diff --git a/uk/ac/sanger/artemis/circular/Block.java b/uk/ac/sanger/artemis/circular/Block.java
index 8a24bc6adbd521ae3d7510c9cd1831164855affa..5265b6670e41550ee76ece435195effae8c03048 100644
--- a/uk/ac/sanger/artemis/circular/Block.java
+++ b/uk/ac/sanger/artemis/circular/Block.java
@@ -610,7 +610,7 @@ public class Block implements Transferable
* @param x x position
* @param y y position
*/
- public void setBlockLocation(int x, int y, final TrackViewer viewer)
+ public void setBlockLocation(int x, int y, final TrackManager viewer)
{
if(current_dna.isCircular())
{
diff --git a/uk/ac/sanger/artemis/circular/DNADraw.java b/uk/ac/sanger/artemis/circular/DNADraw.java
index 86be7aa9d55c3be7a8de86e9d91f531535c8ead6..ecd09010fc420a83d03f2e1679a12662d1a7b9ec 100644
--- a/uk/ac/sanger/artemis/circular/DNADraw.java
+++ b/uk/ac/sanger/artemis/circular/DNADraw.java
@@ -61,7 +61,11 @@ import java.awt.dnd.DropTargetDragEvent;
import java.awt.dnd.DropTargetDropEvent;
import java.awt.dnd.DropTargetEvent;
import java.awt.dnd.DropTargetListener;
+import java.io.BufferedReader;
+import java.io.File;
import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
import javax.swing.JButton;
import javax.swing.JCheckBoxMenuItem;
@@ -87,7 +91,6 @@ public class DNADraw extends ScrollPanel
implements Printable, DragGestureListener,
DragSourceListener, DropTargetListener
{
-
private static final long serialVersionUID = 1L;
public static JScrollPane jsp;
private DNADraw current_dna;
@@ -130,7 +133,7 @@ public class DNADraw extends ScrollPanel
private Graph userGraph;
protected static int Y_SHIFT = -35;
protected static int THETA = -90;
- private TrackViewer viewer;
+ private TrackManager trackManager;
private AffineTransform original;
// linear plot variables
@@ -197,7 +200,28 @@ public class DNADraw extends ScrollPanel
this.addMouseListener(mouseListener);
}
-
+ private String getVersion()
+ {
+ final ClassLoader cl = this.getClass().getClassLoader();
+ try
+ {
+ String line;
+ InputStream in = cl.getResourceAsStream("etc/versions");
+ BufferedReader reader = new BufferedReader(new InputStreamReader(in));
+ while((line = reader.readLine()) != null)
+ {
+ if(line.startsWith("DNAPlot"))
+ return line.substring( "DNAPlot".length() ).trim();
+ }
+ reader.close();
+ in.close();
+ }
+ catch (Exception ex)
+ {
+ }
+ return null;
+ }
+
/**
* Add list of features to a track
* @param features
@@ -956,7 +980,7 @@ public class DNADraw extends ScrollPanel
* @param g
* @return
*/
- private boolean containsGraph(Graph g)
+ protected boolean containsGraph(Graph g)
{
int ncomponents = getComponentCount();
for(int i=0; i<ncomponents; i++)
@@ -1099,7 +1123,7 @@ public class DNADraw extends ScrollPanel
public void actionPerformed(ActionEvent e)
{
Wizard.readEntry(DNADraw.this, getBases());
- viewer.refresh();
+ trackManager.refresh();
repaint();
}
});
@@ -1141,7 +1165,13 @@ public class DNADraw extends ScrollPanel
fileMenu.add(printPreview);
fileMenu.add(new JSeparator());
-
+ fileMenu.add(TrackManager.getExportTrackTemplateMenuItem(null, this));
+
+ if(trackManager == null)
+ trackManager = new TrackManager(DNADraw.this);
+ fileMenu.add(trackManager.getImportTrackTemplateMenuItem(null));
+ fileMenu.add(new JSeparator());
+
final JMenuItem fileMenuExit;
if(!close)
fileMenuExit = new JMenuItem("Exit");
@@ -1199,7 +1229,11 @@ public class DNADraw extends ScrollPanel
graph_menu.add(gc);
final JCheckBoxMenuItem gcPlot = new JCheckBoxMenuItem("Draw");
- gcPlot.setState(false);
+
+ if(gcGraph == null)
+ gcPlot.setState(false);
+ else
+ gcPlot.setState(true);
gcPlot.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent event)
@@ -1236,8 +1270,12 @@ public class DNADraw extends ScrollPanel
JMenu gcSkew = new JMenu("GC Skew");
graph_menu.add(gcSkew);
- final JCheckBoxMenuItem gcSkewPlot = new JCheckBoxMenuItem("GC Skew plot");
- gcSkewPlot.setState(false);
+ final JCheckBoxMenuItem gcSkewPlot = new JCheckBoxMenuItem("Draw");
+ if(gcSkewGraph == null)
+ gcSkewPlot.setState(false);
+ else
+ gcSkewPlot.setState(true);
+
gcSkewPlot.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent event)
@@ -1277,8 +1315,11 @@ public class DNADraw extends ScrollPanel
JMenu user = new JMenu("User");
graph_menu.add(user);
- final JCheckBoxMenuItem userPlot = new JCheckBoxMenuItem("User plot");
- userPlot.setState(false);
+ final JCheckBoxMenuItem userPlot = new JCheckBoxMenuItem("Draw");
+ if(userGraph == null)
+ userPlot.setState(false);
+ else
+ userPlot.setState(true);
userPlot.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent event)
@@ -1377,12 +1418,12 @@ public class DNADraw extends ScrollPanel
if(getArtemisEntryGroup() != null)
{
- viewer = new TrackViewer(DNADraw.this);
+ trackManager = new TrackManager(DNADraw.this);
tracksMenu.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- viewer.setVisible(true);
+ trackManager.setVisible(true);
}
});
}
@@ -1685,7 +1726,7 @@ public class DNADraw extends ScrollPanel
{
Point loc = e.getLocation();
Block b = (Block)t.getTransferData(Block.BLOCK);
- b.setBlockLocation(loc.x,loc.y,viewer);
+ b.setBlockLocation(loc.x,loc.y,trackManager);
DNADraw.this.repaint();
}
catch(Exception ufe){}
@@ -1725,110 +1766,6 @@ public class DNADraw extends ScrollPanel
{
return block;
}
-
- public static void main(String arg[])
- {
- final Wizard wiz = new Wizard(null);
- final DNADraw dna = wiz.getDNADraw();
-
- /**
- final DNADraw dna = new DNADraw();
- final String seq =
- "taaaggtagaattggaaaaattggaaaaattggaaaaatcatgtgatcac"+
- "tgtaaaacaactaacaaatgcaagaatgattatgataaaaataaatgtga"+
- "aaagtgtaaaacgagatgtcaacaatatgataattttattcttaaatgga"+
- "aaactctattcgatatacaatctaagaaatacaaagaattgtatgaacca"+
- "atagatacaaaaaactctacttatgatcatgttgaaaattttgtacaaaa"+
- "gttgaaaaaatataaaaatgaatgttctgttgaaagcgtttctgaatatc"+
- "ttcatgaaacaagtaagtgtttgaattataaatttgatgaaaatgatggt"+
- "tcttctaatatacgatcatatgcttttgaagaaacaccaaaaagttataa"+
- "agaagcttgcagttgtacattaccttctaagaatccattggataattgtc"+
- "ctaccgatcaaaacaaagatgtatgtaaggaattacaaacttttaccttc"+
- "tgctcgaagaatgattatgataataatcttgataattggaacgcatacct"+
- "tgttcttaatagttcagatgataataaaggtgtattgattcctccaagaa"+
- "gaagacatttatgtacaagacctatcactgcatataattatagaaaaggt"+
- "gataaagaaattttaaaaaaaaaacttcttacttctgctttcagtcaagg"+
- "acaattgttaggtcaaaaatataaatcggaagaagagttgtgctttgagg"+
- "caatgaaatatagttatgcagattattccgatataattaaaggaactgat"+
- "atgatggacacttcattatctgaaaaaattaaaaaaatatttgaaacatc"+
- "aaatcaagacactgaagattgtaaaacatggtgggaaaaaaatagaagtc"+
- "atgtatggcacgctatgttatgtggatatatatcaaaaaacaaaaatgag"+
- "aacattaacccaaaatggtgtaatgtacctactgaagatggaactgatca"+
- "attcttaagatggttaattgaatgggcaatgcaagcatgtaaagaaaaga"+
- "aacgtgtaagggattcattaaaaacaaaatgtcgttgttcaaacaaagat"+
- "aattttaaagcgtcagaattattaagacaacctggatgtcagaatgatat"+
- "tagaaaatatattagcttgaatatattgatacaaaattcaatggaaaatc"+
- "taaatataaaatataaaaaattcaaagatcaatcttcaggtttagggttc"+
- "agggtttagggttcagggtttagggtttagggttcagggttttaggttta"+
- "gggttcagggtttagggttcagggtttagggtttagggttcagggtttta"+
- "gggtttagggttcagggtttagggtttaggtttagggtttaggtttaggg"+
- "ttcagggtttaggtttagggttcagggtttaggtttagggttcagggttt"+
- "agggttcagggttcagggtttagggttccggtttagggttcagggttcag"+
- "ggtttagggtttagggtttagggttcagggttcaggtttagggtttaggg"+
- "ttcagggtttagggtttaggtttcagggtttagggtttagggtttagggt"+
- "ttaggtttagggtttagggtttaggtttagggtttagggttcatggttta"+
- "gggtttagggtttagggtttagggtttagggtttaggtttagggttgtgg"+
- "tttagggtttagggtttagggttcagggtttagggtttagggttcagggt";
-
- Bases bases = new Bases(new uk.ac.sanger.artemis.io.RawStreamSequence(seq));
-
- dna.setBases( bases );
- int sequenceLength = bases.getLength();
-
-
- // set sequence length and
- Hashtable lineAttr = new Hashtable();
- lineAttr.put("lsize",new Integer(1));
- lineAttr.put("circular",new Boolean(true));
- lineAttr.put("start",new Integer(0));
- lineAttr.put("end",new Integer(sequenceLength));
- dna.setLineAttributes(lineAttr);
-
- // set ticks
- int div;
- if(sequenceLength < 1000)
- div = 100;
- else if(sequenceLength < 10000)
- div = 1000;
- else if(sequenceLength < 100000)
- div = 10000;
- else
- div = 100000;
- int tick = sequenceLength/div;
- tick = tick*(div/10);
- dna.setMinorTickInterval(tick);
- dna.setTickInterval(tick);
-
- final List features = new Vector();
- features.add(new Feature("a", 20, 250, 2));
- features.add(new Feature("b", 300, 550, 2));
-
- final Track track = new Track(0.9);
- dna.setGeneticMarker(new Vector());
- dna.addFeaturesToTrack(features, track, true);
-
- final Track track2 = new Track(0.8);
- dna.addFeatureToTrack(new Feature("cc", 1400, 1555, 5), track2, true);
- **/
-
- //
- final JFrame f = new JFrame("DNA Viewer");
-
- Dimension d = f.getToolkit().getScreenSize();
- jsp = new JScrollPane(dna);
- jsp.getViewport().setBackground(Color.white);
- f.getContentPane().add(jsp);
- f.setJMenuBar(dna.createMenuBar());
-
- //dna.add(new Graph(dna));
- f.pack();
- f.setLocation(((int)d.getWidth()-f.getWidth())/4,
- ((int)d.getHeight()-f.getHeight())/2);
-
-
- //dna.add(dna.new BlockPanel(dna));
- f.setVisible(true);
- }
public int getBasesPerLine()
@@ -1901,6 +1838,83 @@ public class DNADraw extends ScrollPanel
{
this.borderHeight2 = borderHeight2;
}
+
+ public TrackManager getTrackManager()
+ {
+ return trackManager;
+ }
+
+ public void setTrackManager(TrackManager trackManager)
+ {
+ this.trackManager = trackManager;
+ }
+
+ public Graph getGcGraph()
+ {
+ return gcGraph;
+ }
+
+ public void setGcGraph(Graph gcGraph)
+ {
+ this.gcGraph = gcGraph;
+ }
+
+ public Graph getGcSkewGraph()
+ {
+ return gcSkewGraph;
+ }
+
+ public void setGcSkewGraph(Graph gcSkewGraph)
+ {
+ this.gcSkewGraph = gcSkewGraph;
+ }
+
+ public Graph getUserGraph()
+ {
+ return userGraph;
+ }
+
+ public void setUserGraph(Graph userGraph)
+ {
+ this.userGraph = userGraph;
+ }
+
+ public static void main(String arg[])
+ {
+ final Wizard wiz;
+
+ if(arg.length > 0 && arg[0].equals("-t"))
+ {
+ final File fileTemplate = new File(arg[1]);
+ wiz = new Wizard(fileTemplate);
+ }
+ else
+ wiz = new Wizard((DNADraw)null);
+ final DNADraw dna = wiz.getDNADraw();
+
+ //
+ final String version = dna.getVersion();
+ final JFrame f = new JFrame();
+ if(version == null)
+ f.setTitle("DNA Plot");
+ else
+ f.setTitle("DNA Plot :: "+version);
+
+ Dimension d = f.getToolkit().getScreenSize();
+ jsp = new JScrollPane(dna);
+ jsp.getViewport().setBackground(Color.white);
+ f.getContentPane().add(jsp);
+ f.setJMenuBar(dna.createMenuBar());
+
+ //dna.add(new Graph(dna));
+ f.pack();
+ f.setLocation(((int)d.getWidth()-f.getWidth())/4,
+ ((int)d.getHeight()-f.getHeight())/2);
+
+
+ //dna.add(dna.new BlockPanel(dna));
+ f.setVisible(true);
+ }
/*class BlockPanel extends JPanel
{
diff --git a/uk/ac/sanger/artemis/circular/Graph.java b/uk/ac/sanger/artemis/circular/Graph.java
index d82cd9066b551da8d1d9280ddc4508bdb6872880..156ad5677a402474f2eb70502a3c0bbeefee79d2 100644
--- a/uk/ac/sanger/artemis/circular/Graph.java
+++ b/uk/ac/sanger/artemis/circular/Graph.java
@@ -102,26 +102,7 @@ public abstract class Graph extends JPanel
int nvalues = bases.getLength()/getBaseStepSize();
if(value_array == null)
- {
- value_array = new float [nvalues];
- gcAverage = 0;
- for(int i=0; i<nvalues; i++)
- {
- int start = (i*getBaseStepSize())+1;
- int end = start+getWindowSize();
-
- if(end > bases.getLength())
- end = bases.getLength();
-
- value_array[i] = calculateValue(start, end);
- if(value_array[i] > maxValue)
- maxValue = value_array[i];
- if(value_array[i] < minValue)
- minValue = value_array[i];
- gcAverage += value_array[i];
- }
- gcAverage = gcAverage/nvalues;
- }
+ calcGraphValues();
int minPos = (int)((ddiameter/2.d)*getTrack());
int maxPos = minPos + (int)((ddiameter/2.d)*getGraphHeight());
@@ -181,31 +162,10 @@ public abstract class Graph extends JPanel
int borderHeight2 = getCurrentDna().getBorderHeight2();
Bases bases = getBases();
-
int nvalues = bases.getLength()/getBaseStepSize();
if(value_array == null)
- {
- value_array = new float [nvalues];
- gcAverage = 0;
- for(int i=0; i<nvalues; i++)
- {
- int start = (i*getBaseStepSize())+1;
- int end = start+getWindowSize();
-
- if(end > bases.getLength())
- end = bases.getLength();
-
- value_array[i] = calculateValue(start, end);
- if(value_array[i] > maxValue)
- maxValue = value_array[i];
- if(value_array[i] < minValue)
- minValue = value_array[i];
- gcAverage += value_array[i];
- }
- gcAverage = gcAverage/nvalues;
- }
-
+ calcGraphValues();
int minPos = (int)(lineHeight*(1-getTrack()));
int maxPos = minPos + (int)(lineHeight*getGraphHeight());
@@ -239,6 +199,30 @@ public abstract class Graph extends JPanel
}
}
+ protected void calcGraphValues()
+ {
+ Bases bases = getBases();
+ int nvalues = bases.getLength()/getBaseStepSize();
+ value_array = new float [nvalues];
+ gcAverage = 0;
+ for(int i=0; i<nvalues; i++)
+ {
+ int start = (i*getBaseStepSize())+1;
+ int end = start+getWindowSize();
+
+ if(end > bases.getLength())
+ end = bases.getLength();
+
+ value_array[i] = calculateValue(start, end);
+ if(value_array[i] > maxValue)
+ maxValue = value_array[i];
+ if(value_array[i] < minValue)
+ minValue = value_array[i];
+ gcAverage += value_array[i];
+ }
+ gcAverage = gcAverage/nvalues;
+ }
+
protected int getWindowSize()
{
return windowSize;
@@ -514,6 +498,55 @@ public abstract class Graph extends JPanel
repaint();
}
+ /**
+ * Used to write out options to template file
+ * @return
+ */
+ protected String getOptionsStr()
+ {
+ return "height="+getGraphHeight()+" window_size="+getWindowSize()+
+ " base_step_size="+getBaseStepSize()+" track="+getTrack()+
+ " minus_colour="+getMinusColour().getRed()+":"+
+ getMinusColour().getGreen()+":"+
+ getMinusColour().getBlue()+
+ " plus_colour="+getPlusColour().getRed()+":"+
+ getPlusColour().getGreen()+":"+
+ getPlusColour().getBlue();
+ }
+
+ /**
+ * Used when reading in a template file
+ * @param options
+ */
+ protected void setOptionsStr(final String options[])
+ {
+ for(int i=0; i<options.length; i++)
+ {
+ if(options[i].startsWith("height"))
+ setGraphHeight(Float.parseFloat(options[i+1]));
+ else if(options[i].startsWith("window_size"))
+ setWindowSize(Integer.parseInt(options[i+1]));
+ else if(options[i].startsWith("base_step_size"))
+ setBaseStepSize(Integer.parseInt(options[i+1]));
+ else if(options[i].startsWith("track"))
+ setTrack(Double.parseDouble(options[i+1]));
+ else if(options[i].startsWith("minus_colour"))
+ {
+ String col[] = options[i+1].split(":");
+ setMinusColour(new Color(Integer.parseInt(col[0]),
+ Integer.parseInt(col[1]),
+ Integer.parseInt(col[2])));
+ }
+ else if(options[i].startsWith("plus_colour"))
+ {
+ String col[] = options[i+1].split(":");
+ setPlusColour(new Color(Integer.parseInt(col[0]),
+ Integer.parseInt(col[1]),
+ Integer.parseInt(col[2])));
+ }
+ }
+ }
+
private void setColorButton(final JButton button,
final Color col,
final ActionListener okListener,
diff --git a/uk/ac/sanger/artemis/circular/Track.java b/uk/ac/sanger/artemis/circular/Track.java
index 4c0c2bf556460b55d51c1313b0523fb1a2deaee3..eda2666b36cefac9a53fd17b1636cfcb62e7e51c 100644
--- a/uk/ac/sanger/artemis/circular/Track.java
+++ b/uk/ac/sanger/artemis/circular/Track.java
@@ -21,6 +21,11 @@
package uk.ac.sanger.artemis.circular;
import java.awt.Color;
+import java.io.IOException;
+import java.io.Writer;
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+import java.util.Date;
import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.Feature;
@@ -28,6 +33,7 @@ import uk.ac.sanger.artemis.FeatureKeyPredicate;
import uk.ac.sanger.artemis.FeatureKeyQualifierPredicate;
import uk.ac.sanger.artemis.FeaturePredicate;
import uk.ac.sanger.artemis.io.Key;
+import uk.ac.sanger.artemis.util.FileDocument;
public class Track
{
@@ -235,4 +241,126 @@ public class Track
{
this.colour = colour;
}
+
+ protected void setPropertiesFromTemplate(final String line)
+ {
+ final String properties[] = line.split("\t");
+
+ setPosition(Double.parseDouble(properties[0]));
+ setSize(Float.parseFloat(properties[1]));
+ setShowForward(Boolean.parseBoolean(properties[2]));
+ setShowReverse(Boolean.parseBoolean(properties[3]));
+ setNotQualifier(Boolean.parseBoolean(properties[4]));
+ setAny(Boolean.parseBoolean(properties[5]));
+
+ if(properties[6].equals("null"))
+ setKeyStr(null);
+ else
+ setKeyStr(properties[6]);
+ if(properties[7].equals("null"))
+ setQualifier(null);
+ else
+ setQualifier(properties[7]);
+ if(properties[8].equals("null"))
+ setQualifierValue(null);
+ else
+ setQualifierValue(properties[8]);
+ if(properties[9].equals("null"))
+ setColour(null);
+ else
+ {
+ String colourRGB[] = properties[9].split(":");
+ Color colour = new Color(Integer.parseInt(colourRGB[0]),
+ Integer.parseInt(colourRGB[1]),
+ Integer.parseInt(colourRGB[2]));
+ setColour(colour);
+ }
+ }
+
+ /**
+ * Write the track properties out
+ * @param writer
+ * @throws IOException
+ */
+ protected void write(final Writer writer) throws IOException
+ {
+ writer.write(position+"\t"+
+ size+"\t"+
+ showForward+"\t"+
+ showReverse+"\t"+
+ isNotQualifier()+"\t"+
+ any+"\t"+
+ keyStr+"\t"+
+ qualifier+"\t"+
+ qualifierValue+"\t"+
+ ( colour != null ?
+ colour.getRed()+":"+colour.getGreen()+":"+colour.getBlue() : null)+"\t"+
+ ( entry != null ? entry.getName()+"\t"+entry.getRootDocument() : null )+
+ "\n");
+ }
+
+ /**
+ * Write a header line for the track properties
+ * @param writer
+ * @throws IOException
+ */
+ protected static void writeHeader(final Writer writer, final DNADraw dna) throws IOException
+ {
+ DateFormat dateFormat = new SimpleDateFormat("dd/MM/yyyy HH:mm:ss");
+ writer.write("## DNA Plot :: track template (created: "+
+ dateFormat.format(new Date())+")\n");
+ writer.write("# line attributes: start="+dna.getStart()+
+ " end="+dna.getEnd()+" " +
+ "line_size="+dna.getLineSize()+
+ " circular="+dna.isCircular());
+
+ if(!dna.isCircular())
+ writer.write(" line_height="+dna.getLineHeight()+
+ " bases_per_line="+dna.getBasesPerLine());
+
+ writer.write("\n# tick marks: major="+dna.getTickInterval()+
+ " minor="+dna.getMinorTickInterval()+"\n");
+
+ // graphs
+ if(dna.getUserGraph() != null && dna.containsGraph(dna.getUserGraph()))
+ {
+ FileDocument doc = (FileDocument) ((UserGraph)dna.getUserGraph()).getDocument();
+ String fileName = doc.getFile().getAbsolutePath();
+
+ writer.write("# User Graph: "+dna.getUserGraph().getOptionsStr()+
+ " file_name="+fileName+"\n");
+ }
+ if(dna.getGcGraph() != null && dna.containsGraph(dna.getGcGraph()))
+ writer.write("# GC Graph: "+dna.getGcGraph().getOptionsStr()+"\n");
+ if(dna.getGcSkewGraph() != null && dna.containsGraph(dna.getGcSkewGraph()))
+ writer.write("# GC Skew Graph: "+dna.getGcSkewGraph().getOptionsStr()+"\n");
+
+ writer.write(
+ "# Columns are:\n"+
+ "# POS - track position\n"+
+ "# SIZE - track size\n"+
+ "# FWD - show forward strand features\n"+
+ "# REV - show reverse strand features\n"+
+ "# NOT - use NOT\n"+
+ "# ANY - show any features\n"+
+ "# KEY - show features of this key\n"+
+ "# QUAL - show features with this qualifier\n"+
+ "# VAL - show features with this qualifier value(s)\n"+
+ "# COL - colour for this track e.g. 255:0:0 (R:G:B) or NULL\n"+
+ "# NAME - file entry name or null\n"+
+ "# DIR - root directory for this file\n#\n");
+ writer.write(
+ "#POS\t"+
+ "SIZE\t"+
+ "FWD\t"+
+ "REV\t"+
+ "NOT \t"+
+ "ANY\t"+
+ "KEY\t"+
+ "QUAL\t"+
+ "VAL\t"+
+ "COL\t"+
+ "NAME\t"+
+ "DIR\n");
+ }
}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/circular/TrackViewer.java b/uk/ac/sanger/artemis/circular/TrackManager.java
similarity index 75%
rename from uk/ac/sanger/artemis/circular/TrackViewer.java
rename to uk/ac/sanger/artemis/circular/TrackManager.java
index 833f744b0fb8da4542001d1e2a54e74969ecc713..aec1accef32d8122e1feed990a08ff7ead3342d4 100644
--- a/uk/ac/sanger/artemis/circular/TrackViewer.java
+++ b/uk/ac/sanger/artemis/circular/TrackManager.java
@@ -29,13 +29,24 @@ import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.Writer;
import java.util.StringTokenizer;
import java.util.Vector;
import javax.swing.JButton;
import javax.swing.JCheckBox;
+import javax.swing.JFileChooser;
import javax.swing.JFrame;
import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
@@ -51,11 +62,12 @@ import uk.ac.sanger.artemis.FeaturePredicateVector;
import uk.ac.sanger.artemis.FeatureVector;
import uk.ac.sanger.artemis.components.KeyChoice;
import uk.ac.sanger.artemis.components.QualifierChoice;
+import uk.ac.sanger.artemis.components.StickyFileChooser;
import uk.ac.sanger.artemis.io.Key;
import uk.ac.sanger.artemis.io.Range;
import uk.ac.sanger.artemis.io.RangeVector;
-class TrackViewer extends JFrame
+class TrackManager extends JFrame
{
private static final long serialVersionUID = 1L;
private DNADraw dnaDraw;
@@ -70,21 +82,147 @@ class TrackViewer extends JFrame
private TextFieldFloat trackSize[];
private TextFieldFloat trackPosition[];
- public TrackViewer(final DNADraw dnaDraw)
+ public TrackManager(final DNADraw dnaDraw)
{
super("Track Manager");
this.dnaDraw = dnaDraw;
setDefaultCloseOperation(JFrame.HIDE_ON_CLOSE);
+
+ createMenu();
JScrollPane jsp = new JScrollPane(getPanelComponents());
getContentPane().add(jsp);
pack();
}
- protected void refresh()
+ /**
+ * Create a menu for the track manager.
+ */
+ private void createMenu()
{
- getContentPane().removeAll();
- getContentPane().add(getPanelComponents());
- pack();
+ final JMenu menuFile = new JMenu("File");
+ final JMenuBar menuBar = new JMenuBar();
+ setJMenuBar(menuBar);
+ menuBar.add(menuFile);
+ menuFile.add(getExportTrackTemplateMenuItem(this, dnaDraw));
+ menuFile.add(getImportTrackTemplateMenuItem(this));
+ final JMenuItem closeMenu = new JMenuItem("Close");
+ closeMenu.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ TrackManager.this.setVisible(false);
+ }
+ });
+ menuFile.add(closeMenu);
+ }
+
+ protected JMenuItem getImportTrackTemplateMenuItem(final JFrame f)
+ {
+ final JMenuItem readTemplate = new JMenuItem("Import Track Template...");
+ readTemplate.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent arg0)
+ {
+ StickyFileChooser fileDialog = new StickyFileChooser();
+ int status = fileDialog.showOpenDialog(f);
+ if(status == JFileChooser.CANCEL_OPTION)
+ return;
+
+ final File fileRead = fileDialog.getSelectedFile();
+ if(!fileRead.exists())
+ {
+ JOptionPane.showMessageDialog(f,
+ fileRead.getName()+" not found.",
+ "Problem Reading File",
+ JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ try
+ {
+ final FileReader reader = new FileReader(fileRead);
+ BufferedReader inputStream = new BufferedReader(reader);
+ String inLine = null;
+
+ Track[] tracks = Wizard.getTracks();
+ int trackCount = 0;
+
+ while ((inLine = inputStream.readLine()) != null)
+ {
+ if(inLine.startsWith("#") || inLine.trim().equals(""))
+ continue;
+
+ if(trackCount >= tracks.length)
+ {
+ addTrack();
+ tracks = Wizard.getTracks();
+ }
+ tracks[trackCount].setPropertiesFromTemplate(inLine);
+ trackCount++;
+ }
+ inputStream.close();
+ reader.close();
+ refresh();
+ }
+ catch(FileNotFoundException e)
+ {
+ e.printStackTrace();
+ }
+ catch(IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ });
+ return readTemplate;
+ }
+
+ /**
+ * Menu Item with associated ActionListener for exporting the properties
+ * of this track.
+ * @param f
+ * @return
+ */
+ protected static JMenuItem getExportTrackTemplateMenuItem(final JFrame f,
+ final DNADraw dnaDraw)
+ {
+ final JMenuItem saveTemplate = new JMenuItem("Export Track Template...");
+ saveTemplate.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent arg0)
+ {
+ StickyFileChooser fileDialog = new StickyFileChooser();
+ int status = fileDialog.showSaveDialog(f);
+ if(status == JFileChooser.CANCEL_OPTION)
+ return;
+
+ final File fileWrite = fileDialog.getSelectedFile();
+ if(fileWrite.exists())
+ {
+ status = JOptionPane.showConfirmDialog(f, fileWrite.getName()+
+ " exists. Overwrite?",
+ "Selected File Exists",
+ JOptionPane.OK_CANCEL_OPTION);
+ if(status == JFileChooser.CANCEL_OPTION)
+ return;
+ }
+
+ final Track[] tracks = Wizard.getTracks();
+ try
+ {
+ final Writer writer = new FileWriter(fileWrite);
+ Track.writeHeader(writer, dnaDraw);
+ for(int i=0; i<tracks.length; i++)
+ tracks[i].write(writer);
+ writer.close();
+ }
+ catch(IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ });
+ return saveTemplate;
}
private JPanel getPanelComponents()
@@ -344,9 +482,7 @@ class TrackViewer extends JFrame
pack();
setVisible(true);
- update(Wizard.getTracks(), keyChoice, qualifierChoice, qualifierValue,
- notQualifier, showForward, showReverse,
- showAny, trackSize, trackPosition);
+ update(Wizard.getTracks());
}
});
optionBox.add(deleteTrack, c);
@@ -362,9 +498,7 @@ class TrackViewer extends JFrame
{
public void actionPerformed(ActionEvent e)
{
- update(tracks, keyChoice, qualifierChoice, qualifierValue,
- notQualifier, showForward, showReverse,
- showAny, trackSize, trackPosition);
+ update(tracks);
}
});
@@ -378,36 +512,39 @@ class TrackViewer extends JFrame
{
public void actionPerformed(ActionEvent e)
{
- Entry entry;
- if(Wizard.getTracks().length > 0)
- entry = Wizard.getTracks()[0].getEntry();
- else
- entry = dnaDraw.getArtemisEntryGroup().elementAt(0);
-
- Wizard.addTrack( entry );
- getContentPane().removeAll();
-
- JScrollPane jsp = new JScrollPane(getPanelComponents());
- getContentPane().add(jsp);
- pack();
-
- setVisible(true);
+ addTrack();
}
});
return optionBox;
}
- private void update(final Track[] tracks,
- final KeyChoice keyChoice[],
- final QualifierChoice qualifierChoice[],
- final JTextField qualifierValue[] ,
- final JCheckBox notQualifier[],
- final JCheckBox showForward[],
- final JCheckBox showReverse[],
- final JCheckBox showAny[],
- final TextFieldFloat trackSize[],
- final TextFieldFloat trackPosition[])
+ protected void refresh()
+ {
+ getContentPane().removeAll();
+ JScrollPane jsp = new JScrollPane(getPanelComponents());
+ getContentPane().add(jsp);
+ pack();
+ }
+
+ private void addTrack()
+ {
+ Entry entry;
+ if(Wizard.getTracks().length > 0)
+ entry = Wizard.getTracks()[0].getEntry();
+ else
+ entry = dnaDraw.getArtemisEntryGroup().elementAt(0);
+
+ Wizard.addTrack( entry );
+ refresh();
+ setVisible(true);
+ }
+
+ /**
+ * Update the tracks based on the Track Manager settings
+ * @param tracks
+ */
+ protected void update(final Track[] tracks)
{
// update tracks
for(int i=0; i<tracks.length; i++)
@@ -472,15 +609,21 @@ class TrackViewer extends JFrame
}
tracks[i].setShowForward(showForward[i].isSelected());
tracks[i].setShowReverse(showReverse[i].isSelected());
+ tracks[i].setNotQualifier(!notQualifier[i].isSelected());
tracks[i].setSize((float) trackSize[i].getValue());
tracks[i].setPosition(trackPosition[i].getValue());
}
// update viewer
+ updateDNADraw(dnaDraw, tracks);
+ }
+
+
+ private static void updateDNADraw(final DNADraw dnaDraw, final Track[] tracks)
+ {
dnaDraw.getBlock().removeAll(dnaDraw.getBlock());
final FeatureVector features = dnaDraw.getArtemisEntryGroup().getAllFeatures();
-
for(int i=0; i<features.size(); i++)
{
Feature f = features.elementAt(i);
diff --git a/uk/ac/sanger/artemis/circular/UserGraph.java b/uk/ac/sanger/artemis/circular/UserGraph.java
index 4b3346250aa8572f59f444839ac965d4c152a85f..fe6cd2fc9eca6ae9e5a824430d9be2d039834aca 100644
--- a/uk/ac/sanger/artemis/circular/UserGraph.java
+++ b/uk/ac/sanger/artemis/circular/UserGraph.java
@@ -55,12 +55,15 @@ public class UserGraph extends Graph
* The average calculated by readData ().
**/
private float average_value = 0;
+
+ private Document document;
public UserGraph(DNADraw currentDna, final Document document)
throws IOException
{
super(currentDna);
+ this.document = document;
final Reader document_reader = document.getReader();
LinePushBackReader pushback_reader =
@@ -147,5 +150,10 @@ public class UserGraph extends Graph
}
average_value /= seqLength;
}
+
+ public Document getDocument()
+ {
+ return document;
+ }
}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/circular/Wizard.java b/uk/ac/sanger/artemis/circular/Wizard.java
index 34cada978d1c283a5c682e6068e91dda02cf2fa7..495b81743d75622c00de3a0c5dcd129ec1b1c24d 100644
--- a/uk/ac/sanger/artemis/circular/Wizard.java
+++ b/uk/ac/sanger/artemis/circular/Wizard.java
@@ -24,14 +24,21 @@ package uk.ac.sanger.artemis.circular;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
import java.util.Vector;
import java.util.Hashtable;
import javax.swing.Box;
import javax.swing.ButtonGroup;
+import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
+import javax.swing.JProgressBar;
import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
import javax.swing.JSeparator;
@@ -43,10 +50,17 @@ import uk.ac.sanger.artemis.Feature;
import uk.ac.sanger.artemis.FeatureVector;
import uk.ac.sanger.artemis.Options;
import uk.ac.sanger.artemis.SimpleEntryGroup;
+import uk.ac.sanger.artemis.components.EntryFileDialog;
+import uk.ac.sanger.artemis.components.MessageDialog;
+import uk.ac.sanger.artemis.components.StickyFileChooser;
+import uk.ac.sanger.artemis.components.Utilities;
+import uk.ac.sanger.artemis.io.EntryInformation;
import uk.ac.sanger.artemis.io.Range;
import uk.ac.sanger.artemis.io.RangeVector;
import uk.ac.sanger.artemis.sequence.Bases;
import uk.ac.sanger.artemis.sequence.NoSequenceException;
+import uk.ac.sanger.artemis.util.Document;
+import uk.ac.sanger.artemis.util.DocumentFactory;
import uk.ac.sanger.artemis.util.OutOfRangeException;
@@ -73,6 +87,18 @@ public class Wizard
// option 2 - edit existing dna
if(n == 0)
dna = getDNADrawFromFile(dna_current);
+ else if(n == 3)
+ {
+ StickyFileChooser chooser = new StickyFileChooser();
+ chooser.showOpenDialog(null);
+
+ File fileTemplate = chooser.getSelectedFile();
+ if(!fileTemplate.exists())
+ JOptionPane.showMessageDialog(null,
+ fileTemplate.getName()+" cannot be found!",
+ "Missing File", JOptionPane.WARNING_MESSAGE);
+ loadTemplate(fileTemplate);
+ }
else if(n == 1 || n == 2)
{
Vector block = new Vector();
@@ -165,8 +191,286 @@ public class Wizard
s = la.getEnd();
dna.setEnd(s);
+ }
+ }
+
+ /**
+ * Open a DNA plot based on a template file
+ * @param template
+ */
+ public Wizard(final File template)
+ {
+ loadTemplate(template);
+ }
+
+ /**
+ * Load from a template file
+ * @param template
+ */
+ private void loadTemplate(final File template)
+ {
+ final JFrame f = new JFrame();
+ f.setUndecorated(true);
+ JPanel panel = (JPanel) f.getContentPane();
+ JProgressBar progress = new JProgressBar(1,10);
+ progress.setStringPainted(true);
+ progress.setString("Reading from "+template.getName()+" ");
+ progress.setValue(2);
+ progress.setPreferredSize(new Dimension(350, progress.getPreferredSize().height));
+ panel.add(progress, BorderLayout.CENTER);
+ f.pack();
+ Utilities.centreFrame(f);
+ f.setVisible(true);
+
+ if(dna == null)
+ dna = new DNADraw();
+ Options.getOptions();
+
+
+ try
+ {
+ final FileReader reader = new FileReader(template);
+ final BufferedReader inputStream = new BufferedReader(reader);
+ final EntryGroup entryGroup = new SimpleEntryGroup();
+ final Hashtable fileEntrys = new Hashtable();
+ Vector v_tracks = new Vector();
+ String inLine = null;
+ String lineAttrStr[] = null;
+ String tickMarksStr[] = null;
+ String gcGraphStr[] = null;
+ String gcSkewGraphStr[] = null;
+ String userGraphStr[] = null;
+
+ String lineAttrStart = "# line attributes:";
+ String tickMarksStart = "# tick marks:";
+ String gcGraphStart = "# GC Graph:";
+ String gcSkewGraphStart = "# GC Skew Graph:";
+ String userGraphStart = "# User Graph:";
+
+ while((inLine = inputStream.readLine()) != null)
+ {
+ if(inLine.startsWith("#") || inLine.trim().equals(""))
+ {
+ if(inLine.startsWith(lineAttrStart))
+ lineAttrStr = inLine.substring(lineAttrStart.length()).trim().split("[=\\s]");
+ else if(inLine.startsWith(tickMarksStart))
+ tickMarksStr = inLine.substring(tickMarksStart.length()).trim().split("[=\\s]");
+ else if(inLine.startsWith(gcGraphStart))
+ gcGraphStr = inLine.substring(gcGraphStart.length()).trim().split("[=\\s]");
+ else if(inLine.startsWith(gcSkewGraphStart))
+ gcSkewGraphStr = inLine.substring(gcSkewGraphStart.length()).trim().split("[=\\s]");
+ else if(inLine.startsWith(userGraphStart))
+ userGraphStr = inLine.substring(userGraphStart.length()).trim().split("[=\\s]");
+ continue;
+ }
+
+ String properties[] = inLine.split("\t");
+ String fileName = properties[11] + File.separator + properties[10];
+ Entry entry;
+ if(!fileEntrys.containsKey(fileName))
+ {
+ progress.setString("Reading "+properties[10]);
+ progress.setValue(4);
+ entry = getEntry(fileName, entryGroup);
+ if(entry == null)
+ continue;
+ fileEntrys.put(fileName, entry);
+ }
+ else
+ {
+ entry = (Entry)fileEntrys.get(fileName);
+ }
+
+ Track track = new Track(.9,entry);
+ track.setPropertiesFromTemplate(inLine);
+ v_tracks.add(track);
+ }
+ inputStream.close();
+ reader.close();
+
+ progress.setString("Read template "+template.getName());
+ progress.setValue(7);
+ Track[] newTracks = new Track[v_tracks.size()];
+ for(int i=0; i<v_tracks.size(); i++)
+ newTracks[i] = (Track) v_tracks.get(i);
+
+ Wizard.tracks = newTracks;
+
+ dna.setArtemisEntryGroup(entryGroup);
+
+ int sequenceLength = entryGroup.getSequenceEntry().getBases().getLength();
+
+ Hashtable lineAttr = new Hashtable();
+ lineAttr.put("lsize", new Integer(1));
+ lineAttr.put("circular", new Boolean(true));
+ lineAttr.put("start", new Integer(0));
+ lineAttr.put("end", new Integer(sequenceLength));
+ if(lineAttrStr != null)
+ {
+ for(int i=0; i<lineAttrStr.length; i++)
+ {
+ if(lineAttrStr[i].startsWith("line_size"))
+ lineAttr.put("lsize", new Integer(lineAttrStr[i+1]));
+ else if(lineAttrStr[i].startsWith("circular"))
+ lineAttr.put("circular", new Boolean(lineAttrStr[i+1]));
+ else if(lineAttrStr[i].startsWith("line_height"))
+ dna.setLineHeight(Float.parseFloat(lineAttrStr[i+1]));
+ else if(lineAttrStr[i].startsWith("bases_per_line"))
+ dna.setBasesPerLine(Integer.parseInt(lineAttrStr[i+1]));
+ }
+ }
+ dna.setLineAttributes(lineAttr);
+
+ final int div;
+ if(sequenceLength < 1000)
+ div = 100;
+ else if(sequenceLength < 10000)
+ div = 1000;
+ else if(sequenceLength < 100000)
+ div = 10000;
+ else
+ div = 100000;
+ int tick = sequenceLength / div;
+ tick = tick * (div / 10);
+ int tick2 = tick / 2;
+ tick = tick2 * 2;
+
+ if(tickMarksStr != null)
+ {
+ for(int i=0; i<tickMarksStr.length; i++)
+ {
+ if(tickMarksStr[i].startsWith("major"))
+ tick = Integer.parseInt(tickMarksStr[i+1]);
+ else if(tickMarksStr[i].startsWith("minor"))
+ tick2 = Integer.parseInt(tickMarksStr[i+1]);
+ }
+ }
+
+ dna.setGeneticMarker(new Vector());
+ dna.setRestrictionEnzyme(new Vector());
+ dna.setMinorTickInterval(tick2);
+ dna.setTickInterval(tick);
+
+ TrackManager trackManager = dna.getTrackManager();
+ if(trackManager == null)
+ {
+ trackManager = new TrackManager(dna);
+ dna.setTrackManager(trackManager);
+ }
+ trackManager.update(tracks);
+ loadGraphs(gcGraphStr, gcSkewGraphStr, userGraphStr, dna, progress);
+ }
+ catch(FileNotFoundException e)
+ {
+ e.printStackTrace();
+ }
+ catch(IOException e)
+ {
+ e.printStackTrace();
+ }
+ catch(NoSequenceException e)
+ {
+ e.printStackTrace();
+ }
+ f.dispose();
+ }
+
+ /**
+ *
+ * @param gcGraphStr
+ * @param gcSkewGraphStr
+ * @param userGraphStr
+ * @param dna
+ */
+ private void loadGraphs(final String gcGraphStr[],
+ final String gcSkewGraphStr[],
+ final String userGraphStr[],
+ final DNADraw dna,
+ final JProgressBar progress)
+ {
+ if(gcGraphStr != null)
+ {
+ if(progress != null)
+ progress.setString("Calculating GC graph points");
+ GCGraph gcGraph = new GCGraph(dna);
+ gcGraph.setOptionsStr(gcGraphStr);
+ dna.setGcGraph(gcGraph);
+ gcGraph.calcGraphValues();
+ dna.add(gcGraph);
+ }
+ if(gcSkewGraphStr != null)
+ {
+ if(progress != null)
+ progress.setString("Calculating GC Skew graph points");
+ GCSkewGraph gcSkewGraph = new GCSkewGraph(dna);
+ gcSkewGraph.setOptionsStr(gcSkewGraphStr);
+ dna.setGcSkewGraph(gcSkewGraph);
+ gcSkewGraph.calcGraphValues();
+ dna.add(gcSkewGraph);
+ }
+ if(userGraphStr != null)
+ {
+ String fileName = null;
+ for(int i=0;i<userGraphStr.length; i++)
+ {
+ if(userGraphStr[i].startsWith("file_name"))
+ fileName = userGraphStr[i+1];
+ }
+ final uk.ac.sanger.artemis.util.Document document =
+ new uk.ac.sanger.artemis.util.FileDocument(new File(fileName));
+ try
+ {
+ if(progress != null)
+ progress.setString("Calculating user graph points");
+ UserGraph userGraph = new UserGraph(dna, document);
+ userGraph.setOptionsStr(userGraphStr);
+ dna.setUserGraph(userGraph);
+ userGraph.calcGraphValues();
+ dna.add(userGraph);
+ }
+ catch(IOException e)
+ {
+ e.printStackTrace();
+ return;
+ }
+ }
+ }
+
+ private Entry getEntry(final String entryFileName, final EntryGroup entryGroup)
+ throws NoSequenceException
+ {
+ final Document entry_document = DocumentFactory.makeDocument(entryFileName);
+ final EntryInformation artemis_entry_information =
+ Options.getArtemisEntryInformation();
+
+ final uk.ac.sanger.artemis.io.Entry new_embl_entry =
+ EntryFileDialog.getEntryFromFile(null, entry_document,
+ artemis_entry_information,
+ false);
+
+ if(new_embl_entry == null) // the read failed
+ return null;
+ Entry entry = null;
+ try
+ {
+ Bases bases = null;
+ if(entryGroup.getSequenceEntry() != null)
+ bases = entryGroup.getSequenceEntry().getBases();
+ if(bases == null)
+ entry = new Entry(new_embl_entry);
+ else
+ entry = new Entry(bases,new_embl_entry);
+
+ entryGroup.add(entry);
+ }
+ catch(OutOfRangeException e)
+ {
+ new MessageDialog(null, "read failed: one of the features in " +
+ entryFileName + " has an out of range " +
+ "location: " + e.getMessage());
}
+ return entry;
}
/**
@@ -377,10 +681,8 @@ public class Wizard
JRadioButton[] radioButtons;
- if(dna_current != null)
- radioButtons = new JRadioButton[3];
- else
- radioButtons = new JRadioButton[2];
+ radioButtons = new JRadioButton[3];
+
final ButtonGroup group = new ButtonGroup();
radioButtons[0] = new JRadioButton("Read in sequence file");
group.add(radioButtons[0]);
@@ -390,14 +692,20 @@ public class Wizard
bdown.add(radioButtons[0]);
bdown.add(radioButtons[1]);
+ radioButtons[0].setSelected(true);
if(dna_current != null)
{
radioButtons[2] = new JRadioButton("Edit current dna display");
group.add(radioButtons[2]);
radioButtons[2].setSelected(true);
- bdown.add(radioButtons[2]);
}
-
+ else
+ {
+ radioButtons[2] = new JRadioButton("Read template file");
+ group.add(radioButtons[2]);
+ }
+ bdown.add(radioButtons[2]);
+
JPanel pane = new JPanel(new BorderLayout());
pane.add(bdown);
JOptionPane.showMessageDialog(null,
@@ -408,8 +716,10 @@ public class Wizard
return 0;
else if(radioButtons[1].isSelected())
return 1;
- else if(radioButtons[2].isSelected())
+ else if(radioButtons[2].isSelected() && dna_current != null)
return 2;
+ else if(radioButtons[2].isSelected())
+ return 3;
return 1;
}