diff --git a/uk/ac/sanger/artemis/components/variant/GraphPanel.java b/uk/ac/sanger/artemis/components/variant/GraphPanel.java
new file mode 100644
index 0000000000000000000000000000000000000000..0409e059188f760916269161c8ac47f4b84ec90d
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/variant/GraphPanel.java
@@ -0,0 +1,331 @@
+package uk.ac.sanger.artemis.components.variant;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.geom.GeneralPath;
+import java.io.IOException;
+import java.text.DecimalFormat;
+
+import javax.swing.JCheckBox;
+import javax.swing.JLabel;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JTextField;
+
+import uk.ac.sanger.artemis.FeatureVector;
+import uk.ac.sanger.artemis.components.variant.BCFReader.BCFReaderIterator;
+
+
+public class GraphPanel extends JPanel
+{
+ private static final long serialVersionUID = 1L;
+
+
+ protected boolean autoWinSize = true;
+ protected int userWinSize = 1;
+ protected JPopupMenu popup = new JPopupMenu();
+ private VCFview vcfView;
+
+ private static String TYPES[] = { "SNP", "DP" };
+ private int type = 0; // 0 - SNP; 1 - DP
+
+ public GraphPanel(final VCFview vcfView)
+ {
+ super();
+ this.vcfView = vcfView;
+ setBackground(Color.white);
+ initPopupMenu(this);
+ }
+
+ /**
+ * Override
+ */
+ protected void paintComponent(Graphics g)
+ {
+ super.paintComponent(g);
+ Graphics2D g2 = (Graphics2D)g;
+
+ float pixPerBase = vcfView.getPixPerBaseByWidth();
+ int sbeg = vcfView.getBaseAtStartOfView();
+ int send = sbeg+vcfView.getBasesInView();
+
+ int windowSize;
+ if(autoWinSize)
+ {
+ windowSize = (vcfView.getBasesInView()/300);
+ userWinSize = windowSize;
+ }
+ else
+ windowSize = userWinSize;
+ if(windowSize < 1)
+ windowSize = 1;
+
+ int nBins = Math.round((send-sbeg+1.f)/windowSize);
+ int snpCount[] = new int[nBins];
+ int max = 0;
+ for(int i=0; i<snpCount.length; i++)
+ snpCount[i] = 0;
+
+ AbstractVCFReader readers[] = vcfView.getVcfReaders();
+ FeatureVector features = vcfView.getCDSFeaturesInRange(sbeg, send);
+ for(int i=0; i<readers.length; i++)
+ {
+ max = countAll(readers[i], sbeg, send, windowSize, nBins, features, snpCount, max);
+ }
+
+ g2.setColor(Color.red);
+ g2.setStroke(new BasicStroke(1.f));
+
+ if(windowSize == 1)
+ {
+ GeneralPath shape = new GeneralPath();
+ shape.moveTo(0,getHeight());
+ for(int i=0; i<snpCount.length; i++)
+ {
+ float xpos1 = ((i*windowSize) )*pixPerBase;
+ float xpos2 = ((i*windowSize) + windowSize)*pixPerBase;
+
+ shape.lineTo(xpos1,getHeight());
+ shape.lineTo(xpos1,
+ getHeight() - (((float)snpCount[i]/(float)max)*getHeight()));
+ shape.lineTo(xpos2,
+ getHeight() - (((float)snpCount[i]/(float)max)*getHeight()));
+
+ shape.lineTo(xpos2,getHeight());
+ }
+
+ shape.lineTo(getWidth(),getHeight());
+ g2.fill(shape);
+ }
+ else
+ {
+ for(int i=1; i<snpCount.length; i++)
+ {
+ int x0 = (int) (((i*windowSize) - windowSize/2.f)*pixPerBase);
+ int y0 = (int) (getHeight() - (((float)snpCount[i-1]/(float)max)*getHeight()));
+ int x1 = (int) ((((i+1)*windowSize) - windowSize/2.f)*pixPerBase);
+ int y1 = (int) (getHeight() - (((float)snpCount[i]/(float)max)*getHeight()));
+
+ g2.drawLine(x0, y0, x1, y1);
+ }
+ }
+
+ DecimalFormat df = new DecimalFormat("0.00##");
+ String maxStr = TYPES[type]+" : "+df.format((float)max/(float)windowSize);
+ FontMetrics fm = getFontMetrics(getFont());
+ g2.setColor(Color.black);
+
+ int xpos = getWidth() - fm.stringWidth(maxStr) - 10;
+ g2.drawString(maxStr, xpos, fm.getHeight());
+ }
+
+ private int countAll(AbstractVCFReader reader, int sbeg, int send, int windowSize,
+ int nBins, FeatureVector features, int snpCount[], int max)
+ {
+ if(vcfView.isConcatenate())
+ {
+ String[] contigs = reader.getSeqNames();
+ for(int j=0; j<contigs.length; j++)
+ {
+ int offset = vcfView.getSequenceOffset(contigs[j]);
+ int nextOffset;
+ if(j<contigs.length-1)
+ nextOffset = vcfView.getSequenceOffset(contigs[j+1]);
+ else
+ nextOffset = vcfView.seqLength;
+
+ if( (offset >= sbeg && offset < send) ||
+ (offset < sbeg && sbeg < nextOffset) )
+ {
+ int thisStart = sbeg - offset;
+ if(thisStart < 1)
+ thisStart = 1;
+ int thisEnd = send - offset;
+
+ max = count(reader, contigs[j], thisStart, thisEnd, windowSize, nBins, features, snpCount, max);
+ }
+ }
+ return max;
+ }
+ else
+ return count(reader, vcfView.getChr(), sbeg, send, windowSize, nBins, features, snpCount, max);
+ }
+
+ private int count(AbstractVCFReader reader, String chr, int sbeg, int send, int windowSize,
+ int nBins, FeatureVector features, int snpCount[], int max)
+ {
+ if(reader instanceof BCFReader)
+ {
+ try
+ {
+ BCFReader bcfReader = (BCFReader)reader;
+ BCFReaderIterator it = bcfReader.query(chr, sbeg, send);
+
+ VCFRecord record;
+ while((record = it.next()) != null)
+ {
+ max = calc(record, features, reader, windowSize, nBins, snpCount, max);
+ }
+ }
+ catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ else
+ {
+ TabixReader.Iterator iter =
+ ((TabixReader)reader).query(chr+":"+sbeg+"-"+send); // get the iterator
+ if (iter == null)
+ return max;
+ try
+ {
+ String s;
+ while ((s = iter.next()) != null)
+ {
+ VCFRecord record = VCFRecord.parse(s);
+ max = calc(record, features, reader, windowSize, nBins, snpCount, max);
+ }
+ }
+ catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ return max;
+ }
+
+ private int calc(VCFRecord record, FeatureVector features,
+ AbstractVCFReader reader, int windowSize, int nBins, int snpCount[], int max)
+ {
+ int pos = record.getPos() + vcfView.getSequenceOffset(record.getChrom());
+ if(!vcfView.showVariant(record, features, pos, reader.isVcf_v4()))
+ return max;
+
+ int bin = (int)((pos-vcfView.getBaseAtStartOfView()) / windowSize);
+ if(bin < 0 || bin > nBins-1)
+ return max;
+
+ if(type == 1)
+ {
+ int dp = 0;
+ try
+ {
+ dp = Integer.parseInt(record.getInfoValue("DP"));
+ }
+ catch(Exception e){ e.printStackTrace(); }
+ snpCount[bin]+=dp;
+ }
+ else
+ snpCount[bin]+=1;
+
+ if(snpCount[bin] > max)
+ max = snpCount[bin];
+
+ return max;
+ }
+
+ private void initPopupMenu(final JPanel graphPanel)
+ {
+ final JMenuItem setScale = new JMenuItem("Set the Window Size...");
+ setScale.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent _)
+ {
+ GridBagLayout gridbag = new GridBagLayout();
+ GridBagConstraints c = new GridBagConstraints();
+ JPanel pane = new JPanel(gridbag);
+ final JTextField newWinSize = new JTextField(Integer.toString(userWinSize), 10);
+ final JLabel lab = new JLabel("Window size:");
+ c.gridy = 0;
+ pane.add(lab, c);
+ pane.add(newWinSize, c);
+
+ final JCheckBox autoSet = new JCheckBox("Automatically set window size", false);
+ autoSet.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ lab.setEnabled(!autoSet.isSelected());
+ newWinSize.setEnabled(!autoSet.isSelected());
+ }
+ });
+ c.gridy = 1;
+ c.gridwidth = GridBagConstraints.REMAINDER;
+ pane.add(autoSet, c);
+
+ String window_options[] = { "OK", "Cancel" };
+ int select = JOptionPane.showOptionDialog(null, pane, "Window Size",
+ JOptionPane.DEFAULT_OPTION, JOptionPane.QUESTION_MESSAGE, null,
+ window_options, window_options[0]);
+
+ if (select == 1)
+ return;
+ autoWinSize = autoSet.isSelected();
+ try
+ {
+ userWinSize = Integer.parseInt(newWinSize.getText().trim());
+ }
+ catch (NumberFormatException nfe)
+ {
+ return;
+ }
+ graphPanel.repaint();
+ }
+ });
+ popup.add(setScale);
+
+ addMouseListener(new PopupListener());
+ }
+
+ /**
+ * @param type the type to set
+ */
+ protected void setType(int type)
+ {
+ this.type = type;
+ }
+
+ /**
+ * Popup menu listener
+ */
+ class PopupListener extends MouseAdapter
+ {
+ JMenuItem gotoMateMenuItem;
+ JMenuItem showDetails;
+
+ public void mouseClicked(MouseEvent e)
+ {
+ }
+
+ public void mousePressed(MouseEvent e)
+ {
+ maybeShowPopup(e);
+ }
+
+ public void mouseReleased(MouseEvent e)
+ {
+ maybeShowPopup(e);
+ }
+
+ private void maybeShowPopup(MouseEvent e)
+ {
+ if(e.isPopupTrigger())
+ {
+ popup.show(e.getComponent(),
+ e.getX(), e.getY());
+ }
+ }
+ }
+}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index 3e62a9c709a3655547b61fcce0fded33a2367d91..5b9ceda46286e55da09f0f4cc6acff8d1e081ed7 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -54,6 +54,7 @@ import java.util.List;
import java.util.Vector;
import java.util.regex.Pattern;
+import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
import javax.swing.JButton;
import javax.swing.JCheckBox;
@@ -131,6 +132,8 @@ public class VCFview extends JPanel
private String chr;
private VCFRecord mouseVCF;
private int mouseOverIndex = -1;
+
+ private GraphPanel graphPanel;
//record of where a mouse drag starts
private int dragStart = -1;
@@ -222,7 +225,8 @@ public class VCFview extends JPanel
vcfPanel.add(jspView, BorderLayout.CENTER);
JPanel bottomPanel = new JPanel(new BorderLayout());
- GraphPanel graphPanel = new GraphPanel(this);
+ graphPanel = new GraphPanel(this);
+ graphPanel.setBorder(BorderFactory.createMatteBorder(1, 0, 1, 0, Color.gray));
graphPanel.setPreferredSize(new Dimension(900, 100));
graphPanel.setVisible(false);
@@ -565,6 +569,33 @@ public class VCFview extends JPanel
}
});
view.add(viewFasta);
+
+ JMenu graph = new JMenu("Graph");
+ popup.add(graph);
+
+ final JCheckBoxMenuItem graphSNP = new JCheckBoxMenuItem("SNP");
+ final JCheckBoxMenuItem graphDP = new JCheckBoxMenuItem("Depth (DP)");
+ graph.add(graphSNP);
+ graphSNP.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent e)
+ {
+ graphPanel.setVisible(graphSNP.isSelected());
+ graphDP.setSelected(false);
+ graphPanel.setType(0);
+ graphPanel.repaint();
+ }
+ });
+
+ graph.add(graphDP);
+ graphDP.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent e)
+ {
+ graphPanel.setVisible(graphDP.isSelected());
+ graphSNP.setSelected(false);
+ graphPanel.setType(1);
+ graphPanel.repaint();
+ }
+ });
}
private static EntryGroup getReference(String reference)
@@ -616,13 +647,21 @@ public class VCFview extends JPanel
* @param fileName
* @return
*/
- private String testForURL(String fileName)
+ private String testForURL(String fileName, boolean isBCF)
{
if(!fileName.startsWith("http:"))
return fileName;
- String newFileName = download(fileName, null, ".bcf");
- download(fileName+".bci", newFileName, ".bci");
+ if(isBCF)
+ {
+ String newFileName = download(fileName, null, ".bcf");
+ download(fileName+".bci", newFileName, ".bci");
+ return newFileName;
+ }
+
+ String newFileName = download(fileName, null, ".vcf.gz");
+ download(fileName+".tbi", newFileName, ".tbi");
+
return newFileName;
}
@@ -673,7 +712,7 @@ public class VCFview extends JPanel
{
if(IOUtils.isBCF(fileName))
{
- fileName = testForURL(fileName);
+ fileName = testForURL(fileName, true);
vcfReaders[index] = new BCFReader(new File(fileName));
String hdr = ((BCFReader)vcfReaders[index]).headerToString();
@@ -682,6 +721,7 @@ public class VCFview extends JPanel
return hdr;
}
+ fileName = testForURL(fileName, false);
BlockCompressedInputStream is =
new BlockCompressedInputStream(new FileInputStream(fileName));
vcfReaders[index] = new TabixReader(fileName);
@@ -790,6 +830,13 @@ public class VCFview extends JPanel
return offsetLengths.get(refName);
}
+ public void repaint()
+ {
+ super.repaint();
+ if(graphPanel != null && graphPanel.isVisible())
+ graphPanel.repaint();
+ }
+
protected void paintComponent(Graphics g)
{
super.paintComponent(g);
@@ -892,7 +939,7 @@ public class VCFview extends JPanel
}
}
- private FeatureVector getCDSFeaturesInRange(int start, int end)
+ protected FeatureVector getCDSFeaturesInRange(int start, int end)
{
if(entryGroup == null)
return null;