From 643e0b8b683629a6bd2e3a0744fa2a80b1490c97 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Thu, 15 Nov 2012 12:19:54 +0000
Subject: [PATCH] add svg support
---
art | 5 +-
.../artemis/components/FeatureDisplay.java | 41 ++++-
uk/ac/sanger/artemis/components/Plot.java | 26 ++-
.../artemis/components/PrintArtemis.java | 166 +++++++++++++++---
4 files changed, 195 insertions(+), 43 deletions(-)
mode change 100755 => 100644 art
diff --git a/art b/art
old mode 100755
new mode 100644
index 16cf2c2af..16f98d7dd
--- a/art
+++ b/art
@@ -6,8 +6,6 @@
# necessary a symbolic link can be made to this script from
# /usr/local/bin/ or elsewhere.
-# $Header: //tmp/pathsoft/artemis/art,v 1.26 2009-09-21 15:45:47 tjc Exp $
-
# resolve links - $0 may be a link
PRG=$0
progname=`basename $0`
@@ -30,6 +28,9 @@ LIBDIR=/nfs/pathsoft/prod/javalibs
CLASSPATH=$ARTEMIS_HOME:$ARTEMIS_HOME/lib/biojava.jar:$ARTEMIS_HOME/lib/jemAlign.jar:$ARTEMIS_HOME/lib/jakarta-regexp-1.2.jar:$ARTEMIS_HOME/lib/macos.jar:$ARTEMIS_HOME/lib/postgresql-8.4-701.jdbc3.jar:$CLASSPATH
+# batik jars
+CLASSPATH=$CLASSPATH:$ARTEMIS_HOME/lib/batik/batik-awt-util.jar:$ARTEMIS_HOME/lib/batik/batik-dom.jar:$ARTEMIS_HOME/lib/batik/batik-ext.jar:$ARTEMIS_HOME/lib/batik/batik-svggen.jar:$ARTEMIS_HOME/lib/batik/batik-util.jar:$ARTEMIS_HOME/lib/batik/batik-xml.jar
+
# j2ssh jars
CLASSPATH=$CLASSPATH:$ARTEMIS_HOME/lib/j2ssh/commons-logging.jar:$ARTEMIS_HOME/lib/j2ssh/j2ssh-core.jar:$ARTEMIS_HOME/lib/j2ssh/
diff --git a/uk/ac/sanger/artemis/components/FeatureDisplay.java b/uk/ac/sanger/artemis/components/FeatureDisplay.java
index 8c279573a..bc6cb235c 100644
--- a/uk/ac/sanger/artemis/components/FeatureDisplay.java
+++ b/uk/ac/sanger/artemis/components/FeatureDisplay.java
@@ -68,6 +68,8 @@ import javax.swing.UIManager;
import javax.swing.ImageIcon;
import javax.swing.JFrame;
+import org.apache.batik.svggen.SVGGraphics2D;
+
/**
* This component is used for displaying an Entry.
*
@@ -1890,8 +1892,19 @@ public class FeatureDisplay extends EntryGroupPanel
// draw fwd bases
if(getScaleFactor() == 0)
- g.drawString(forward_visible_bases, offset * getFontWidth(),
- yposition + getFontAscent() + 1);
+ {
+ if(!(g instanceof SVGGraphics2D))
+ g.drawString(forward_visible_bases, offset * getFontWidth(),
+ yposition + getFontAscent() + 1);
+ else
+ {
+ // for svg graphics
+ for(int i=0;i<forward_visible_bases.length();i++)
+ g.drawString(String.valueOf(forward_visible_bases.charAt(i)),
+ (offset+i)*getFontWidth(),
+ yposition + getFontAscent() + 1);
+ }
+ }
else
{
for(int base_index = 0; base_index < forward_sequence_length;
@@ -1914,8 +1927,19 @@ public class FeatureDisplay extends EntryGroupPanel
// draw bwd bases
if(getScaleFactor() == 0)
- g.drawString(reverse_visible_bases, offset * getFontWidth(),
- yposition + getFontAscent() + 1);
+ {
+ if(!(g instanceof SVGGraphics2D))
+ g.drawString(reverse_visible_bases, offset * getFontWidth(),
+ yposition + getFontAscent() + 1);
+ else
+ {
+ // for svg graphics
+ for(int i=0;i<reverse_visible_bases.length();i++)
+ g.drawString(String.valueOf(reverse_visible_bases.charAt(i)),
+ (offset+i)*getFontWidth(),
+ yposition + getFontAscent() + 1);
+ }
+ }
else
{
for(int base_index = 0; base_index < reverse_sequence_length;
@@ -2200,8 +2224,15 @@ public class FeatureDisplay extends EntryGroupPanel
else
draw_x_position = (int)((offset + frame_start + 1) * getScaleValue());
- g.drawString(codons, draw_x_position,
+ if(!(g instanceof SVGGraphics2D))
+ g.drawString(codons, draw_x_position,
draw_y_position + getFontAscent() + 1);
+ else
+ {
+ for(int i=0;i<codons.length();i++)
+ g.drawString(String.valueOf(codons.charAt(i)), draw_x_position+(i*getFontWidth() ),
+ draw_y_position + getFontAscent() + 1);
+ }
}
/**
diff --git a/uk/ac/sanger/artemis/components/Plot.java b/uk/ac/sanger/artemis/components/Plot.java
index 2063ea330..5a24f1de1 100644
--- a/uk/ac/sanger/artemis/components/Plot.java
+++ b/uk/ac/sanger/artemis/components/Plot.java
@@ -51,6 +51,8 @@ import javax.swing.JMenuItem;
import javax.swing.JScrollBar;
import javax.swing.JPopupMenu;
+import org.apache.batik.svggen.SVGGraphics2D;
+
/**
* This class implements a simple plot component.
* @author Kim Rutherford
@@ -682,11 +684,17 @@ public abstract class Plot extends JPanel
if(offscreen == null || lastPaintHeight != height)
offscreen = createImage(width, height);
- Graphics og = offscreen.getGraphics();
- og.setClip(0, 0, width, height);
- og.setColor(Color.WHITE);
- og.fillRect(0, 0, width, height);
-
+ final Graphics og;
+ if(g instanceof SVGGraphics2D)
+ og = g;
+ else
+ {
+ og = offscreen.getGraphics();
+ og.setClip(0, 0, width, height);
+ og.setColor(Color.WHITE);
+ og.fillRect(0, 0, width, height);
+ }
+
// Redraw the graph on the canvas using the algorithm from the
// constructor.
@@ -703,8 +711,12 @@ public abstract class Plot extends JPanel
numPlots = drawMultiValueGraph(og,lines);
drawLabels(og,numPlots);
- g.drawImage(offscreen, 0, 0, null);
- og.dispose();
+
+ if( !(g instanceof SVGGraphics2D) )
+ {
+ g.drawImage(offscreen, 0, 0, null);
+ og.dispose();
+ }
lastPaintHeight = height;
}
diff --git a/uk/ac/sanger/artemis/components/PrintArtemis.java b/uk/ac/sanger/artemis/components/PrintArtemis.java
index f72fef4d4..4abd4784b 100644
--- a/uk/ac/sanger/artemis/components/PrintArtemis.java
+++ b/uk/ac/sanger/artemis/components/PrintArtemis.java
@@ -29,9 +29,24 @@ import java.awt.print.Printable;
import java.awt.print.PrinterException;
import java.awt.print.PrinterJob;
import java.awt.event.*;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.io.UnsupportedEncodingException;
+import java.io.Writer;
+
import javax.swing.*;
-import java.io.*;
+import org.apache.batik.dom.GenericDOMImplementation;
+import org.apache.batik.svggen.SVGGeneratorContext;
+import org.apache.batik.svggen.SVGGraphics2D;
+import org.apache.batik.svggen.SVGGraphics2DIOException;
+import org.w3c.dom.DOMImplementation;
+import org.w3c.dom.Document;
+
+import uk.ac.sanger.artemis.Options;
import uk.ac.sanger.artemis.editor.ScrollPanel;
/**
@@ -66,15 +81,45 @@ public class PrintArtemis extends ScrollPanel implements Printable
}
/**
- *
* Override paintComponent to draw entry
- *
*/
- public void paintComponent(Graphics g)
+ public void paintComponent(Graphics g2d)
{
// let UI delegate paint first (incl. background filling)
- super.paintComponent(g);
- Graphics2D g2d = (Graphics2D)g.create();
+ super.paintComponent(g2d);
+
+ // feature list
+ if(featListDisplay.isSelected())
+ {
+ FeatureList flist = entry.getFeatureList();
+ Point ploc = flist.getViewport().getViewPosition();
+ try
+ {
+ int translateX = 0;
+ if(selectDisplay.isSelected())
+ translateX += entry.getSelectionInfoDisplay().getHeight();
+ if(groupsDisplay.isSelected())
+ translateX += entry.getEntryGroupDisplay().getHeight();
+ if(plotsDisplay.isSelected())
+ translateX += entry.getBasePlotGroup().getHeight();
+ if(jamDisplay.isSelected() && entry.getBamPanel() != null && entry.getBamPanel().isVisible())
+ translateX += entry.getBamPanel().getHeight()-1;
+ if(vcfDisplay.isSelected() && entry.getVcfView() != null && entry.getVcfView().isVisible())
+ translateX += entry.getVcfPanel().getHeight();
+ if(onelineDisplay.isSelected())
+ translateX += entry.getOneLinePerEntryDisplay().getHeight();
+ if(featDisplay.isSelected())
+ translateX += entry.getFeatureDisplay().getHeight();
+ if(baseDisplay.isSelected())
+ translateX += entry.getBaseDisplay().getHeight();
+
+ translateX-=2+ploc.y;
+ g2d.translate(0,translateX);
+ flist.paintComponent(g2d);
+ g2d.translate(0,-translateX);
+ }
+ catch(IllegalArgumentException e){} // thrown if the list is not visible
+ }
// selection info
if(selectDisplay.isSelected())
@@ -128,24 +173,9 @@ public class PrintArtemis extends ScrollPanel implements Printable
entry.getBaseDisplay().paintComponent(g2d);
g2d.translate(0,entry.getBaseDisplay().getHeight());
}
-
- // feature list
- if(featListDisplay.isSelected())
- {
- FeatureList flist = entry.getFeatureList();
- Point ploc = flist.getViewport().getViewPosition();
- try
- {
- BufferedImage offScreen = new BufferedImage(flist.getViewport().getWidth(),
- flist.getViewport().getHeight(), BufferedImage.TYPE_INT_RGB);
- Graphics og = offScreen.getGraphics();
- og.translate(0,-ploc.y);
- flist.paintComponent(og);
- g2d.drawImage(offScreen, 0, 0, null);
- }
- catch(IllegalArgumentException e){} // thrown if the list is not visible
- }
}
+
+
/**
@@ -153,7 +183,7 @@ public class PrintArtemis extends ScrollPanel implements Printable
* Set the size of the image
*
*/
- private void setImageSize()
+ private Dimension getImageSize()
{
height = 0;
width = entry.getFeatureDisplay().getDisplayWidth();
@@ -185,9 +215,14 @@ public class PrintArtemis extends ScrollPanel implements Printable
if(featListDisplay.isSelected())
height += entry.getFeatureList().getViewport().getExtentSize().height;
- setPreferredSize(new Dimension(width,height));
+ return new Dimension(width,height);
}
+ private void setImageSize()
+ {
+ setPreferredSize(getImageSize());
+ }
+
/**
*
* Display a print preview page
@@ -391,6 +426,15 @@ public class PrintArtemis extends ScrollPanel implements Printable
f.setVisible(true);
}
+ private String[] getImageFormats()
+ {
+ final String fmts[] = javax.imageio.ImageIO.getWriterFormatNames();
+ final String tmpFmts[] = new String[fmts.length+1];
+ System.arraycopy(fmts, 0, tmpFmts, 0, fmts.length);
+ tmpFmts[tmpFmts.length-1] = "svg";
+ return tmpFmts;
+ }
+
/**
*
* Print to a jpeg or png file
@@ -399,7 +443,7 @@ public class PrintArtemis extends ScrollPanel implements Printable
public void print()
{
// file chooser
- StickyFileChooser fc = new StickyFileChooser();
+ final StickyFileChooser fc = new StickyFileChooser();
File fselect = new File(fc.getCurrentDirectory()+
System.getProperty("file.separator")+
"artemis.png");
@@ -413,9 +457,27 @@ public class PrintArtemis extends ScrollPanel implements Printable
YBox.add(labFormat);
Box bacross = Box.createHorizontalBox();
- JComboBox formatSelect =
- new JComboBox(javax.imageio.ImageIO.getWriterFormatNames());
+ final JComboBox formatSelect = new JComboBox(getImageFormats());
formatSelect.setSelectedItem("png");
+ formatSelect.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent arg0)
+ {
+ String selected;
+ if(fc.getSelectedFile() != null)
+ {
+ selected = fc.getSelectedFile().getAbsolutePath();
+ String fmts[] = getImageFormats();
+ for(int i=0; i<fmts.length; i++)
+ selected = selected.replaceAll("."+fmts[i]+"$", "");
+ }
+ else
+ selected = "artemis";
+
+ fc.setSelectedFile(new File(selected+"."+
+ formatSelect.getSelectedItem()));
+ }
+ });
Dimension d = formatSelect.getPreferredSize();
formatSelect.setMaximumSize(d);
@@ -488,6 +550,13 @@ public class PrintArtemis extends ScrollPanel implements Printable
// remove file extension
String fsave = fc.getSelectedFile().getAbsolutePath().toLowerCase();
+
+ if(fsave.endsWith(".svg"))
+ {
+ createSVG(fc.getSelectedFile());
+ return;
+ }
+
if(fsave.endsWith(".png") ||
fsave.endsWith(".jpg") ||
fsave.endsWith(".jpeg") )
@@ -514,6 +583,45 @@ public class PrintArtemis extends ScrollPanel implements Printable
}
}
+ private void createSVG(final File fout)
+ {
+ final DOMImplementation domImpl =
+ GenericDOMImplementation.getDOMImplementation();
+ final Document doc = domImpl.createDocument(
+ "http://www.w3.org/2000/svg", "svg", null);
+
+ SVGGeneratorContext ctx = SVGGeneratorContext.createDefault(doc);
+ ctx.setComment("Generated by Artemis with Batik SVG Generator");
+ final SVGGraphics2D svgG = new SVGGraphics2D(ctx, true);
+ svgG.setFont(Options.getOptions().getFont());
+ final FontMetrics fm = svgG.getFontMetrics();
+ final Dimension d = getImageSize();
+ svgG.setSVGCanvasSize( new Dimension(
+ d.width+fm.stringWidth(" "), d.height+fm.getHeight()) );
+ paintComponent(svgG);
+
+ try
+ {
+ final Writer out = new OutputStreamWriter(
+ new FileOutputStream(fout), "UTF-8");
+ svgG.stream(out, true);
+ }
+ catch (UnsupportedEncodingException e)
+ {
+ e.printStackTrace();
+ }
+ catch (SVGGraphics2DIOException e)
+ {
+ e.printStackTrace();
+ }
+ catch (FileNotFoundException e)
+ {
+ e.printStackTrace();
+ }
+
+ return;
+ }
+
protected void doPrintActions()
{
final PrinterJob pj=PrinterJob.getPrinterJob();
@@ -575,7 +683,7 @@ public class PrintArtemis extends ScrollPanel implements Printable
public int print(Graphics g, PageFormat pf, int pageIndex) throws PrinterException
{
setImageSize();
- Graphics2D g2 = (Graphics2D) g;
+ Graphics2D g2 = (Graphics2D)g.create();
// RepaintManager.currentManager(this).setDoubleBufferingEnabled(false);
Dimension d = this.getSize(); //get size of document
--
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