diff --git a/uk/ac/sanger/artemis/components/EntryEdit.java b/uk/ac/sanger/artemis/components/EntryEdit.java
index 9c422c8bfd4ad17d0f11d9c020621a699434b4ba..4507e41b11a730c2d561abd9c2f961a6a47e1fb3 100644
--- a/uk/ac/sanger/artemis/components/EntryEdit.java
+++ b/uk/ac/sanger/artemis/components/EntryEdit.java
@@ -1873,7 +1873,7 @@ public class EntryEdit extends JFrame
vcfPanel.removeAll();
vcfView = new VCFview(null, vcfPanel, vcfFiles,
feature_display.getMaxVisibleBases(), 1, null, null,
- feature_display);
+ this, feature_display);
feature_display.addDisplayAdjustmentListener(vcfView);
feature_display.getSelection().addSelectionChangeListener(vcfView);
diff --git a/uk/ac/sanger/artemis/components/MultiComparator.java b/uk/ac/sanger/artemis/components/MultiComparator.java
index 751605414e3f96373794bc47dd72670f43d8d195..b9a64b897040179a9cc5739a90d08ab8ad26dd26 100644
--- a/uk/ac/sanger/artemis/components/MultiComparator.java
+++ b/uk/ac/sanger/artemis/components/MultiComparator.java
@@ -1067,7 +1067,7 @@ public class MultiComparator extends JFrame
VCFview vcfView = new VCFview(null, thisVCFPanel, vcfFiles,
feature_display.getMaxVisibleBases(), 1, null, null,
- feature_display);
+ null, feature_display);
feature_display.addDisplayAdjustmentListener(vcfView);
feature_display.getSelection().addSelectionChangeListener(vcfView);
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index 52bf4d9fa62aa12d7edde14055e8f78db9e9e0dd..c7f62a5a3d81b4506e90b5a4eb816ba01b136c8d 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -191,6 +191,7 @@ public class VCFview extends JPanel
final int seqLength,
final String chr,
final String reference,
+ final EntryEdit entry_edit,
final FeatureDisplay feature_display)
{
super();
@@ -198,6 +199,7 @@ public class VCFview extends JPanel
this.nbasesInView = nbasesInView;
this.seqLength = seqLength;
this.chr = chr;
+
this.feature_display = feature_display;
this.vcfPanel = vcfPanel;
this.vcfFiles = vcfFiles;
@@ -266,7 +268,8 @@ public class VCFview extends JPanel
addMouseListener(new PopupListener());
//
- createMenus(frame, jspView);
+ createTopPanel(frame, jspView, entry_edit);
+ createMenus(jspView);
setDisplay();
if(feature_display == null)
@@ -282,151 +285,8 @@ public class VCFview extends JPanel
}
}
- private void createMenus(final JFrame frame, final JScrollPane jspView)
- {
- final JComponent topPanel;
- if(feature_display != null)
- topPanel = new JPanel(new FlowLayout(FlowLayout.LEADING, 0, 0));
- else
- {
- markNewStops.setSelected(false);
- markNewStops.setEnabled(false);
- topPanel = new JMenuBar();
-
- if(frame != null)
- frame.setJMenuBar((JMenuBar)topPanel);
-
- JMenu fileMenu = new JMenu("File");
- topPanel.add(fileMenu);
-
- JMenuItem printImage = new JMenuItem("Save As Image Files (png/jpeg)...");
- printImage.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- PrintVCFview part = new PrintVCFview(VCFview.this);
- part.print();
- }
- });
- fileMenu.add(printImage);
-
- JMenuItem printPS = new JMenuItem("Print...");
- printPS.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- PrintVCFview part = new PrintVCFview(VCFview.this);
- part.validate();
- part.doPrintActions();
- }
- });
- fileMenu.add(printPS);
-
-
- JMenuItem close = new JMenuItem("Close");
- fileMenu.add(close);
- close.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- VCFview.this.setVisible(false);
- Component comp = VCFview.this;
-
- while( !(comp instanceof JFrame) )
- comp = comp.getParent();
- ((JFrame)comp).dispose();
- }
- });
-
- JButton zoomIn = new JButton("-");
- Insets ins = new Insets(1,1,1,1);
- zoomIn.setMargin(ins);
- zoomIn.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- setZoomLevel((int) (VCFview.this.nbasesInView * 1.1));
- }
- });
- topPanel.add(zoomIn);
-
- JButton zoomOut = new JButton("+");
- zoomOut.setMargin(ins);
- zoomOut.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- setZoomLevel((int) (VCFview.this.nbasesInView * .9));
- }
- });
- topPanel.add(zoomOut);
- }
-
- final JComboBox combo = new JComboBox(vcfReaders[0].getSeqNames());
- combo.setEditable(true);
- JTextComponent editor = (JTextComponent) combo.getEditor().getEditorComponent();
- editor.setDocument(new AutoCompleteComboDocument(combo));
-
- if(vcfReaders[0].getSeqNames().length > 1)
- combo.addItem("Combine References");
-
- if(chr == null)
- this.chr = vcfReaders[0].getSeqNames()[0];
-
- combo.setSelectedItem(this.chr);
- combo.setMaximumRowCount(20);
-
- combo.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent e)
- {
- if(combo.getSelectedItem().equals("Combine References"))
- concatSequences = true;
- else
- {
- VCFview.this.chr = (String) combo.getSelectedItem();
- concatSequences = false;
- }
- repaint();
- }
- });
- topPanel.add(combo);
- if(topPanel instanceof JPanel)
- vcfPanel.add(topPanel, BorderLayout.NORTH);
-
- // auto hide top panel
- final JCheckBox buttonAutoHide = new JCheckBox("Hide", true);
- buttonAutoHide.setToolTipText("Auto-Hide");
- topPanel.add(buttonAutoHide);
- final MouseMotionListener mouseMotionListener = new MouseMotionListener()
- {
- public void mouseDragged(MouseEvent event)
- {
- handleCanvasMouseDrag(event);
- }
-
- public void mouseMoved(MouseEvent e)
- {
- findVariantAtPoint(e.getPoint());
-
- int thisHgt = HEIGHT;
- if (thisHgt < 5)
- thisHgt = 15;
-
- int y = (int) (e.getY() - jspView.getViewport().getViewRect().getY());
- if (y < thisHgt)
- topPanel.setVisible(true);
- else
- {
- if (buttonAutoHide.isSelected())
- topPanel.setVisible(false);
- }
-
- }
- };
- addMouseMotionListener(mouseMotionListener);
-
-
+ private void createMenus(final JScrollPane jspView)
+ {
// popup menu
popup = new JPopupMenu();
@@ -718,6 +578,167 @@ public class VCFview extends JPanel
popup.add(labels);
}
+ private void createTopPanel(final JFrame frame, final JScrollPane jspView, final EntryEdit entry_edit)
+ {
+ final JComponent topPanel;
+ if(feature_display != null)
+ topPanel = new JPanel(new FlowLayout(FlowLayout.LEADING, 0, 0));
+ else
+ {
+ markNewStops.setSelected(false);
+ markNewStops.setEnabled(false);
+ topPanel = new JMenuBar();
+ if(frame != null)
+ frame.setJMenuBar((JMenuBar)topPanel);
+
+ JMenu fileMenu = new JMenu("File");
+ topPanel.add(fileMenu);
+
+ JMenuItem printImage = new JMenuItem("Save As Image Files (png/jpeg)...");
+ printImage.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ PrintVCFview part = new PrintVCFview(VCFview.this);
+ part.print();
+ }
+ });
+ fileMenu.add(printImage);
+
+ JMenuItem printPS = new JMenuItem("Print...");
+ printPS.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ PrintVCFview part = new PrintVCFview(VCFview.this);
+ part.validate();
+ part.doPrintActions();
+ }
+ });
+ fileMenu.add(printPS);
+
+
+ JMenuItem close = new JMenuItem("Close");
+ fileMenu.add(close);
+ close.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ VCFview.this.setVisible(false);
+ Component comp = VCFview.this;
+
+ while( !(comp instanceof JFrame) )
+ comp = comp.getParent();
+ ((JFrame)comp).dispose();
+ }
+ });
+
+ JButton zoomIn = new JButton("-");
+ Insets ins = new Insets(1,1,1,1);
+ zoomIn.setMargin(ins);
+ zoomIn.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ setZoomLevel((int) (VCFview.this.nbasesInView * 1.1));
+ }
+ });
+ topPanel.add(zoomIn);
+
+ JButton zoomOut = new JButton("+");
+ zoomOut.setMargin(ins);
+ zoomOut.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ setZoomLevel((int) (VCFview.this.nbasesInView * .9));
+ }
+ });
+ topPanel.add(zoomOut);
+ }
+
+ final JComboBox combo = new JComboBox(vcfReaders[0].getSeqNames());
+ combo.setEditable(true);
+ JTextComponent editor = (JTextComponent) combo.getEditor().getEditorComponent();
+ editor.setDocument(new AutoCompleteComboDocument(combo));
+
+ if(vcfReaders[0].getSeqNames().length > 1)
+ combo.addItem("Combine References");
+
+ if(chr == null)
+ this.chr = vcfReaders[0].getSeqNames()[0];
+
+ combo.setSelectedItem(this.chr);
+ combo.setMaximumRowCount(20);
+
+ combo.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ if(combo.getSelectedItem().equals("Combine References"))
+ concatSequences = true;
+ else
+ {
+ VCFview.this.chr = (String) combo.getSelectedItem();
+ concatSequences = false;
+ }
+ repaint();
+ }
+ });
+ topPanel.add(combo);
+ if(topPanel instanceof JPanel)
+ vcfPanel.add(topPanel, BorderLayout.NORTH);
+
+ // auto hide top panel
+ final JCheckBox buttonAutoHide = new JCheckBox("Hide", true);
+ buttonAutoHide.setToolTipText("Auto-Hide");
+ topPanel.add(buttonAutoHide);
+ final MouseMotionListener mouseMotionListener = new MouseMotionListener()
+ {
+ public void mouseDragged(MouseEvent event)
+ {
+ handleCanvasMouseDrag(event);
+ }
+
+ public void mouseMoved(MouseEvent e)
+ {
+ findVariantAtPoint(e.getPoint());
+
+ int thisHgt = HEIGHT;
+ if (thisHgt < 5)
+ thisHgt = 15;
+
+ int y = (int) (e.getY() - jspView.getViewport().getViewRect().getY());
+ if (y < thisHgt)
+ topPanel.setVisible(true);
+ else
+ {
+ if (buttonAutoHide.isSelected())
+ topPanel.setVisible(false);
+ }
+
+ }
+ };
+ addMouseMotionListener(mouseMotionListener);
+
+
+ if(feature_display != null)
+ {
+ JButton close = new JButton("Close");
+ topPanel.add(close);
+ close.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ setVisible(false);
+ if(entry_edit != null)
+ entry_edit.setNGDivider();
+ else
+ vcfPanel.setVisible(false);
+ }
+ });
+ }
+ }
private void addToViewMenu(final int thisBamIndex)
{
@@ -1825,7 +1846,8 @@ public class VCFview extends JPanel
JFrame f = new JFrame();
new VCFview(f, (JPanel) f.getContentPane(), vcfFileList,
- nbasesInView, 100000000, null, reference, null);
+ nbasesInView, 100000000, null, reference, null, null);
+
f.pack();
f.setVisible(true);
}