diff --git a/uk/ac/sanger/artemis/components/alignment/JamView.java b/uk/ac/sanger/artemis/components/alignment/JamView.java
index 7a9bfe53cabbd69ee0213e012b53e63e076a2768..2a06ec63657b11fda2cb9b7c3fd296ba1630b961 100644
--- a/uk/ac/sanger/artemis/components/alignment/JamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/JamView.java
@@ -26,6 +26,7 @@ package uk.ac.sanger.artemis.components.alignment;
import java.awt.BasicStroke;
import java.awt.BorderLayout;
import java.awt.Color;
+import java.awt.Component;
import java.awt.Cursor;
import java.awt.Dimension;
import java.awt.FontMetrics;
@@ -33,6 +34,7 @@ import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
+import java.awt.Insets;
import java.awt.Point;
import java.awt.Rectangle;
import java.awt.Stroke;
@@ -46,7 +48,7 @@ import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
-import java.awt.event.MouseMotionAdapter;
+import java.awt.event.MouseMotionListener;
import java.awt.event.WindowEvent;
import java.awt.event.WindowFocusListener;
import java.io.BufferedReader;
@@ -405,7 +407,7 @@ public class JamView extends JPanel
ruler.repaint();
int ypos = 0;
- drawSelectionRange(g2, pixPerBase, start, end);
+
String refSeq = null;
int refSeqStart = start;
@@ -429,7 +431,7 @@ public class JamView extends JPanel
g2.setColor(light_grey);
g2.fillRect(xpos, ypos-11,
jspView.getViewport().getWidth()+(ALIGNMENT_PIX_PER_BASE*2), 11);
-
+ drawSelectionRange(g2, pixPerBase, start, end);
g2.setColor(Color.black);
g2.drawString(refSeq, xpos, ypos);
@@ -444,6 +446,8 @@ public class JamView extends JPanel
e.printStackTrace();
}
}
+ else
+ drawSelectionRange(g2, pixPerBase, start, end);
boolean drawn[] = new boolean[readsInView.size()];
@@ -804,37 +808,71 @@ public class JamView extends JPanel
* Add the alignment view to the supplied <code>JPanel</code> in
* a <code>JScrollPane</code>.
* @param mainPanel panel to add the alignment to
- * @param showTopanel true in standalone mode to show buttons in
- * a panel at the top rather than in a popup menu.
+ * @param autohide automatically hide the top panel containing the buttons
*/
public void addJamToPanel(final JPanel mainPanel,
- final boolean showTopanel)
+ final boolean autohide,
+ final FeatureDisplay feature_display)
{
this.mainPanel = mainPanel;
- popup = new JPopupMenu();
-
- JPanel topPanel = null;
+
+ if(feature_display != null)
+ {
+ this.feature_display = feature_display;
+ this.selection = feature_display.getSelection();
+ }
+
+ final JPanel topPanel = new JPanel(new GridBagLayout());
GridBagConstraints gc = new GridBagConstraints();
- combo = new JComboBox(seqNames);
- combo.setEditable(false);
- if(showTopanel)
+ // auto hide top panel
+ final JCheckBox buttonAutoHide = new JCheckBox("Auto-hide", autohide);
+ final MouseMotionListener mouseMotionListener = new MouseMotionListener()
{
- topPanel = new JPanel(new GridBagLayout());
- combo.addItemListener(new ItemListener()
+ public void mouseDragged(MouseEvent event)
{
- public void itemStateChanged(ItemEvent e)
+ handleCanvasMouseDragOrClick(event);
+ }
+
+ public void mouseMoved(MouseEvent e)
+ {
+ int thisHgt = HEIGHT;
+ if (thisHgt < 5)
+ thisHgt = 15;
+
+ int y = (int) (e.getY() - jspView.getViewport().getViewRect().getY());
+ if (y < thisHgt)
{
- laststart = -1;
- lastend = -1;
- setZoomLevel(JamView.this.nbasesInView);
+ if (!containsComponent(topPanel, mainPanel))
+ mainPanel.add(topPanel, BorderLayout.NORTH);
}
- });
- gc.fill = GridBagConstraints.NONE;
- gc.anchor = GridBagConstraints.NORTHWEST;
- topPanel.add(combo, gc);
- }
-
+ else
+ {
+ if (buttonAutoHide.isSelected() && containsComponent(topPanel, mainPanel))
+ mainPanel.remove(topPanel);
+ }
+ mainPanel.repaint();
+ mainPanel.revalidate();
+ }
+ };
+ addMouseMotionListener(mouseMotionListener);
+
+ combo = new JComboBox(seqNames);
+ combo.setEditable(false);
+
+ combo.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ laststart = -1;
+ lastend = -1;
+ setZoomLevel(JamView.this.nbasesInView);
+ }
+ });
+ gc.fill = GridBagConstraints.NONE;
+ gc.anchor = GridBagConstraints.NORTHWEST;
+ topPanel.add(combo, gc);
+
checkBoxSingle = new JCheckBox("Single Reads");
checkBoxSingle.addActionListener(new ActionListener()
{
@@ -843,31 +881,25 @@ public class JamView extends JPanel
repaint();
}
});
- if(topPanel != null)
- topPanel.add(checkBoxSingle, gc);
- else
- popup.add(checkBoxSingle);
+ topPanel.add(checkBoxSingle, gc);
checkBoxSNPs = new JCheckBox("SNPs");
checkBoxSNPs.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- if(checkBoxSNPs.isSelected() && bases == null)
+ if (checkBoxSNPs.isSelected() && bases == null)
{
JOptionPane.showMessageDialog(null,
- "No reference sequence supplied to identify SNPs.",
- "SNPs", JOptionPane.INFORMATION_MESSAGE);
+ "No reference sequence supplied to identify SNPs.", "SNPs",
+ JOptionPane.INFORMATION_MESSAGE);
}
repaint();
}
});
- if(topPanel != null)
- topPanel.add(checkBoxSNPs, gc);
- else
- popup.add(checkBoxSNPs, gc);
-
- if (topPanel != null)
+ topPanel.add(checkBoxSNPs, gc);
+
+ if (feature_display == null)
{
final JTextField baseText = new JTextField(10);
JButton goTo = new JButton("GoTo:");
@@ -888,14 +920,12 @@ public class JamView extends JPanel
}
}
});
-
topPanel.add(goTo, gc);
topPanel.add(baseText, gc);
- }
- if (topPanel != null)
- {
JButton zoomIn = new JButton("+");
+ Insets ins = new Insets(0,0,0,0);
+ zoomIn.setMargin(ins);
zoomIn.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -923,23 +953,23 @@ public class JamView extends JPanel
});
topPanel.add(zoomOut, gc);
}
+
+ topPanel.add(buttonAutoHide, gc);
- mainPanel.setPreferredSize(new Dimension(800,400));
- jspView = new JScrollPane(this,
- JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
+ mainPanel.setPreferredSize(new Dimension(800, 400));
+ jspView = new JScrollPane(this, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
-
+
setDisplay(1, nbasesInView, null);
mainPanel.setLayout(new BorderLayout());
-
- if(topPanel != null)
- mainPanel.add(topPanel, BorderLayout.NORTH);
+
+ mainPanel.add(topPanel, BorderLayout.NORTH);
mainPanel.add(jspView, BorderLayout.CENTER);
jspView.getVerticalScrollBar().setValue(
jspView.getVerticalScrollBar().getMaximum());
- if(topPanel != null)
+ if (feature_display == null)
{
addKeyListener(new KeyAdapter()
{
@@ -967,24 +997,32 @@ public class JamView extends JPanel
}
});
}
-
+
addMouseListener(new PopupListener());
setFocusable(true);
requestFocusInWindow();
- addFocusListener(new FocusListener()
+ addFocusListener(new FocusListener()
{
- public void focusGained(FocusEvent fe) {}
- public void focusLost(FocusEvent fe) {}
+ public void focusGained(FocusEvent fe){}
+ public void focusLost(FocusEvent fe){}
});
- // Listen for mouse motion events so that we can select ranges of bases.
- addMouseMotionListener(new MouseMotionAdapter()
+ }
+
+ /**
+ * Check to see if this component is contained by the display
+ * (FeatureDisplay) component.
+ * @return
+ */
+ private boolean containsComponent(JPanel topPanel, JPanel mainPanel)
+ {
+ Component[] c = mainPanel.getComponents();
+ for(int i=0; i<c.length; i++)
{
- public void mouseDragged(MouseEvent event)
- {
- // adjust for scrollbar
- handleCanvasMouseDrag(event);
- }
- });
+ if(c[i].equals(topPanel))
+ return true;
+ }
+
+ return false;
}
public void setVisible(boolean visible)
@@ -1144,12 +1182,6 @@ public class JamView extends JPanel
{
return jspView;
}
-
- public void setFeatureDisplay(FeatureDisplay feature_display)
- {
- this.feature_display = feature_display;
- this.selection = feature_display.getSelection();;
- }
public void setBases(Bases bases)
{
@@ -1168,71 +1200,31 @@ public class JamView extends JPanel
/**
* Handle a mouse drag event on the drawing canvas.
**/
- private void handleCanvasMouseDrag(final MouseEvent event)
+ private void handleCanvasMouseDragOrClick(final MouseEvent event)
{
- if(event.isShiftDown())
+ if(!showBaseAlignment || event.isShiftDown())
return;
String refName = (String) combo.getSelectedItem();
int seqLength = seqLengths.get(refName);
- float pixPerBase = ((float)getWidth())/(float)(seqLength);
-
+ float pixPerBase = ((float)getWidth())/(float)(seqLength);
+ int start = (int) Math.round(event.getPoint().getX()/pixPerBase);
+ if(start < 1)
+ start = 1;
+ if(start > seqLength)
+ start = seqLength;
-
-/* MarkerRange drag_range = getMarkerRangeFromPosition(event.getPoint());
- selection.setMarkerRange(marker_range);
- if(drag_range == null)
- return;
-
- final MarkerRange selected_range = getSelection().getMarkerRange();
-
- // if the start and current positions of the drag are not on the
- // same Strand then ignore this event
- if(selected_range != null &&
- drag_range.getStrand() != selected_range.getStrand())
- return;
-
- try
+ MarkerRange drag_range;
+ try
{
- // user has dragged off the screen so use a marker at position 1
- if(drag_range.getStart().getPosition() < 1)
- drag_range = new MarkerRange(drag_range.getStrand(), 1, 1);
-
- // user has dragged off the screen so use a marker at position the
- // end of the sequence
- if(drag_range.getEnd().getPosition() > getSequenceLength())
- drag_range = new MarkerRange(drag_range.getStrand(),
- getSequenceLength(),
- getSequenceLength());
+ drag_range = new MarkerRange (bases.getForwardStrand(), start, start);
+ getSelection().setMarkerRange(drag_range);
+ repaint();
}
- catch(OutOfRangeException e)
+ catch (OutOfRangeException e)
{
- throw new Error("internal error - unexpected OutOfRangeException");
+ e.printStackTrace();
}
-
- final boolean start_base_is_visible = baseVisible(drag_range.getStart());
- final boolean end_base_is_visible = baseVisible(drag_range.getEnd());
-
- if(!start_base_is_visible)
- makeBaseVisible(drag_range.getStart());
-
- if(!end_base_is_visible)
- makeBaseVisible(drag_range.getEnd());
-
- // scrolling was necessary so update the visible features vector
- if(!start_base_is_visible || !end_base_is_visible)
- needVisibleFeatureVectorUpdate();
-
- final MarkerRange new_marker_range;
-
- if(click_range == null)
- new_marker_range = drag_range;
- else
- new_marker_range = selected_range.combineRanges(drag_range, true);
-
- getSelection().setMarkerRange(new_marker_range);
-
- repaint();*/
}
private Selection getSelection()
@@ -1277,15 +1269,14 @@ public class JamView extends JPanel
}
/**
- *
* Popup menu listener
- *
*/
class PopupListener extends MouseAdapter
{
public void mouseClicked(MouseEvent e)
{
JamView.this.requestFocus();
+ handleCanvasMouseDragOrClick(e);
}
public void mousePressed(MouseEvent e)
@@ -1428,7 +1419,7 @@ public class JamView extends JPanel
public void windowLostFocus(WindowEvent e){}
});
- view.addJamToPanel((JPanel)frame.getContentPane(), true);
+ view.addJamToPanel((JPanel)frame.getContentPane(), false, null);
frame.pack();
view.jspView.getVerticalScrollBar().setValue(