From a16c16b46bd7c1c6bc642a93bbcb985d92ecfdfb Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 19 Aug 2008 08:23:32 +0000
Subject: [PATCH] updates for linear plot
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8569 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/circular/Block.java | 25 +--
uk/ac/sanger/artemis/circular/DNADraw.java | 194 +++++++++++++--------
uk/ac/sanger/artemis/circular/Graph.java | 13 +-
uk/ac/sanger/artemis/circular/Wizard.java | 4 +-
4 files changed, 144 insertions(+), 92 deletions(-)
diff --git a/uk/ac/sanger/artemis/circular/Block.java b/uk/ac/sanger/artemis/circular/Block.java
index 8e3e31e3f..fc1d68792 100644
--- a/uk/ac/sanger/artemis/circular/Block.java
+++ b/uk/ac/sanger/artemis/circular/Block.java
@@ -374,14 +374,15 @@ public class Block implements Transferable
int lineNumberEnd = Math.round((float)(bend-1)/((float)basesPerLine) + 0.5f)-1;
float singleBaseWidth = current_dna.getSingleBaseWidth();
- int border2 = current_dna.getBorder2();
+ int borderWidth2 = current_dna.getBorderWidth2();
+ int borderHeight2 = current_dna.getBorderHeight2();
int ypos = (int) ( (lineNumberStart*current_dna.getLineHeight()) - (strokeSize/2.f) -
((1-track.getPosition())*current_dna.getLineHeight()) +
- border2+current_dna.getLineHeight());
+ borderHeight2+current_dna.getLineHeight());
- int xstart = (int) ((bstart-(lineNumberStart*basesPerLine))*singleBaseWidth)+border2;
- int xend = (int) ((bend-(lineNumberEnd*basesPerLine))*singleBaseWidth)+border2;
+ int xstart = (int) ((bstart-(lineNumberStart*basesPerLine))*singleBaseWidth)+borderWidth2;
+ int xend = (int) ((bend-(lineNumberEnd*basesPerLine))*singleBaseWidth)+borderWidth2;
BasicStroke basicstroke = new BasicStroke(
strokeSize,
@@ -415,29 +416,29 @@ public class Block implements Transferable
if(lineNumberEnd > lineNumberStart)
{
- g2.drawLine(xstart,ypos,current_dna.getWidth()-border2,ypos);
+ g2.drawLine(xstart,ypos,current_dna.getWidth()-borderWidth2,ypos);
r = new Rectangle();
r.setLocation(xstart,ypos);
- r.setSize(current_dna.getWidth()-border2-xstart,(int)strokeSize);
+ r.setSize(current_dna.getWidth()-borderWidth2-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);
+ borderHeight2+current_dna.getLineHeight());
+ g2.drawLine(borderWidth2,ypos,current_dna.getWidth()-borderWidth2,ypos);
r = new Rectangle();
- r.setLocation(border2,ypos);
- r.setSize(current_dna.getWidth()-border2-border2,(int)strokeSize);
+ r.setLocation(borderWidth2,ypos);
+ r.setSize(current_dna.getWidth()-borderWidth2-borderWidth2,(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;
+ borderHeight2+current_dna.getLineHeight());
+ xstart = borderWidth2;
}
g2.drawLine(xstart,ypos,xend,ypos);
diff --git a/uk/ac/sanger/artemis/circular/DNADraw.java b/uk/ac/sanger/artemis/circular/DNADraw.java
index 0ab0f4a48..459816f31 100644
--- a/uk/ac/sanger/artemis/circular/DNADraw.java
+++ b/uk/ac/sanger/artemis/circular/DNADraw.java
@@ -137,9 +137,10 @@ public class DNADraw extends ScrollPanel
private JMenuItem linearPlotOptions = new JMenuItem("Linear plot...");;
private int numberOfLines;
private int basesPerLine = 20000;
- private float lineHeight = 100.f;
+ private float lineHeight = 200.f;
private float singleBaseWidth;
- private int border2;
+ private int borderWidth2;
+ private int borderHeight2;
public DNADraw()
{
@@ -282,6 +283,7 @@ public class DNADraw extends ScrollPanel
if(!isCircular())
setPreferredSize(linearPanelSize);
+ basesPerLine = majorTick;
calculateTickPosistions();
}
@@ -372,6 +374,12 @@ public class DNADraw extends ScrollPanel
protected void drawLinearPanel(Graphics2D g2)
{
+ RenderingHints qualityHints = new RenderingHints(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ qualityHints.put(RenderingHints.KEY_RENDERING,
+ RenderingHints.VALUE_RENDER_QUALITY);
+ g2.setRenderingHints(qualityHints);
+
FontMetrics fm = g2.getFontMetrics();
double hgt = fm.getAscent();
g2.setColor(Color.black);
@@ -386,11 +394,15 @@ public class DNADraw extends ScrollPanel
{
System.out.println("No line size specified using default!");
}
- g2.setStroke(new BasicStroke((float)lineSize));
-
- border2 = border.width/2;
- g2.setStroke(new BasicStroke((float)lineSize));
+ borderWidth2 = border.width/2;
+ borderHeight2 = border.height/2;
+
+ BasicStroke basicstroke = new BasicStroke(
+ lineSize,
+ BasicStroke.CAP_BUTT,
+ BasicStroke.JOIN_MITER);
+ g2.setStroke(basicstroke);
int lastBase = getEnd();
numberOfLines = Math.round( (lastBase/basesPerLine) + 0.5f);
@@ -404,14 +416,14 @@ public class DNADraw extends ScrollPanel
for(int i=0; i<numberOfLines; i++)
{
- int ypos = (int) (border2+lineHeight+(lineHeight*i));
+ int ypos = (int) (borderHeight2+lineHeight+(lineHeight*i));
if(i<numberOfLines-1)
- g2.drawLine(border2,ypos,getWidth()-border2,ypos);
+ g2.drawLine(borderWidth2,ypos,getWidth()-borderWidth2,ypos);
else
{
- int lastLineWidth = (int) ((lastBase-(i*basesPerLine))*singleBaseWidth)+border2;
- g2.drawLine(border2,ypos,lastLineWidth,ypos);
+ int lastLineWidth = (int) ((lastBase-(i*basesPerLine))*singleBaseWidth)+borderWidth2;
+ g2.drawLine(borderWidth2,ypos,lastLineWidth,ypos);
}
}
@@ -427,8 +439,8 @@ public class DNADraw extends ScrollPanel
int tick = ((Integer)enumTk.nextElement()).intValue();
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 ypos = (int) (borderHeight2+lineHeight+(lineHeight*lineNumber));
+ int xpos = (int) ((tick-(lineNumber*basesPerLine))*singleBaseWidth)+borderWidth2;
int y = ypos+(int)((lineSize+widDash)/2);
g2.drawLine(xpos,ypos,xpos,y);
@@ -443,8 +455,8 @@ public class DNADraw extends ScrollPanel
if(lineNumber < 0)
lineNumber = 0;
- int ypos = (int) (border2+lineHeight+(lineHeight*lineNumber));
- int xpos = (int) ((tick-(lineNumber*basesPerLine))*singleBaseWidth)+border2;
+ int ypos = (int) (borderHeight2+lineHeight+(lineHeight*lineNumber));
+ int xpos = (int) ((tick-(lineNumber*basesPerLine))*singleBaseWidth)+borderWidth2;
int y = ypos+(int)((lineSize+widDash)/2);
g2.drawLine(xpos,ypos,xpos,y);
@@ -602,7 +614,11 @@ public class DNADraw extends ScrollPanel
}
if(majorTicks == null || minorTicks == null)
+ {
calculateTickPosistions();
+ if(majorTick>0)
+ basesPerLine = majorTick;
+ }
//major ticks
drawCircularTicks(g2,ddiameter,ddiameter2,diameter,origin,
widthPanel,heightPanel,rad,pi,widDash,fm,
@@ -744,7 +760,7 @@ public class DNADraw extends ScrollPanel
* Calculate the tick marks to be drawn
*
*/
- protected void calculateTickPosistions()
+ protected void calculateTickPosistions()
{
minorTicks = new Vector();
majorTicks = new Vector();
@@ -905,11 +921,26 @@ public class DNADraw extends ScrollPanel
drawLinearPanel(g2);
if(gcGraph != null && containsGraph(gcGraph))
- gcGraph.draw(g2);
+ {
+ if(isCircular())
+ gcGraph.draw(g2);
+ else
+ gcGraph.drawLinear(g2);
+ }
if(gcSkewGraph != null && containsGraph(gcSkewGraph))
- gcSkewGraph.draw(g2);
+ {
+ if(isCircular())
+ gcSkewGraph.draw(g2);
+ else
+ gcSkewGraph.drawLinear(g2);
+ }
if(userGraph != null && containsGraph(userGraph))
- userGraph.draw(g2);
+ {
+ if(isCircular())
+ userGraph.draw(g2);
+ else
+ userGraph.drawLinear(g2);
+ }
}
/**
@@ -1065,18 +1096,16 @@ public class DNADraw extends ScrollPanel
fileMenu.add(readInEntry);
// print
- final JMenu printMenu = new JMenu("Print");
+ final JMenuItem printMenu = new JMenuItem("Print...");
fileMenu.add(printMenu);
- JMenuItem print = new JMenuItem("Print postscript");
- print.addActionListener(new ActionListener()
+ printMenu.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
doPrintActions();
}
});
- printMenu.add(print);
JMenuItem printImage = new JMenuItem("Save As jpeg/png Image...");
printImage.addActionListener(new ActionListener()
@@ -1087,7 +1116,7 @@ public class DNADraw extends ScrollPanel
pdnai.printAsSinglePage();
}
});
- printMenu.add(printImage);
+ fileMenu.add(printImage);
// print preview
JMenuItem printPreview = new JMenuItem("Print Preview...");
@@ -1349,7 +1378,7 @@ public class DNADraw extends ScrollPanel
optionMenu.add(tracksMenu);
- JMenuItem line = new JMenuItem("DNA Properties...");
+ /*JMenuItem line = new JMenuItem("DNA Properties...");
line.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1364,7 +1393,7 @@ public class DNADraw extends ScrollPanel
f.setVisible(true);
}
});
- optionMenu.add(line);
+ optionMenu.add(line);*/
JMenuItem tickMarks = new JMenuItem("Tick marks...");
@@ -1421,6 +1450,17 @@ public class DNADraw extends ScrollPanel
});
optionMenu.add(reSites);
+ linearPlotOptions.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showLinearPlotOptions();
+ }
+ });
+ linearPlotOptions.setEnabled(!isCircular());
+ optionMenu.add(linearPlotOptions);
+ optionMenu.addSeparator();
+
final JCheckBoxMenuItem labelTick = new JCheckBoxMenuItem("Show tick numbers", labelTicks);
labelTick.addItemListener(new ItemListener()
{
@@ -1433,50 +1473,7 @@ public class DNADraw extends ScrollPanel
});
optionMenu.add(labelTick);
-
- linearPlotOptions.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- GridBagLayout grid = new GridBagLayout();
- GridBagConstraints c = new GridBagConstraints();
- c.ipady = 3;
- c.ipadx = 5;
-
- JPanel optionBox = new JPanel(grid);
- c.gridx = 1;
- c.gridy = 0;
- c.anchor = GridBagConstraints.WEST;
- TextFieldFloat lineHeightField = new TextFieldFloat();
- lineHeightField.setValue(getLineHeight());
- optionBox.add(lineHeightField, c);
- c.gridx = 0;
- c.anchor = GridBagConstraints.EAST;
- optionBox.add(new JLabel("Line Height"), c);
-
- c.gridx = 1;
- c.gridy = 1;
- c.anchor = GridBagConstraints.WEST;
- TextFieldInt basesPerLineField = new TextFieldInt();
- basesPerLineField.setValue(getBasesPerLine());
- optionBox.add(basesPerLineField, c);
- c.gridx = 0;
- c.anchor = GridBagConstraints.EAST;
- optionBox.add(new JLabel("Bases Per Line"), c);
-
- JOptionPane.showMessageDialog(DNADraw.this, optionBox,
- "Linear Plot Options", JOptionPane.QUESTION_MESSAGE);
-
- setLineHeight( (float) lineHeightField.getValue() );
- setBasesPerLine(basesPerLineField.getValue());
- revalidate();
- repaint();
- }
- });
- linearPlotOptions.setEnabled(!isCircular());
- optionMenu.add(linearPlotOptions);
-
- final JCheckBoxMenuItem asCircular = new JCheckBoxMenuItem("Circular Plot", isCircular());
+ final JCheckBoxMenuItem asCircular = new JCheckBoxMenuItem("Display as Circular Plot", isCircular());
asCircular.addItemListener(new ItemListener()
{
@@ -1508,6 +1505,45 @@ public class DNADraw extends ScrollPanel
return menuBar;
}
+ /**
+ * Provide options for the linear plot
+ */
+ private void showLinearPlotOptions()
+ {
+ GridBagLayout grid = new GridBagLayout();
+ GridBagConstraints c = new GridBagConstraints();
+ c.ipady = 3;
+ c.ipadx = 5;
+
+ JPanel optionBox = new JPanel(grid);
+ c.gridx = 1;
+ c.gridy = 0;
+ c.anchor = GridBagConstraints.WEST;
+ TextFieldFloat lineHeightField = new TextFieldFloat();
+ lineHeightField.setValue(getLineHeight());
+ optionBox.add(lineHeightField, c);
+ c.gridx = 0;
+ c.anchor = GridBagConstraints.EAST;
+ optionBox.add(new JLabel("Line Height"), c);
+
+ c.gridx = 1;
+ c.gridy = 1;
+ c.anchor = GridBagConstraints.WEST;
+ TextFieldInt basesPerLineField = new TextFieldInt();
+ basesPerLineField.setValue(getBasesPerLine());
+ optionBox.add(basesPerLineField, c);
+ c.gridx = 0;
+ c.anchor = GridBagConstraints.EAST;
+ optionBox.add(new JLabel("Bases Per Line"), c);
+
+ JOptionPane.showMessageDialog(null, optionBox,
+ "Linear Plot Options", JOptionPane.QUESTION_MESSAGE);
+
+ setLineHeight( (float) lineHeightField.getValue() );
+ setBasesPerLine(basesPerLineField.getValue());
+ revalidate();
+ repaint();
+ }
public void setCloseAndDispose(boolean close, JFrame mainFrame)
{
@@ -1829,15 +1865,27 @@ public class DNADraw extends ScrollPanel
}
- public int getBorder2()
+ public int getBorderWidth2()
+ {
+ return borderWidth2;
+ }
+
+
+ public void setBorderWidth2(int borderWidth2)
+ {
+ this.borderWidth2 = borderWidth2;
+ }
+
+
+ public int getBorderHeight2()
{
- return border2;
+ return borderHeight2;
}
- public void setBorder2(int border2)
+ public void setBorderHeight2(int borderHeight2)
{
- this.border2 = border2;
+ this.borderHeight2 = borderHeight2;
}
/*class BlockPanel extends JPanel
diff --git a/uk/ac/sanger/artemis/circular/Graph.java b/uk/ac/sanger/artemis/circular/Graph.java
index 104821322..0e37dba22 100644
--- a/uk/ac/sanger/artemis/circular/Graph.java
+++ b/uk/ac/sanger/artemis/circular/Graph.java
@@ -177,7 +177,8 @@ public abstract class Graph extends JPanel
int basesPerLine = getCurrentDna().getBasesPerLine();
float lineHeight = getCurrentDna().getLineHeight();
float singleBaseWidth = getCurrentDna().getSingleBaseWidth();
- int border2 = getCurrentDna().getBorder2();
+ int borderWidth2 = getCurrentDna().getBorderWidth2();
+ int borderHeight2 = getCurrentDna().getBorderHeight2();
Bases bases = getBases();
@@ -205,6 +206,7 @@ public abstract class Graph extends JPanel
gcAverage = gcAverage/nvalues;
}
+
int minPos = (int)(lineHeight*(1-getTrack()));
int maxPos = minPos + (int)(lineHeight*getGraphHeight());
@@ -224,15 +226,14 @@ public abstract class Graph extends JPanel
else
g2.setColor(getMinusColour());
- int val = minPos - (int)( ((xA-minValue)/(maxValue-minValue))*(maxPos-minPos) );
-
int basePos = (i*getBaseStepSize())+1;
int lineNumber = Math.round((float)(basePos-1)/((float)basesPerLine) + 0.5f)-1;
- int xpos = (int) ((basePos-(lineNumber*basesPerLine))*singleBaseWidth)+border2;
+ int ypos = (int)(borderHeight2 + (lineNumber*lineHeight)
+ + (lineHeight*getGraphHeight()));
- int ypos = (int) ( (lineNumber*lineHeight) - (strokeSize/2.f) -
- (getTrack()*lineHeight) + border2);
+ int val = minPos - (int)( ((xA-minValue)/(maxValue-minValue))*(maxPos-minPos) );
+ int xpos = (int) ((basePos-(lineNumber*basesPerLine))*singleBaseWidth)+borderWidth2;
g2.drawLine(xpos, avVal+ypos, xpos, val+ypos);
}
diff --git a/uk/ac/sanger/artemis/circular/Wizard.java b/uk/ac/sanger/artemis/circular/Wizard.java
index d06c415e6..304bc8c84 100644
--- a/uk/ac/sanger/artemis/circular/Wizard.java
+++ b/uk/ac/sanger/artemis/circular/Wizard.java
@@ -250,10 +250,12 @@ public class Wizard
div = 100000;
int tick = entry.getBases().getLength()/div;
tick = tick*(div/10);
+ int tick2 = tick/2;
+ tick = tick2*2;
dna_current.setGeneticMarker(block);
dna_current.setRestrictionEnzyme(new Vector());
- dna_current.setMinorTickInterval(tick);
+ dna_current.setMinorTickInterval(tick2);
dna_current.setTickInterval(tick);
}
catch(OutOfRangeException e)
--
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