diff --git a/uk/ac/sanger/artemis/circular/digest/CircularGenomeController.java b/uk/ac/sanger/artemis/circular/digest/CircularGenomeController.java
index cf05244fabc4b73852c6326eb2a1039078d35a82..f7e854f25decaf52c4aef3b2a977a025d4e05a04 100644
--- a/uk/ac/sanger/artemis/circular/digest/CircularGenomeController.java
+++ b/uk/ac/sanger/artemis/circular/digest/CircularGenomeController.java
@@ -124,7 +124,7 @@ public class CircularGenomeController
final DNADraw dna = Utils.createDNADrawFromReportDetails(rd, entryGroup);
final InSilicoGelPanel inSilicoGelPanel =
- new InSilicoGelPanel(rd.length, rd.cutSites, dna.getHeight());
+ new InSilicoGelPanel(rd.length, rd.cutSites, dna.getHeight(), output);
MouseMotionListener mouseMotionListener = new MouseMotionAdapter()
{
diff --git a/uk/ac/sanger/artemis/circular/digest/CutSite.java b/uk/ac/sanger/artemis/circular/digest/CutSite.java
index cc6c63618dd3611544990f505f943f7986842cfc..350a2e72558598b50f138c6296bbf774e1acaf96 100644
--- a/uk/ac/sanger/artemis/circular/digest/CutSite.java
+++ b/uk/ac/sanger/artemis/circular/digest/CutSite.java
@@ -20,6 +20,7 @@ package uk.ac.sanger.artemis.circular.digest;
public class CutSite
{
+ private String enzymeName;
private int fivePrime;
private int threePrime;
private int fivePrimeRev;
@@ -27,10 +28,12 @@ public class CutSite
private boolean forward = false;
private boolean highlighted = false;
- CutSite(String fivePrimeStr, String threePrimeStr,
+ CutSite(final String enzymeName,
+ String fivePrimeStr, String threePrimeStr,
String fivePrimeRevStr, String threePrimeRevStr,
String strand)
{
+ this.enzymeName = enzymeName;
this.fivePrime = Integer.parseInt(fivePrimeStr);
this.threePrime = Integer.parseInt(threePrimeStr);
if(!fivePrimeRevStr.equals("."))
@@ -76,4 +79,9 @@ public class CutSite
{
this.highlighted = highlighted;
}
+
+ public String getEnzymeName()
+ {
+ return enzymeName;
+ }
}
diff --git a/uk/ac/sanger/artemis/circular/digest/EmbossTableParser.java b/uk/ac/sanger/artemis/circular/digest/EmbossTableParser.java
index 4c02fd5633d12c13d3786cf0af919ee85aea71bc..6540ecc0a7cba14a23f45d0032db739c0f0a2e23 100644
--- a/uk/ac/sanger/artemis/circular/digest/EmbossTableParser.java
+++ b/uk/ac/sanger/artemis/circular/digest/EmbossTableParser.java
@@ -55,7 +55,8 @@ public class EmbossTableParser
if ("Start".equals(parts[0]))
continue;
- CutSite cutSite = new CutSite(parts[5], parts[6], parts[7], parts[8], parts[2]);
+ CutSite cutSite = new CutSite(
+ parts[3], parts[5], parts[6], parts[7], parts[8], parts[2]);
list.add(cutSite);
}
return list;
diff --git a/uk/ac/sanger/artemis/circular/digest/InSilicoGelPanel.java b/uk/ac/sanger/artemis/circular/digest/InSilicoGelPanel.java
index ad1f059824c258093877d6cb4f796a012535fd31..311e2c706858fa71bf1e404e22eddbb9d8f59620 100644
--- a/uk/ac/sanger/artemis/circular/digest/InSilicoGelPanel.java
+++ b/uk/ac/sanger/artemis/circular/digest/InSilicoGelPanel.java
@@ -28,14 +28,22 @@ import java.awt.event.ActionListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
import java.util.List;
import java.util.Vector;
import javax.swing.ButtonGroup;
+import javax.swing.JMenuItem;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JRadioButtonMenuItem;
+import uk.ac.sanger.artemis.components.FileViewer;
+
public class InSilicoGelPanel extends JPanel
implements ActionListener
{
@@ -48,13 +56,21 @@ public class InSilicoGelPanel extends JPanel
private int MIN_FRAGMENT_LENGTH = Integer.MAX_VALUE;
private boolean drawLog = false;
private JPopupMenu popup;
+ private File restrictOutput;
-
+ /**
+ * @param genomeLength
+ * @param cutSites
+ * @param panelHeight
+ * @param restrictOutput
+ */
public InSilicoGelPanel(final int genomeLength,
final List<CutSite> cutSites,
- final int panelHeight)
+ final int panelHeight,
+ final File restrictOutput)
{
- this.panelHeight = panelHeight;
+ this.panelHeight = panelHeight;
+ this.restrictOutput = restrictOutput;
setBackground(Color.white);
setPreferredSize(new Dimension(160,panelHeight));
@@ -70,7 +86,7 @@ public class InSilicoGelPanel extends JPanel
else
{
len = cutSite.getFivePrime()-lastSite;
- System.out.println(i+" **** "+len.toString());
+
FragmentBand band = new FragmentBand();
band.genomeFragmentLength = len;
band.bandCutSite = cutSite;
@@ -90,7 +106,7 @@ public class InSilicoGelPanel extends JPanel
genomeFragments.add(band);
if(len > MAX_FRAGMENT_LENGTH)
MAX_FRAGMENT_LENGTH = len;
- System.out.println(len.toString());
+ //System.out.println(len.toString());
MouseListener popupListener = new PopupListener();
addMouseListener(popupListener);
@@ -106,6 +122,10 @@ public class InSilicoGelPanel extends JPanel
group.add(linearScale);
group.add(logScale);
linearScale.setSelected(true);
+
+ JMenuItem showCutSites = new JMenuItem("Show cut site details");
+ popup.add(showCutSites);
+ showCutSites.addActionListener(this);
}
/**
@@ -135,7 +155,7 @@ public class InSilicoGelPanel extends JPanel
else
y = gelHeight+marginHeight-(int)( ((float)(gelHeight)/
(float)(MAX_FRAGMENT_LENGTH-MIN_FRAGMENT_LENGTH)) * fragmentLength );
-
+
if(!genomeFragments.get(i).bandCutSite.isHighlighted())
{
g2D.setStroke(stroke);
@@ -143,11 +163,50 @@ public class InSilicoGelPanel extends JPanel
}
else
{
+ g2D.setColor(Color.black);
+ g2D.drawString(genomeFragments.get(i).bandCutSite.getEnzymeName(),
+ marginWidth+marginWidth+2, y);
g2D.setStroke(stroke2);
g2D.setColor(Color.yellow);
}
g2D.drawLine(marginWidth, y, marginWidth+marginWidth, y);
}
+
+ drawScale(g2D, stroke,gelHeight);
+ }
+
+ /**
+ * Draw the fragment length scale
+ * @param g2D
+ * @param stroke
+ * @param gelHeight
+ */
+ private void drawScale(Graphics2D g2D, BasicStroke stroke, int gelHeight)
+ {
+ g2D.setColor(Color.black);
+ g2D.setStroke(stroke);
+ NumberFormat formatter = new DecimalFormat("#0.0");
+
+ int nscale = 8;
+ if(isDrawLog())
+ nscale = 5;
+
+ float range = (MAX_FRAGMENT_LENGTH-MIN_FRAGMENT_LENGTH)/(float)nscale;
+ for(int i=0;i<nscale+1; i++)
+ {
+ float length = MIN_FRAGMENT_LENGTH+(range*i);
+
+ int y;
+ if(isDrawLog())
+ y = getLogValue((int)length, marginHeight, gelHeight);
+ else
+ y = gelHeight+marginHeight-(int)( ((float)(gelHeight)/
+ (float)(MAX_FRAGMENT_LENGTH-MIN_FRAGMENT_LENGTH)) * length );
+
+ g2D.drawLine(marginWidth, y, marginWidth-10, y);
+
+ g2D.drawString(formatter.format(length/1000)+"kb",0,y);
+ }
}
private static final double LOG10SCALE = 1.d/Math.log(10);
@@ -206,11 +265,34 @@ public class InSilicoGelPanel extends JPanel
public void actionPerformed(ActionEvent e)
{
- JRadioButtonMenuItem radioButton = (JRadioButtonMenuItem)e.getSource();
- if(radioButton.isSelected())
+ if (e.getSource() instanceof JRadioButtonMenuItem)
{
- setDrawLog(radioButton.getText().startsWith("Log"));
- repaint();
+ JRadioButtonMenuItem radioButton = (JRadioButtonMenuItem) e.getSource();
+ if (radioButton.isSelected())
+ {
+ setDrawLog(radioButton.getText().startsWith("Log"));
+ repaint();
+ }
+ }
+ else
+ {
+ final FileViewer viewer = new FileViewer(
+ restrictOutput.getName(), true, false);
+ BufferedReader br;
+ try
+ {
+ br = new BufferedReader(new FileReader(restrictOutput));
+
+ StringBuffer buff = new StringBuffer();
+ String line;
+ while ((line = br.readLine()) != null)
+ buff.append(line + "\n");
+ viewer.getTextPane().setText(buff.toString());
+ }
+ catch (Exception e2)
+ {
+ e2.printStackTrace();
+ }
}
}
}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/circular/digest/Utils.java b/uk/ac/sanger/artemis/circular/digest/Utils.java
index 0740ee24c55d40fda310423b3e0fb845a97fbf68..fd19e72fd3b6c2ff2a9adc4d9c1f9dbdc5ce3cbd 100644
--- a/uk/ac/sanger/artemis/circular/digest/Utils.java
+++ b/uk/ac/sanger/artemis/circular/digest/Utils.java
@@ -140,10 +140,7 @@ public class Utils
counter++;
continue;
}
-
- //circularFeature = createFeature(lastCutPosFwd, cutSite.getEnd(), counter, sequenceLength);
- //dna.addFeatureToTrack(circularFeature, forward, false);
- //System.out.println(lastCutPosFwd+".."+cutSite.getEnd()+"="+(cutSite.getEnd()-lastCutPosFwd));
+
addFeature(lastCutPos, cutSite.getFivePrime(),
counter, newEntry, dna, cutSite.isForward());
lastCutPos = cutSite.getFivePrime();
@@ -168,8 +165,17 @@ public class Utils
return dna;
}
+ /**
+ * Add a new feature to the entry with the given coordinates
+ * @param coord1
+ * @param coord2
+ * @param counter
+ * @param newEntry
+ * @param dna
+ * @param isForward
+ */
private static void addFeature(int coord1, int coord2,
- int counter, Entry newEntry,
+ int counter, Entry entry,
DNADraw dna, boolean isForward)
{
String colour;
@@ -184,8 +190,7 @@ public class Utils
{
QualifierVector qualifiers = new QualifierVector();
qualifiers.add(new Qualifier("colour",colour));
- final MarkerRange r;
-
+ final MarkerRange r;
if(isForward)
qualifiers.add(new Qualifier("note","plus"));
@@ -200,18 +205,16 @@ public class Utils
dna.getArtemisEntryGroup().getSequenceEntry().getBases().getReverseStrand(),
coord1,coord2);*/
- int len = r.getCount();
+ //int len = r.getCount();
uk.ac.sanger.artemis.io.Feature f = new uk.ac.sanger.artemis.io.EmblStreamFeature(
new Key("misc_feature"),
r.createLocation(),
qualifiers);
- newEntry.add(new uk.ac.sanger.artemis.Feature(f), false);
+ entry.add(new uk.ac.sanger.artemis.Feature(f), false);
- if(!isForward)
- {
- System.out.println(counter+" "+coord1+".."+coord2+" "+f.getLocation().toStringShort());
- }
+ //if(!isForward)
+ // System.out.println(counter+" "+coord1+".."+coord2+" "+f.getLocation().toStringShort());
}
catch (Exception e)
{