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Commit 918d46e2 authored by tjc's avatar tjc
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use popup menu 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11897 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent 50bf227c
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uk/ac/sanger/artemis/components/alignment/JamView.java
+ 86
− 87
View file @ 918d46e2
......@@ -26,14 +26,12 @@ 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.FlowLayout;
import java.awt.FontMetrics;
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;
......@@ -64,8 +62,11 @@ import java.util.Vector;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JFrame;
import javax.swing.JMenuBar;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
......@@ -118,9 +119,9 @@ public class JamView extends JPanel
private Bases bases;
private JScrollPane jspView;
private JComboBox combo;
private JCheckBox checkBoxSingle;
private JCheckBox checkBoxSNPs;
private JCheckBox checkBoxStackView;
private boolean isSingle = false;
private boolean isSNPs = false;
private boolean isStackView = false;
private FeatureDisplay feature_display;
private Selection selection;
......@@ -331,7 +332,7 @@ public class JamView extends JPanel
}
}
inputSam.close();
System.out.println("readFromBamPicard "+start+".."+end);
//System.out.println("readFromBamPicard "+start+".."+end);
}
/**
......@@ -382,7 +383,7 @@ public class JamView extends JPanel
else
readFromBam(start, end);
if(!checkBoxStackView.isSelected() || pixPerBase*3 >= ALIGNMENT_PIX_PER_BASE)
if(!isStackView || pixPerBase*3 >= ALIGNMENT_PIX_PER_BASE)
Collections.sort(readsInView, new SAMRecordComparator());
setCursor(cdone);
}
......@@ -399,7 +400,7 @@ public class JamView extends JPanel
drawBaseAlignment(g2, seqLength, pixPerBase, start, end);
else
{
if(!checkBoxStackView.isSelected())
if(!isStackView)
drawLineView(g2, seqLength, pixPerBase, start, end);
else
drawStackView(g2, seqLength, pixPerBase, start, end);
......@@ -568,7 +569,7 @@ public class JamView extends JPanel
xpos = block.getReferenceStart()-1+j;
int refPos = xpos-refSeqStart+1;
if(checkBoxSNPs.isSelected() && refSeq != null && refPos > 0 && refPos < refSeq.length())
if(isSNPs && refSeq != null && refPos > 0 && refPos < refSeq.length())
{
if(readSeq.charAt(readPos) != refSeq.charAt(refPos))
g2.setColor(Color.red);
......@@ -611,7 +612,7 @@ public class JamView extends JPanel
if( !samRecord.getReadPairedFlag() || // read is not paired in sequencing
samRecord.getMateUnmappedFlag() ) // mate is unmapped
{
if(checkBoxSingle.isSelected())
if(isSingle)
{
int ypos = (getHeight() - scaleHeight) - samRecord.getReadString().length();
g2.setColor(Color.orange);
......@@ -782,7 +783,7 @@ public class JamView extends JPanel
}
drawRead(g2, samRecord, pixPerBase, stroke, ypos);
if (checkBoxSNPs.isSelected())
if (isSNPs)
showSNPsOnReads(g2, samRecord, pixPerBase, ypos);
}
......@@ -859,7 +860,7 @@ public class JamView extends JPanel
g2.drawLine((int) (thisStart * pixPerBase), ypos,
(int) (thisEnd * pixPerBase), ypos);
if (checkBoxSNPs.isSelected())
if (isSNPs)
showSNPsOnReads(g2, thisRead, pixPerBase, ypos);
}
......@@ -950,19 +951,25 @@ public class JamView extends JPanel
* @param autohide automatically hide the top panel containing the buttons
*/
public void addJamToPanel(final JPanel mainPanel,
final JFrame frame,
final boolean autohide,
final FeatureDisplay feature_display)
{
this.mainPanel = mainPanel;
final JComponent topPanel;
if(feature_display != null)
{
this.feature_display = feature_display;
this.selection = feature_display.getSelection();
topPanel = new JPanel(new FlowLayout(FlowLayout.LEADING, 0, 0));
}
else
{
topPanel = new JMenuBar();
frame.setJMenuBar((JMenuBar)topPanel);
}
final JPanel topPanel = new JPanel(new GridBagLayout());
GridBagConstraints gc = new GridBagConstraints();
// auto hide top panel
final JCheckBox buttonAutoHide = new JCheckBox("Hide", autohide);
......@@ -983,13 +990,12 @@ public class JamView extends JPanel
int y = (int) (e.getY() - jspView.getViewport().getViewRect().getY());
if (y < thisHgt)
{
if (!containsComponent(topPanel, mainPanel))
mainPanel.add(topPanel, BorderLayout.NORTH);
topPanel.setVisible(true);
}
else
{
if (buttonAutoHide.isSelected() && containsComponent(topPanel, mainPanel))
mainPanel.remove(topPanel);
if (buttonAutoHide.isSelected())
topPanel.setVisible(false);
}
mainPanel.repaint();
mainPanel.revalidate();
......@@ -999,7 +1005,6 @@ public class JamView extends JPanel
combo = new JComboBox(seqNames);
combo.setEditable(false);
combo.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
......@@ -1009,52 +1014,13 @@ public class JamView extends JPanel
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()
{
public void actionPerformed(ActionEvent e)
{
repaint();
}
});
topPanel.add(checkBoxSingle, gc);
checkBoxSNPs = new JCheckBox("SNPs");
checkBoxSNPs.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
if (checkBoxSNPs.isSelected() && bases == null)
{
JOptionPane.showMessageDialog(null,
"No reference sequence supplied to identify SNPs.", "SNPs",
JOptionPane.INFORMATION_MESSAGE);
}
repaint();
}
});
topPanel.add(checkBoxSNPs, gc);
checkBoxStackView = new JCheckBox("Stack");
checkBoxStackView.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
laststart = -1;
lastend = -1;
repaint();
}
});
topPanel.add(checkBoxStackView, gc);
topPanel.add(combo);
if(feature_display == null)
{
final JTextField baseText = new JTextField(10);
final JTextField baseText = new JTextField(8);
JButton goTo = new JButton("GoTo:");
goTo.setToolTipText("Go to base position");
goTo.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
......@@ -1072,8 +1038,8 @@ public class JamView extends JPanel
}
}
});
topPanel.add(goTo, gc);
topPanel.add(baseText, gc);
topPanel.add(goTo);
topPanel.add(baseText);
JButton zoomIn = new JButton("-");
Insets ins = new Insets(1,1,1,1);
......@@ -1087,7 +1053,7 @@ public class JamView extends JPanel
goToBasePosition(startBase);
}
});
topPanel.add(zoomIn, gc);
topPanel.add(zoomIn);
JButton zoomOut = new JButton("+");
zoomOut.setMargin(ins);
......@@ -1102,10 +1068,10 @@ public class JamView extends JPanel
goToBasePosition(startBase);
}
});
topPanel.add(zoomOut, gc);
topPanel.add(zoomOut);
}
topPanel.add(buttonAutoHide, gc);
topPanel.add(buttonAutoHide);
mainPanel.setPreferredSize(new Dimension(900, 400));
......@@ -1116,6 +1082,7 @@ public class JamView extends JPanel
setDisplay(1, nbasesInView, null);
mainPanel.setLayout(new BorderLayout());
if(topPanel instanceof JPanel)
mainPanel.add(topPanel, BorderLayout.NORTH);
mainPanel.add(jspView, BorderLayout.CENTER);
......@@ -1159,21 +1126,48 @@ public class JamView extends JPanel
});
}
/**
* Check to see if this component is contained by the display
* (FeatureDisplay) component.
* @return
*/
private boolean containsComponent(JPanel topPanel, JPanel mainPanel)
private void createViewMenu(JComponent view)
{
JCheckBoxMenuItem checkBoxSingle = new JCheckBoxMenuItem("Single Reads");
checkBoxSingle.addActionListener(new ActionListener()
{
Component[] c = mainPanel.getComponents();
for(int i=0; i<c.length; i++)
public void actionPerformed(ActionEvent e)
{
if(c[i].equals(topPanel))
return true;
repaint();
isSingle = !isSingle;
}
});
view.add(checkBoxSingle);
return false;
JCheckBoxMenuItem checkBoxSNPs = new JCheckBoxMenuItem("SNPs");
checkBoxSNPs.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
if (isSNPs && bases == null)
{
JOptionPane.showMessageDialog(null,
"No reference sequence supplied to identify SNPs.", "SNPs",
JOptionPane.INFORMATION_MESSAGE);
}
isSNPs = !isSNPs;
repaint();
}
});
view.add(checkBoxSNPs);
JCheckBoxMenuItem checkBoxStackView = new JCheckBoxMenuItem("Stack View");
checkBoxStackView.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
laststart = -1;
lastend = -1;
isStackView = !isStackView;
repaint();
}
});
view.add(checkBoxStackView);
}
public void setVisible(boolean visible)
......@@ -1207,15 +1201,15 @@ public class JamView extends JPanel
if(pixPerBase*3 > ALIGNMENT_PIX_PER_BASE)
{
pixPerBase = ALIGNMENT_PIX_PER_BASE;
checkBoxSingle.setVisible(false);
jspView.getVerticalScrollBar().setValue(0);
jspView.setColumnHeaderView(ruler);
showBaseAlignment = true;
}
else if(jspView != null)
{
checkBoxSingle.setVisible(true);
jspView.setColumnHeaderView(null);
jspView.getVerticalScrollBar().setValue(
jspView.getVerticalScrollBar().getMaximum());
showBaseAlignment = false;
}
......@@ -1273,14 +1267,12 @@ public class JamView extends JPanel
if(pixPerBase*3 > ALIGNMENT_PIX_PER_BASE)
{
pixPerBase = ALIGNMENT_PIX_PER_BASE;
checkBoxSingle.setVisible(false);
jspView.getVerticalScrollBar().setValue(0);
jspView.setColumnHeaderView(ruler);
showBaseAlignment = true;
}
else if(jspView != null)
{
checkBoxSingle.setVisible(true);
jspView.setColumnHeaderView(null);
showBaseAlignment = false;
}
......@@ -1471,10 +1463,17 @@ public class JamView extends JPanel
private void maybeShowPopup(MouseEvent e)
{
if(e.isPopupTrigger())
{
if(popup == null)
{
popup = new JPopupMenu();
createViewMenu(popup);
}
popup.show(e.getComponent(),
e.getX(), e.getY());
}
}
}
class SAMRecordComparator implements Comparator<Object>
......@@ -1617,7 +1616,7 @@ public class JamView extends JPanel
public void windowLostFocus(WindowEvent e){}
});
view.addJamToPanel((JPanel)frame.getContentPane(), false, null);
view.addJamToPanel((JPanel)frame.getContentPane(), frame, false, null);
frame.pack();
view.jspView.getVerticalScrollBar().setValue(
......
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