From 65ea2d45f6812649eac1efbf0d9ac9fdb492b485 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 15 Aug 2008 15:24:46 +0000
Subject: [PATCH] draw linear plots fixed and printing single page image files
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8565 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/circular/Block.java | 102 ++++++++---
uk/ac/sanger/artemis/circular/DNADraw.java | 166 +++++++++++++++---
.../artemis/circular/LineAttribute.java | 16 +-
.../artemis/circular/PrintDNAImage.java | 59 +++++--
4 files changed, 269 insertions(+), 74 deletions(-)
diff --git a/uk/ac/sanger/artemis/circular/Block.java b/uk/ac/sanger/artemis/circular/Block.java
index 83035a63d..8e3e31e3f 100644
--- a/uk/ac/sanger/artemis/circular/Block.java
+++ b/uk/ac/sanger/artemis/circular/Block.java
@@ -28,6 +28,7 @@ import java.awt.*;
import java.awt.datatransfer.*;
import java.awt.event.*;
import java.io.IOException;
+import java.util.Vector;
import javax.swing.event.*;
@@ -38,7 +39,7 @@ public class Block implements Transferable
private double angStart;
private double angEnd;
- private Rectangle rect = new Rectangle();
+ private Vector rect;
private boolean drawLabel = false;
final public static DataFlavor BLOCK =
new DataFlavor(Block.class, "Block");
@@ -217,7 +218,7 @@ public class Block implements Transferable
{
public void actionPerformed(ActionEvent e)
{
- dialog.show();
+ dialog.setVisible(true);
}
});
bacross = Box.createHorizontalBox();
@@ -350,7 +351,7 @@ public class Block implements Transferable
f.setVisible(true);
}
- protected void drawLinear(Graphics2D g2)
+ protected void drawLinear(final Graphics2D g2)
{
RenderingHints qualityHints = new RenderingHints(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
@@ -361,31 +362,34 @@ public class Block implements Transferable
String markerLabel = getLabel();
int bstart = getBstart();
int bend = getBend();
+
- float strokeSize2 = getStrokeSize()/2.f;
-
FontMetrics fm = g2.getFontMetrics();
- //double hgt = fm.getAscent();
g2.setColor(getColour());
- double ddiameter = current_dna.getDiameter();
- double heightPanel = current_dna.getHeight();
- Point location = current_dna.getLocationPoint();
- int ymid = (int)(heightPanel/2.);
+ //int shift = (int)getTrack().getPosition();
- int shift = (int)getTrack().getPosition();
- if(shift > 1 && shift < (int)heightPanel)
- ymid = shift;
+ int basesPerLine = current_dna.getBasesPerLine();
+ int lineNumberStart = Math.round((float)(bstart-1)/((float)basesPerLine) + 0.5f)-1;
+ int lineNumberEnd = Math.round((float)(bend-1)/((float)basesPerLine) + 0.5f)-1;
+ float singleBaseWidth = current_dna.getSingleBaseWidth();
+
+ int border2 = current_dna.getBorder2();
+
+ int ypos = (int) ( (lineNumberStart*current_dna.getLineHeight()) - (strokeSize/2.f) -
+ ((1-track.getPosition())*current_dna.getLineHeight()) +
+ border2+current_dna.getLineHeight());
- int start = current_dna.getStart();
- int end = current_dna.getEnd();
- g2.setStroke(new BasicStroke(strokeSize));
+ int xstart = (int) ((bstart-(lineNumberStart*basesPerLine))*singleBaseWidth)+border2;
+ int xend = (int) ((bend-(lineNumberEnd*basesPerLine))*singleBaseWidth)+border2;
+
+ BasicStroke basicstroke = new BasicStroke(
+ strokeSize,
+ BasicStroke.CAP_BUTT,
+ BasicStroke.JOIN_MITER);
+ g2.setStroke(basicstroke);
- int xend = (((int)ddiameter-location.x)*(bend-start)/
- (end-start))+location.x-(int)strokeSize2;
- int xstart = (((int)ddiameter-location.x)*(bstart-start)/
- (end-start))+location.x+(int)strokeSize2;
- if(arrowHead)
+ /*if(arrowHead)
{
xend-=strokeSize2;
int[] xPoints = {xend,xend,xend+(int)strokeSize};
@@ -402,15 +406,52 @@ public class Block implements Transferable
g2.fillPolygon(xPoints,yPoints,3);
g2.drawLine(xstart,ymid,xend,ymid);
}
- else
- g2.drawLine(xstart,ymid,xend,ymid);
+ else*/
+
+ if(rect == null)
+ rect = new Vector();
+ Rectangle r;
+
+ if(lineNumberEnd > lineNumberStart)
+ {
+ g2.drawLine(xstart,ypos,current_dna.getWidth()-border2,ypos);
+ r = new Rectangle();
+ r.setLocation(xstart,ypos);
+ r.setSize(current_dna.getWidth()-border2-xstart,(int)strokeSize);
+ rect.add(r);
+
+ for(int i=lineNumberStart+1; i<lineNumberEnd; i++)
+ {
+ ypos = (int) ( (i*current_dna.getLineHeight()) - (strokeSize/2.f) -
+ ((1-track.getPosition())*current_dna.getLineHeight()) +
+ border2+current_dna.getLineHeight());
+ g2.drawLine(border2,ypos,current_dna.getWidth()-border2,ypos);
+
+ r = new Rectangle();
+ r.setLocation(border2,ypos);
+ r.setSize(current_dna.getWidth()-border2-border2,(int)strokeSize);
+ rect.add(r);
+ }
+
+ ypos = (int) ( (lineNumberEnd*current_dna.getLineHeight()) - (strokeSize/2.f) -
+ ((1-track.getPosition())*current_dna.getLineHeight()) +
+ border2+current_dna.getLineHeight());
+ xstart = border2;
+ }
+
+ g2.drawLine(xstart,ypos,xend,ypos);
+
+ r = new Rectangle();
+ r.setLocation(xstart,ypos);
+ r.setSize(xend-xstart,(int)strokeSize);
+ rect.add(r);
+
+
if(drawLabel)
{
- rect.setLocation(xstart,ymid-(int)strokeSize2);
- rect.setSize(xend-xstart,(int)strokeSize);
int xmid = xstart+(int)(((xend-xstart)/2.)-(fm.stringWidth(markerLabel)/2.));
- g2.drawString(markerLabel,xmid,ymid-strokeSize);
+ g2.drawString(markerLabel,xmid,ypos-strokeSize);
}
}
@@ -718,7 +759,14 @@ public class Block implements Transferable
}
}
else
- return rect.contains(x,y);
+ {
+ for(int i=0; i<rect.size(); i++)
+ {
+ Rectangle r = (Rectangle)rect.get(i);
+ if(r.contains(x,y))
+ return true;
+ }
+ }
return false;
}
diff --git a/uk/ac/sanger/artemis/circular/DNADraw.java b/uk/ac/sanger/artemis/circular/DNADraw.java
index 9cb79185d..27ababfa0 100644
--- a/uk/ac/sanger/artemis/circular/DNADraw.java
+++ b/uk/ac/sanger/artemis/circular/DNADraw.java
@@ -60,7 +60,6 @@ import java.awt.dnd.DropTargetDropEvent;
import java.awt.dnd.DropTargetEvent;
import java.awt.dnd.DropTargetListener;
import java.io.IOException;
-import java.net.URL;
import javax.swing.JButton;
import javax.swing.JCheckBoxMenuItem;
@@ -129,7 +128,14 @@ public class DNADraw extends ScrollPanel
protected static int THETA = -90;
private TrackViewer viewer;
private AffineTransform original;
-
+
+ // linear plot variables
+ private int numberOfLines;
+ private int basesPerLine = 10000;
+ private float lineHeight = 100.f;
+ private float singleBaseWidth;
+ private int border2;
+
public DNADraw()
{
super(new BorderLayout());
@@ -335,8 +341,7 @@ public class DNADraw extends ScrollPanel
protected void paintComponent(Graphics g)
{
super.paintComponent(g);
- Graphics2D g2 = (Graphics2D)g;
-
+ Graphics2D g2 = (Graphics2D)g;
if(isCircular())
drawCircularPanel(g2,true);
@@ -366,7 +371,7 @@ public class DNADraw extends ScrollPanel
double hgt = fm.getAscent();
g2.setColor(Color.black);
double widDash = 4;
-
+
int lineSize = 5;
try
{
@@ -378,18 +383,33 @@ public class DNADraw extends ScrollPanel
}
g2.setStroke(new BasicStroke((float)lineSize));
- double widthPanel = getWidth();
- double ddiameter = widthPanel-border.getWidth();
- int diameter = (int)ddiameter;
- int ymid = getHeight()/2;
+ border2 = border.width/2;
g2.setStroke(new BasicStroke((float)lineSize));
- g2.drawLine(location.x,ymid,
- diameter,ymid);
-
- int start = getStart();
- int end = getEnd();
-
+
+ int lastBase = getEnd();
+ numberOfLines = Math.round( (lastBase/basesPerLine) + 0.5f);
+
+ int height = (int) ((numberOfLines * lineHeight)+border.height);
+ Dimension size = new Dimension(getWidth(),height);
+ setPreferredSize(size);
+ setSize(size);
+
+ singleBaseWidth = (float)(getWidth()-border.width)/(float)basesPerLine;
+
+ for(int i=0; i<numberOfLines; i++)
+ {
+ int ypos = (int) (border2+lineHeight+(lineHeight*i));
+
+ if(i<numberOfLines-1)
+ g2.drawLine(border2,ypos,getWidth()-border2,ypos);
+ else
+ {
+ int lastLineWidth = (int) ((lastBase-(i*basesPerLine))*singleBaseWidth)+border2;
+ g2.drawLine(border2,ypos,lastLineWidth,ypos);
+ }
+ }
+
g2.setColor(Color.black);
g2.setStroke(new BasicStroke(1.f));
@@ -400,25 +420,37 @@ public class DNADraw extends ScrollPanel
while(enumTk.hasMoreElements())
{
int tick = ((Integer)enumTk.nextElement()).intValue();
- int x = ((diameter-location.x)*(tick-start)/(end-start))+location.x;
- int y = ymid+(int)((lineSize+widDash)/2);
- g2.drawLine(x,ymid,x,y);
+ int lineNumber = Math.round((float)(tick-1)/((float)basesPerLine) + 0.5f)-1;
+
+ int ypos = (int) (border2+lineHeight+(lineHeight*lineNumber));
+ int xpos = (int) ((tick-(lineNumber*basesPerLine))*singleBaseWidth)+border2;
+ int y = ypos+(int)((lineSize+widDash)/2);
+
+ g2.drawLine(xpos,ypos,xpos,y);
}
enumTk = majorTicks.elements();
while(enumTk.hasMoreElements())
{
int tick = ((Integer)enumTk.nextElement()).intValue();
- int x = ((diameter-location.x)*(tick-start)/(end-start))+location.x;
- int y = ymid+(lineSize/2)+(int)widDash;
- g2.drawLine(x,ymid,x,y);
+ int lineNumber = Math.round((float)(tick-1)/((float)basesPerLine) + 0.5f)-1;
+
+ if(lineNumber < 0)
+ lineNumber = 0;
+
+ int ypos = (int) (border2+lineHeight+(lineHeight*lineNumber));
+ int xpos = (int) ((tick-(lineNumber*basesPerLine))*singleBaseWidth)+border2;
+ int y = ypos+(int)((lineSize+widDash)/2);
+
+ g2.drawLine(xpos,ypos,xpos,y);
+
String label = Integer.toString(tick);
- x-=(fm.stringWidth(label)/2);
+ xpos-=(fm.stringWidth(label)/2);
y+=hgt;
- g2.drawString(label,x,y);
+ g2.drawString(label,xpos,y);
}
- if(restrictionEnzyme != null)
+ /*if(restrictionEnzyme != null)
{
enumTk = restrictionEnzyme.elements();
while(enumTk.hasMoreElements())
@@ -434,7 +466,7 @@ public class DNADraw extends ScrollPanel
y-=hgt;
g2.drawString(reLabel,x,y);
}
- }
+ }*/
// draw features
Vector markers = getGeneticMarker();
@@ -946,6 +978,14 @@ public class DNADraw extends ScrollPanel
public void setLineAttributes(Hashtable lineAttr)
{
this.lineAttr = lineAttr;
+
+ if(isCircular())
+ {
+ setSize(panelSize);
+ setPreferredSize(panelSize);
+ }
+ revalidate();
+ repaint();
}
@@ -1037,7 +1077,7 @@ public class DNADraw extends ScrollPanel
public void actionPerformed(ActionEvent e)
{
PrintDNAImage pdnai = new PrintDNAImage(current_dna);
- pdnai.print();
+ pdnai.printAsSinglePage();
}
});
printMenu.add(printImage);
@@ -1384,7 +1424,19 @@ public class DNADraw extends ScrollPanel
repaint();
}
});
- optionMenu.add(labelTick);
+ optionMenu.add(labelTick);
+
+ final JCheckBoxMenuItem asCircular = new JCheckBoxMenuItem("Circular Plot", isCircular());
+ asCircular.addItemListener(new ItemListener()
+ {
+
+ public void itemStateChanged(ItemEvent e)
+ {
+ lineAttr.put("circular",new Boolean(asCircular.isSelected()));
+ setLineAttributes(lineAttr);
+ }
+ });
+ optionMenu.add(asCircular);
// help manu
JMenu helpMenu = new JMenu("Help");
@@ -1676,6 +1728,66 @@ public class DNADraw extends ScrollPanel
//dna.add(dna.new BlockPanel(dna));
f.setVisible(true);
}
+
+
+ public int getBasesPerLine()
+ {
+ return basesPerLine;
+ }
+
+
+ public void setBasesPerLine(int basesPerLine)
+ {
+ this.basesPerLine = basesPerLine;
+ }
+
+
+ public int getNumberOfLines()
+ {
+ return numberOfLines;
+ }
+
+
+ public void setNumberOfLines(int numberOfLines)
+ {
+ this.numberOfLines = numberOfLines;
+ }
+
+
+ public float getLineHeight()
+ {
+ return lineHeight;
+ }
+
+
+ public void setLineHeight(float lineHeight)
+ {
+ this.lineHeight = lineHeight;
+ }
+
+
+ public float getSingleBaseWidth()
+ {
+ return singleBaseWidth;
+ }
+
+
+ public void setSingleBaseWidth(float singleBaseWidth)
+ {
+ this.singleBaseWidth = singleBaseWidth;
+ }
+
+
+ public int getBorder2()
+ {
+ return border2;
+ }
+
+
+ public void setBorder2(int border2)
+ {
+ this.border2 = border2;
+ }
/*class BlockPanel extends JPanel
{
diff --git a/uk/ac/sanger/artemis/circular/LineAttribute.java b/uk/ac/sanger/artemis/circular/LineAttribute.java
index 44e13845c..ae0e3b0c6 100644
--- a/uk/ac/sanger/artemis/circular/LineAttribute.java
+++ b/uk/ac/sanger/artemis/circular/LineAttribute.java
@@ -22,12 +22,14 @@
package uk.ac.sanger.artemis.circular;
import javax.swing.Box;
+import javax.swing.ButtonGroup;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
import javax.swing.JPanel;
+import javax.swing.JRadioButton;
import javax.swing.JSlider;
import javax.swing.KeyStroke;
import javax.swing.event.*;
@@ -37,6 +39,7 @@ import java.util.Hashtable;
public class LineAttribute extends JPanel
{
+ private static final long serialVersionUID = 1L;
private Hashtable lineAttr = new Hashtable();
private TextFieldInt start;
private TextFieldInt end;
@@ -52,7 +55,7 @@ public class LineAttribute extends JPanel
Box bacross = Box.createHorizontalBox();
// circular or linear dna
- /*ButtonGroup group = new ButtonGroup();
+ ButtonGroup group = new ButtonGroup();
final JRadioButton jcirc = new JRadioButton("Circular");
jcirc.addActionListener(new ActionListener()
{
@@ -75,15 +78,16 @@ public class LineAttribute extends JPanel
}
});
group.add(jline);
- jcirc.setSelected(true);*/
- lineAttr.put("circular",new Boolean(true));
- /*bacross.add(jcirc);
+ jcirc.setSelected( draw.isCircular() );
+ jline.setSelected( !draw.isCircular() );
+ lineAttr.put("circular",new Boolean(draw.isCircular()));
+ bacross.add(jcirc);
bacross.add(jline);
bacross.add(Box.createHorizontalGlue());
bdown.add(bacross);
// start position
- bdown.add(Box.createVerticalStrut(4));*/
+ bdown.add(Box.createVerticalStrut(4));
bacross = Box.createHorizontalBox();
start = new TextFieldInt();
start.addActionListener(new ActionListener()
@@ -101,7 +105,7 @@ public class LineAttribute extends JPanel
if(draw != null)
start.setValue(draw.getStart());
else
- start.setValue(0);
+ start.setValue(1);
start.setPreferredSize(d);
start.setMaximumSize(d);
diff --git a/uk/ac/sanger/artemis/circular/PrintDNAImage.java b/uk/ac/sanger/artemis/circular/PrintDNAImage.java
index 8498e4410..a3683a7c3 100644
--- a/uk/ac/sanger/artemis/circular/PrintDNAImage.java
+++ b/uk/ac/sanger/artemis/circular/PrintDNAImage.java
@@ -27,6 +27,7 @@ import java.awt.Font;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.print.PageFormat;
+import java.awt.print.Paper;
import java.awt.print.PrinterJob;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
@@ -35,7 +36,6 @@ import java.awt.image.BufferedImage;
import java.awt.image.RenderedImage;
import java.io.File;
import java.io.IOException;
-import java.util.Hashtable;
import javax.swing.BorderFactory;
import javax.swing.Box;
import javax.swing.JComboBox;
@@ -66,20 +66,15 @@ import javax.swing.border.Border;
*/
public class PrintDNAImage extends ScrollPanel
{
+ private static final long serialVersionUID = 1L;
+
/** page format */
private PageFormat format = null;
- /** page number to print */
- private int pageIndex = 0;
+
/** alignment sequence panel */
private DNADraw dna;
- /** prefix of file */
-//private String filePrefix;
/** status field for print preview */
private JTextField statusField = new JTextField("");
- /** number of residues per line */
- private int nResPerLine = 0;
- /** line attributes */
- private Hashtable lineAttr;
/** type (jpeg/png) */
private String type;
@@ -93,7 +88,6 @@ public class PrintDNAImage extends ScrollPanel
super();
this.dna = dna;
- lineAttr = dna.getLineAttributes();
setBackground(Color.white);
}
@@ -118,7 +112,7 @@ public class PrintDNAImage extends ScrollPanel
* Print to a jpeg or png file
*
*/
- public void print()
+/* public void print()
{
if(format == null)
getFormatDialog();
@@ -138,7 +132,7 @@ public class PrintDNAImage extends ScrollPanel
JOptionPane.showMessageDialog(this,
"This option requires Java 1.4 or higher.");
}
- }
+ }*/
/**
@@ -236,7 +230,7 @@ public class PrintDNAImage extends ScrollPanel
{
public void actionPerformed(ActionEvent e)
{
- print();
+ printAsSinglePage();
}
});
printMenu.add(printImage);
@@ -271,7 +265,7 @@ public class PrintDNAImage extends ScrollPanel
String cwd = System.getProperty("user.dir");
JFileChooser fc = new JFileChooser(cwd);
File fselect = new File(cwd+System.getProperty("file.separator")+
- "dna_image.jpeg");
+ "dna.jpg");
fc.setSelectedFile(fselect);
// file name prefix
@@ -287,6 +281,8 @@ public class PrintDNAImage extends ScrollPanel
Box bacross = Box.createHorizontalBox();
JComboBox formatSelect =
new JComboBox(javax.imageio.ImageIO.getWriterFormatNames());
+ formatSelect.setSelectedItem("jpg");
+
Dimension d = formatSelect.getPreferredSize();
formatSelect.setMaximumSize(d);
bacross.add(Box.createHorizontalGlue());
@@ -324,7 +320,42 @@ public class PrintDNAImage extends ScrollPanel
System.out.println("Java 1.4+ is required");
}
}
+
+
+
+
+ /**
+ * Print to one jpeg or png file
+ */
+ public void printAsSinglePage()
+ {
+ //PrinterJob printerJob = PrinterJob.getPrinterJob();
+ format = new PageFormat();
+
+ File file = showOptions();
+
+ Dimension d = dna.getSize();
+ double imageWidth = d.getWidth();
+ double imageHeight = d.getHeight();
+ Paper paper = format.getPaper();
+
+ paper.setSize(imageWidth,imageHeight);
+
+ paper.setImageableArea(0,0,
+ imageWidth,imageHeight+imageHeight);
+ format.setPaper(paper);
+ try
+ {
+ RenderedImage rendImage = createDNAImage(0);
+ writeImageToFile(rendImage,file,type);
+ }
+ catch(NoClassDefFoundError ex)
+ {
+ JOptionPane.showMessageDialog(this,
+ "This option requires Java 1.4 or higher.");
+ }
+ }
}
--
GitLab