diff --git a/uk/ac/sanger/artemis/components/alignment/AbstractGraphPanel.java b/uk/ac/sanger/artemis/components/alignment/AbstractGraphPanel.java
index 17d9d1e01ee13e3bfade8a498ae07beb4ff48ee4..50e1dc6adaa65450887bd348b862e919b04c75a9 100644
--- a/uk/ac/sanger/artemis/components/alignment/AbstractGraphPanel.java
+++ b/uk/ac/sanger/artemis/components/alignment/AbstractGraphPanel.java
@@ -23,12 +23,16 @@
*/
package uk.ac.sanger.artemis.components.alignment;
+import java.awt.Color;
+import java.awt.FontMetrics;
+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.text.DecimalFormat;
import javax.swing.JCheckBox;
import javax.swing.JComponent;
@@ -46,6 +50,9 @@ public class AbstractGraphPanel extends JPanel
protected int end;
protected float pixPerBase;
+ protected BamView bamView;
+ protected int windowSize;
+ protected int max;
protected boolean autoWinSize = true;
protected int userWinSize = 1;
protected JPopupMenu popup = new JPopupMenu();
@@ -61,12 +68,13 @@ public class AbstractGraphPanel extends JPanel
GridBagConstraints c = new GridBagConstraints();
JPanel pane = new JPanel(gridbag);
final JTextField newWinSize = new JTextField(Integer.toString(userWinSize), 10);
+ newWinSize.setEnabled(!autoWinSize);
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);
+ final JCheckBox autoSet = new JCheckBox("Automatically set window size", autoWinSize);
autoSet.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -102,6 +110,23 @@ public class AbstractGraphPanel extends JPanel
addMouseListener(new PopupListener());
}
+
+ /**
+ * Draw maximum average value.
+ * @param g2
+ */
+ protected void drawMax(Graphics2D g2)
+ {
+ DecimalFormat df = new DecimalFormat("0.#");
+ String maxStr = df.format((float)max/(float)windowSize);
+
+ FontMetrics fm = getFontMetrics(getFont());
+ g2.setColor(Color.black);
+
+ int xpos = bamView.getJspView().getVisibleRect().width - fm.stringWidth(maxStr) -
+ bamView.getJspView().getVerticalScrollBar().getWidth();
+ g2.drawString(maxStr, xpos, fm.getHeight());
+ }
protected void setStartAndEnd(int start, int end)
{
diff --git a/uk/ac/sanger/artemis/components/alignment/SnpPanel.java b/uk/ac/sanger/artemis/components/alignment/SnpPanel.java
index 453ae6faef7ccf9faf05ca888beeee404cdf448b..63b65f818f58999842b501b730511bdd8b9bc74b 100644
--- a/uk/ac/sanger/artemis/components/alignment/SnpPanel.java
+++ b/uk/ac/sanger/artemis/components/alignment/SnpPanel.java
@@ -26,7 +26,6 @@ package uk.ac.sanger.artemis.components.alignment;
import java.awt.BasicStroke;
import java.awt.Color;
-import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Graphics2D;
@@ -49,10 +48,10 @@ import net.sf.samtools.SAMRecord;
public class SnpPanel extends AbstractGraphPanel
{
private static final long serialVersionUID = 1L;
- private BamView bamView;
-
private Bases bases;
private float minBaseQualityFilter = 0;
+ private int nBins;
+ private int snpCount[];
public SnpPanel(final BamView bamView, Bases bases)
{
@@ -96,16 +95,18 @@ import net.sf.samtools.SAMRecord;
{
super.paintComponent(g);
Graphics2D g2 = (Graphics2D)g;
-
- if(bases == null)
- return;
-
- List<SAMRecord> readsInView = bamView.getReadsInView();
- if(readsInView == null)
+
+ if(bases == null || nBins == 0 || bamView.getReadsInView() == null)
return;
-
- int windowSize;
-
+ draw(g2);
+ drawMax(g2);
+ }
+
+ protected void init(BamView bamView, float pixPerBase, int start, int end)
+ {
+ this.bamView = bamView;
+ setPixPerBase(pixPerBase);
+ setStartAndEnd(start, end);
if(autoWinSize)
{
windowSize = (bamView.getBasesInView()/300);
@@ -116,36 +117,13 @@ import net.sf.samtools.SAMRecord;
if(windowSize < 1)
windowSize = 1;
-
- int nBins = Math.round((end-start+1.f)/windowSize);
- int max = drawPlot(g2, nBins, windowSize);
-
- String maxStr = Float.toString(max/windowSize);
- FontMetrics fm = getFontMetrics(getFont());
- g2.setColor(Color.black);
-
- int xpos = getWidth() - fm.stringWidth(maxStr) -
- bamView.getJspView().getVerticalScrollBar().getWidth();
- g2.drawString(maxStr, xpos, fm.getHeight());
+ nBins = Math.round((end-start+1.f)/windowSize);
+ max = 0;
+ snpCount = null;
}
-
-
- private int drawPlot(Graphics2D g2, int nBins, int windowSize)
- {
- //lines = CoveragePanel.getLineAttributes(bamView.bamList.size());
- List<SAMRecord> readsInView = bamView.getReadsInView();
-
- int snpCount[] = new int[nBins];
- for(int i=0; i<snpCount.length; i++)
- snpCount[i] = 0;
-
- int max = 0;
- for(int i=0; i<readsInView.size(); i++)
- {
- SAMRecord thisRead = readsInView.get(i);
- max = calculateSNPs(thisRead, windowSize, nBins, snpCount, max);
- }
+ protected void draw(Graphics2D g2)
+ {
g2.setColor(Color.red);
g2.setStroke(new BasicStroke(1.f));
@@ -182,8 +160,6 @@ import net.sf.samtools.SAMRecord;
g2.drawLine(x0, y0, x1, y1);
}
}
-
- return max;
}
/**
@@ -193,12 +169,15 @@ import net.sf.samtools.SAMRecord;
* @param pixPerBase
* @param ypos
*/
- private int calculateSNPs(SAMRecord thisRead,
- int windowSize,
- int nBins,
- int[] snpCount,
- int max)
+ protected void addRecord(SAMRecord thisRead)
{
+ if(snpCount == null)
+ {
+ snpCount = new int[nBins];
+ for(int i=0; i<snpCount.length; i++)
+ snpCount[i] = 0;
+ }
+
int thisStart = thisRead.getAlignmentStart();
int thisEnd = thisRead.getAlignmentEnd();
int offset = bamView.getSequenceOffset(thisRead.getReferenceName());
@@ -241,7 +220,5 @@ import net.sf.samtools.SAMRecord;
{
e.printStackTrace();
}
- return max;
}
-
}
\ No newline at end of file