diff --git a/uk/ac/sanger/artemis/editor/DBViewer.java b/uk/ac/sanger/artemis/editor/DBViewer.java
index 4ee2df49b46c1b5efd418a29367e332f2e69899d..18a4ce0aec1a4f370929af51a253de360b459fa2 100644
--- a/uk/ac/sanger/artemis/editor/DBViewer.java
+++ b/uk/ac/sanger/artemis/editor/DBViewer.java
@@ -25,19 +25,79 @@
package uk.ac.sanger.artemis.editor;
import java.awt.*;
+import java.awt.event.*;
import javax.swing.*;
import java.util.Vector;
import java.util.Enumeration;
-public class DBViewer extends JPanel
+public class DBViewer extends ScrollPanel
{
- Vector hitInfoCollection = null;
+ /** collection of hits */
+ private Vector hitInfoCollection = null;
+ /** query length */
+ private int qlen;
+ /** viewer boundary */
+ private int bound = 10;
+ /** y displacement for each hit */
+ private int ydisp = 5;
+ /** maximum hit score */
+ private float max_score = 0;
+ /** colour the hits by score or by evalue */
+ private boolean colourByScore = false;
+ /** popup menu */
+ private JPopupMenu popup;
+ /** number height */
+ private int hgtNumber;
public DBViewer(FastaTextPane fastaPane)
{
super();
hitInfoCollection = fastaPane.getHitCollection();
+ qlen = fastaPane.getQueryLength();
+
+ Dimension d = new Dimension(500,
+ (hitInfoCollection.size()*ydisp)+(6*bound));
+ setPreferredSize(d);
+ setToolTipText(""); //enable tooltip display
+
+ Enumeration enumHits = hitInfoCollection.elements();
+ while(enumHits.hasMoreElements())
+ {
+ HitInfo hit = (HitInfo)enumHits.nextElement();
+ float score = Float.parseFloat(hit.getScore());
+ if(score > max_score)
+ max_score = score;
+ }
+
+ // Popup menu
+ addMouseListener(new PopupListener());
+ popup = new JPopupMenu();
+
+ JRadioButtonMenuItem colourScore = new JRadioButtonMenuItem("Colour by Score");
+ colourScore.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ setColourByScore(true);
+ }
+ });
+ popup.add(colourScore);
+
+ JRadioButtonMenuItem colourEval = new JRadioButtonMenuItem("Colour by E-value");
+ colourEval.setSelected(true);
+ colourEval.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ setColourByScore(false);
+ }
+ });
+ popup.add(colourEval);
+
+ ButtonGroup butt = new ButtonGroup();
+ butt.add(colourScore);
+ butt.add(colourEval);
}
/**
@@ -50,34 +110,118 @@ public class DBViewer extends JPanel
{
// let UI delegate paint first (incl. background filling)
super.paintComponent(g);
-
+
+ FontMetrics metrics = g.getFontMetrics();
+ hgtNumber = metrics.getAscent();
+
+// Dimension d = new Dimension(500,
+// (hitInfoCollection.size()*ydisp)+(4*bound)+hgtNumber);
+// setPreferredSize(d);
+
Graphics2D g2 = (Graphics2D)g;
- int bound = 10;
- int width = getWidth()-(2*bound);
+ int width = (int)getPreferredSize().getWidth()-(2*bound);
g2.setColor(Color.black);
g2.setStroke(new BasicStroke(3.f));
- g2.drawLine(bound,bound,bound+width,bound);
+ g2.drawLine(bound,bound+hgtNumber,bound+width,bound+hgtNumber);
- int ydisp = bound+5;
+ g2.setStroke(new BasicStroke(1.f));
+ g2.drawLine(bound,bound+hgtNumber,bound,bound+hgtNumber-6);
+ g2.drawString("0",bound,hgtNumber+3);
+
+// draw hits
+ int ypos = bound+ydisp+hgtNumber;
Enumeration enumHits = hitInfoCollection.elements();
while(enumHits.hasMoreElements())
{
- ydisp += 5;
+ ypos += ydisp;
HitInfo hit = (HitInfo)enumHits.nextElement();
- g2.setColor(Color.red);
+ if(colourByScore)
+ {
+ float score = Float.parseFloat(hit.getScore());
+ if(score > max_score/2)
+ g2.setColor(Color.red);
+ else if(score > max_score/4)
+ g2.setColor(Color.blue);
+ else
+ g2.setColor(Color.cyan);
+ }
+ else
+ {
+ double evalue = Double.parseDouble(hit.getEValue());
+ if(evalue < 0.005)
+ g2.setColor(Color.red);
+ else if(evalue < 0.)
+ g2.setColor(Color.blue);
+ else
+ g2.setColor(Color.cyan);
+ }
+
g2.setStroke(new BasicStroke(1.f));
- float hit_unit = (float)width/(float)hit.getQueryLength();
+ float hit_unit = (float)width/(float)qlen;
int start = (int)(bound+(hit_unit*hit.getQueryStart()));
int end = (int)(bound+(hit_unit*hit.getQueryEnd()));
- g2.drawLine(start,bound+ydisp,end,bound+ydisp);
+ g2.drawLine(start,bound+ypos,end,bound+ypos);
- System.out.println(hit.getID()+" "+hit.getQueryStart()+" -> "+hit.getQueryEnd()+
- " start "+start+" end "+end+" width "+width);
+// System.out.println(hit.getID()+" "+hit.getQueryStart()+" -> "+hit.getQueryEnd()+
+// " start "+start+" end "+end+" width "+width);
// ", E = "+hit.getEValue()+" Length = "+hit.getQueryLength());
}
+
+ }
+
+ protected void setColourByScore(boolean colourByScore)
+ {
+ this.colourByScore = colourByScore;
+ repaint();
+ }
+
+ /**
+ *
+ * Popup menu listener
+ *
+ */
+ class PopupListener extends MouseAdapter
+ {
+ 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());
+ }
+ }
+
+
+ /**
+ *
+ * Determine the tool tip to display
+ * @param e mouse event
+ * @return tool tip
+ *
+ */
+ public String getToolTipText(MouseEvent e)
+ {
+ Point loc = e.getPoint();
+ int seqPos = (int)((loc.y-bound-ydisp-bound-ydisp-hgtNumber)/ydisp);
+
+ if(seqPos >= 0 && seqPos<=hitInfoCollection.size())
+ {
+ HitInfo hit = (HitInfo)hitInfoCollection.get(seqPos);
+ return hit.getID();
+ }
+ return null;
}
}
diff --git a/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java b/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java
index 665a1953f8665178f070b578c0fe4b4f76aae28d..0befa1815678dde659ff12f88e4fcea6c94febe8 100644
--- a/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java
+++ b/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java
@@ -70,7 +70,7 @@ public class DataViewInternalFrame extends JInternalFrame
true);//iconifiable
DBViewer dbview = new DBViewer(fastaPane);
JScrollPane dbviewScroll = new JScrollPane(dbview);
- dbviewScroll.setPreferredSize(new Dimension(500,200));
+ dbviewScroll.setPreferredSize(new Dimension(500,300));
jif.getContentPane().add(dbviewScroll);
jif.setLocation(0,0);
jif.setSize(500,300);
diff --git a/uk/ac/sanger/artemis/editor/FastaTextPane.java b/uk/ac/sanger/artemis/editor/FastaTextPane.java
index 38c48a37aba1c584254dffb7cad42a0aefd2c71d..28d8747571e03656594c8e8866b9aaab2dcbac21 100644
--- a/uk/ac/sanger/artemis/editor/FastaTextPane.java
+++ b/uk/ac/sanger/artemis/editor/FastaTextPane.java
@@ -48,6 +48,7 @@ public class FastaTextPane extends JScrollPane
private JTextArea textArea;
private Vector hitInfoCollection = null;
private String format = null;
+ private int qlen;
public FastaTextPane(String dataFile)
{
@@ -155,7 +156,6 @@ public class FastaTextPane extends JScrollPane
streamReader = new InputStreamReader(getInputStream(dataFile));
buffReader = new BufferedReader(streamReader);
- String qlen = null;
String line = null;
int textPosition = 0;
int len = 0;
@@ -200,9 +200,6 @@ public class FastaTextPane extends JScrollPane
hit = getHitInfo(currentID,hitInfoCollection);
hit.setStartPosition(textPosition);
- if(qlen != null)
- hit.setQueryLength(Integer.parseInt(qlen));
-
String going = "";
ind = line.indexOf("GO:");
if(ind > -1)
@@ -284,7 +281,7 @@ public class FastaTextPane extends JScrollPane
else
ind2 = line.indexOf("(");
- qlen = line.substring(ind2+1,ind1).trim();
+ qlen = Integer.parseInt(line.substring(ind2+1,ind1).trim());
}
textPosition += len;
@@ -415,6 +412,17 @@ public class FastaTextPane extends JScrollPane
return sbuff;
}
+ /**
+ *
+ * Get the query sequence length.
+ * @return query sequence length.
+ *
+ */
+ protected int getQueryLength()
+ {
+ return qlen;
+ }
+
protected Vector getHitCollection()
{
return hitInfoCollection;
diff --git a/uk/ac/sanger/artemis/editor/HitInfo.java b/uk/ac/sanger/artemis/editor/HitInfo.java
index c8f84a56cb226cc50739df2a96dc2950ae0f8995..80703f047ca47284f3b6f1d00f5f2f8106e0cf6f 100644
--- a/uk/ac/sanger/artemis/editor/HitInfo.java
+++ b/uk/ac/sanger/artemis/editor/HitInfo.java
@@ -49,8 +49,6 @@ public class HitInfo
private String desc = null;
/** Sequence length */
private String length = null;
- /** Query length */
- private int queryLength = 0;
/** */
private String opt = null;
@@ -245,28 +243,6 @@ public class HitInfo
this.endPosition = endPosition;
}
- /**
- *
- * Set the query sequence length.
- * @param queryLength query sequence length.
- *
- */
- protected void setQueryLength(int queryLength)
- {
- this.queryLength = queryLength;
- }
-
- /**
- *
- * Get the query sequence length.
- * @return query sequence length.
- *
- */
- protected int getQueryLength()
- {
- return queryLength;
- }
-
/**
*