413,6 +447,14 @@ public class VCFview extends JPanel
}
}
+ protected int getBaseAtStartOfView()
+ {
+ if(feature_display != null)
+ return feature_display.getForwardBaseAtLeftEdge();
+ else
+ return scrollBar.getValue();
+ }
+
private void drawVariantCall(Graphics g, String line, int start, int index, float pixPerBase)
{
String parts[] = line.split("\\t");
@@ -437,8 +479,7 @@ public class VCFview extends JPanel
String parts[] = line.split("\\t");
int pos[] = new int[2];
pos[0] = Math.round((Integer.parseInt(parts[1]) - start)*pixPerBase);
- pos[1] = getHeight() - 15 - (vcfFileIndex*(LINE_HEIGHT+5));
-
+ pos[1] = getHeight() - 15 - (vcfFileIndex*(LINE_HEIGHT+5));
return pos;
}
@@ -446,7 +487,7 @@ public class VCFview extends JPanel
{
float pixPerBase = getPixPerBaseByWidth();
String s;
- int start = scrollBar.getValue();
+ int start = getBaseAtStartOfView();
int end = start+nbasesInView;
String region = chr+":"+start+"-"+end;
@@ -618,7 +659,7 @@ public class VCFview extends JPanel
private float getPixPerBaseByWidth()
{
- return (float)getWidth() / (float)nbasesInView;
+ return (float)vcfPanel.getWidth() / (float)nbasesInView;
}
/**
@@ -698,6 +739,25 @@ public class VCFview extends JPanel
}
}
+ private void setDisplay()
+ {
+ Dimension d = new Dimension();
+ d.setSize(nbasesInView*getPixPerBaseByWidth(), tr.length*(LINE_HEIGHT+5));
+ setPreferredSize(d);
+ }
+
+ public void displayAdjustmentValueChanged(DisplayAdjustmentEvent event)
+ {
+ nbasesInView = feature_display.getMaxVisibleBases();
+ setDisplay();
+ repaint();
+ }
+
+ public void selectionChanged(SelectionChangeEvent event)
+ {
+
+ }
+
public static void main(String args[])
{
List<String> vcfFileList = new Vector<String>();
@@ -707,7 +767,7 @@ public class VCFview extends JPanel
System.setProperty("default_directory", System.getProperty("user.dir"));
FileSelectionDialog fileSelection = new FileSelectionDialog(
null, true, "VCFview", "VCF");
- vcfFileList = fileSelection.getBamFiles();
+ vcfFileList = fileSelection.getFiles(".vcf");
reference = fileSelection.getReferenceFile();
if(reference.equals(""))
reference = null;
@@ -766,7 +826,8 @@ public class VCFview extends JPanel
else
{
JFrame f = new JFrame();
- new VCFview(f, vcfFileList, nbasesInView, 100000000, null, reference);
+ new VCFview(f, (JPanel) f.getContentPane(), vcfFileList,
+ nbasesInView, 100000000, null, reference, null);
}
}
}
\ No newline at end of file