diff --git a/.classpath b/.classpath
index 6cb6c677295e1216745131319e1ae767d6ec0707..a071b60b897152574377095ebcbba10e4c73a6e3 100644
--- a/.classpath
+++ b/.classpath
@@ -17,5 +17,11 @@
<classpathentry kind="lib" path="lib/picard/picard.jar"/>
<classpathentry kind="lib" path="lib/picard/sam.jar"/>
<classpathentry kind="lib" path="lib/commons-net-2.2.jar"/>
+ <classpathentry kind="lib" path="lib/batik/batik-awt-util.jar"/>
+ <classpathentry kind="lib" path="lib/batik/batik-dom.jar"/>
+ <classpathentry kind="lib" path="lib/batik/batik-ext.jar"/>
+ <classpathentry kind="lib" path="lib/batik/batik-svggen.jar"/>
+ <classpathentry kind="lib" path="lib/batik/batik-util.jar"/>
+ <classpathentry kind="lib" path="lib/batik/batik-xml.jar"/>
<classpathentry kind="output" path="ant-build/classes/main"/>
</classpath>
diff --git a/ChangeLog b/ChangeLog
index fbadef0ebfb378428aa21c873d7ee1b2038f9b80..7ed00133084c4621843b5c9698d3d2c987357053 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,4 +1,16 @@
Version XX
+ Add SVG (scalable vector graphics) support for Artemis, ACT and DNAPlotter.
+
+ Add support for indexed user graphs using tabix. For example file.plot is a tab
+ delimited file with column 1 containing the sequence name and column 2 the
+ positions:
+ (grep ^"#" file.plot; grep -v ^"#" file.plot | sort -k1,1 -k2,2n) | bgzip > sorted.plot.gz ;
+ tabix -s 1 -b 2 -e 2 sorted.plot.gz
+
+ Option added to show or hide the average line in the graphs.
+
+ BAM coverage heatmap view added.
+
Add Rfam sequence search from the RUN menu.
Base similarity graph for each VCF added to the VCF view.
@@ -13,7 +25,7 @@ Version XX
Coverage plots from read alignments (BAM) can be plotted by their strand.
- Addition of a Project File Manager for grouping files together for
+ Addition of a Project File Manager used to group files together for
launching in Artemis. When a project has been added or updated the details
are saved at the end of each session in '.artemis.project.properties'
in the user's home directory.
diff --git a/Makefile b/Makefile
index 2b20f14ece3af9b84a4e24312cf1947a80b95f5e..ed4aa75a3222ede16e40a62782898bcc73ef2423 100644
--- a/Makefile
+++ b/Makefile
@@ -8,7 +8,7 @@ SHELL=/bin/sh
JAVAC := javac -source 1.5 -target 1.5 $(OPT_FLAGS) $(EXTRA_FLAGS)
-REAL_CLASSPATH := CLASSPATH=lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/picard/sam.jar:lib/commons-net-2.2.jar:.
+REAL_CLASSPATH := CLASSPATH=lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/picard/sam.jar:lib/commons-net-2.2.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:.
NAMES:= \
uk/ac/sanger/artemis/OptionChangeListener \
diff --git a/act b/act
index f7aa1fae3f11804ae4620735b055c2a48bd6347f..4200521ecdb9b2301b3e989c86fcdd295cd31de7 100755
--- a/act
+++ b/act
@@ -31,6 +31,9 @@ ACT_HOME=`dirname "$PRG"`/.
CLASSPATH=$ACT_HOME:$ACT_HOME/lib/JacORB.jar:$ACT_HOME/lib/jemAlign.jar:$ACT_HOME/lib/jakarta-regexp-1.2.jar:$ACT_HOME/lib/macos.jar:$ACT_HOME/lib/chado-14-interface.jar:$ACT_HOME/lib/postgresql-8.4-701.jdbc3.jar:$CLASSPATH
+# batik jars
+CLASSPATH=$CLASSPATH:$ACT_HOME/lib/batik/batik-awt-util.jar:$ACT_HOME/lib/batik/batik-dom.jar:$ACT_HOME/lib/batik/batik-ext.jar:$ACT_HOME/lib/batik/batik-svggen.jar:$ACT_HOME/lib/batik/batik-util.jar:$ACT_HOME/lib/batik/batik-xml.jar
+
# j2ssh jars
CLASSPATH=$CLASSPATH:$ACT_HOME/lib/j2ssh/commons-logging.jar:$ACT_HOME/lib/j2ssh/j2ssh-core.jar:$ACT_HOME/lib/j2ssh/
diff --git a/art b/art
index 16cf2c2afe8c6c6159ad4871913c25d0eb8c6f4d..16f98d7ddb46a161f3f00f1be7a09da05bfbf2f5 100755
--- 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/etc/log4j.properties b/etc/log4j.properties
index d714f791dc537de7e2620242fe4f862020053fe2..1fcb68fee4c8bd8d66b8299cda3a373952c85c67 100644
--- a/etc/log4j.properties
+++ b/etc/log4j.properties
@@ -37,6 +37,7 @@ log4j.logger.uk.ac.sanger.artemis.components.variant=DEBUG, R
log4j.logger.uk.ac.sanger.artemis.io.ReadAndWriteEntry=DEBUG, R
log4j.logger.uk.ac.sanger.artemis.io.GFFStreamFeature=DEBUG, R
log4j.logger.uk.ac.sanger.artemis.util.FTPSeekableStream=DEBUG, R
+log4j.logger.uk.ac.sanger.artemis.plot.UserDataAlgorithm=DEBUG, R
#log4j.logger.com.ibatis.common.jdbc.SimpleDataSource=DEBUG, stdout, R
#log4j.logger.com.ibatis.common.jdbc.ScriptRunner=DEBUG, stdout, R
diff --git a/etc/versions b/etc/versions
index 83ee417ea300c88422ad233affd7d903999c84d8..01440428135bbe52ccd3e3e46e320f373727852f 100644
--- a/etc/versions
+++ b/etc/versions
@@ -1,4 +1,4 @@
-Artemis Release 14.2.2
-ACT Release 11.2.2
-DNAPlotter Release 1.8
+Artemis Release 14.2.3
+ACT Release 11.2.3
+DNAPlotter Release 1.9
BamView 1.2.6
diff --git a/lib/batik/batik-awt-util.jar b/lib/batik/batik-awt-util.jar
new file mode 100644
index 0000000000000000000000000000000000000000..f8d0d8d0aef4defbef79b77cf9ce3e960b24b39e
Binary files /dev/null and b/lib/batik/batik-awt-util.jar differ
diff --git a/lib/batik/batik-dom.jar b/lib/batik/batik-dom.jar
new file mode 100644
index 0000000000000000000000000000000000000000..dab1ab3ba9b27f82062d5d2e000972808f325555
Binary files /dev/null and b/lib/batik/batik-dom.jar differ
diff --git a/lib/batik/batik-ext.jar b/lib/batik/batik-ext.jar
new file mode 100644
index 0000000000000000000000000000000000000000..deaad0cf03a362f3854774104010db6997effb6f
Binary files /dev/null and b/lib/batik/batik-ext.jar differ
diff --git a/lib/batik/batik-svggen.jar b/lib/batik/batik-svggen.jar
new file mode 100644
index 0000000000000000000000000000000000000000..ede092150cd2f19af5d34ae902c3ef4819fbb283
Binary files /dev/null and b/lib/batik/batik-svggen.jar differ
diff --git a/lib/batik/batik-util.jar b/lib/batik/batik-util.jar
new file mode 100644
index 0000000000000000000000000000000000000000..6dd43a696abb84a074f99a45b22c650eb4d8b148
Binary files /dev/null and b/lib/batik/batik-util.jar differ
diff --git a/lib/batik/batik-xml.jar b/lib/batik/batik-xml.jar
new file mode 100644
index 0000000000000000000000000000000000000000..af2fbf6b06948405ff7c30e2c1cea3acb5aafb0b
Binary files /dev/null and b/lib/batik/batik-xml.jar differ
diff --git a/lib/batik/version b/lib/batik/version
new file mode 100644
index 0000000000000000000000000000000000000000..b55ee096feeb1ba544a96cb51064ccd5cfd8e951
--- /dev/null
+++ b/lib/batik/version
@@ -0,0 +1,5 @@
+http://xmlgraphics.apache.org/batik/
+
+SVN (batik-1.8pre) version (13-NOV-2012):
+
+http://people.apache.org/builds/xml-batik/batik-svn-12-11-13.zip
diff --git a/uk/ac/sanger/artemis/circular/PrintDNAImage.java b/uk/ac/sanger/artemis/circular/PrintDNAImage.java
index 603a9bb008ce448cbc55d8fc445148041829647d..74005d93af7f8451d600c8b5e7f572c43bd15106 100644
--- a/uk/ac/sanger/artemis/circular/PrintDNAImage.java
+++ b/uk/ac/sanger/artemis/circular/PrintDNAImage.java
@@ -35,7 +35,13 @@ import java.awt.event.KeyEvent;
import java.awt.image.BufferedImage;
import java.awt.image.RenderedImage;
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.BorderFactory;
import javax.swing.Box;
import javax.swing.JComboBox;
@@ -53,6 +59,17 @@ import javax.swing.JTextField;
import javax.swing.KeyStroke;
import javax.swing.border.Border;
+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.components.PrintArtemis;
+import uk.ac.sanger.artemis.components.StickyFileChooser;
+
@@ -225,18 +242,15 @@ public class PrintDNAImage extends ScrollPanel
f.setVisible(true);
}
-
/**
- *
* Provide some options for the image created
- *
*/
private File showOptions()
{
- String cwd = System.getProperty("user.dir");
- JFileChooser fc = new JFileChooser(cwd);
- File fselect = new File(cwd+System.getProperty("file.separator")+
- "dna.jpg");
+ final StickyFileChooser fc = new StickyFileChooser();
+ File fselect = new File(fc.getCurrentDirectory()+
+ System.getProperty("file.separator")+
+ "dnaplotter.png");
fc.setSelectedFile(fselect);
// file name prefix
@@ -250,10 +264,28 @@ public class PrintDNAImage extends ScrollPanel
bdown.add(labFormat);
Box bacross = Box.createHorizontalBox();
- JComboBox formatSelect =
- new JComboBox(javax.imageio.ImageIO.getWriterFormatNames());
- formatSelect.setSelectedItem("jpg");
-
+ final JComboBox formatSelect = new JComboBox(PrintArtemis.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[] = PrintArtemis.getImageFormats();
+ for(int i=0; i<fmts.length; i++)
+ selected = selected.replaceAll("."+fmts[i]+"$", "");
+ }
+ else
+ selected = "dnaplotter";
+
+ fc.setSelectedFile(new File(selected+"."+
+ formatSelect.getSelectedItem()));
+ }
+ });
+
Dimension d = formatSelect.getPreferredSize();
formatSelect.setMaximumSize(d);
bacross.add(Box.createHorizontalGlue());
@@ -291,9 +323,6 @@ public class PrintDNAImage extends ScrollPanel
System.out.println("Java 1.4+ is required");
}
}
-
-
-
/**
* Print to one jpeg or png file
@@ -310,10 +339,15 @@ public class PrintDNAImage extends ScrollPanel
Dimension d = dna.getSize();
double imageWidth = d.getWidth();
double imageHeight = d.getHeight();
- Paper paper = format.getPaper();
+ if(type.equals("svg"))
+ {
+ createSVG(file, d);
+ return;
+ }
+
+ Paper paper = format.getPaper();
paper.setSize(imageWidth,imageHeight);
-
paper.setImageableArea(0,0,
imageWidth,imageHeight+imageHeight);
format.setPaper(paper);
@@ -329,6 +363,42 @@ public class PrintDNAImage extends ScrollPanel
"This option requires Java 1.4 or higher.");
}
}
+
+ private void createSVG(final File fout, Dimension d)
+ {
+ 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 DNAPlotter with Batik SVG Generator");
+ final SVGGraphics2D svgG = new SVGGraphics2D(ctx, true);
+ svgG.setFont(Options.getOptions().getFont());
+ svgG.setSVGCanvasSize(d);
+ 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;
+ }
}
diff --git a/uk/ac/sanger/artemis/components/AlignmentViewer.java b/uk/ac/sanger/artemis/components/AlignmentViewer.java
index e8d30b680561d660fcc42fe8bfac62ab23be649e..19666975697068eea1cd7a757948defd32395d60 100644
--- a/uk/ac/sanger/artemis/components/AlignmentViewer.java
+++ b/uk/ac/sanger/artemis/components/AlignmentViewer.java
@@ -40,6 +40,9 @@ import java.util.Vector;
import java.util.Comparator;
import java.util.Arrays;
import javax.swing.*;
+
+import org.apache.batik.svggen.SVGGraphics2D;
+
import java.io.FileWriter;
import java.io.IOException;
@@ -1172,14 +1175,25 @@ public class AlignmentViewer extends CanvasPanel
if(offscreen == null)
offscreen = createImage(canvas_width, canvas_height);
- Graphics og = offscreen.getGraphics();
- og.setClip(0,0,canvas_width,canvas_height);
+ final Graphics og;
+ if(!(g instanceof SVGGraphics2D))
+ {
+ og = offscreen.getGraphics();
+ og.setClip(0,0,canvas_width,canvas_height);
+ }
+ else
+ og = g;
+
og.setColor(Color.white);
og.fillRect(0, 0, canvas_width, canvas_height);
drawAlignments(og);
drawLabels(og);
- g.drawImage(offscreen, 0, 0, null);
- og.dispose();
+
+ if(!(g instanceof SVGGraphics2D))
+ {
+ g.drawImage(offscreen, 0, 0, null);
+ og.dispose();
+ }
}
}
diff --git a/uk/ac/sanger/artemis/components/BasePlot.java b/uk/ac/sanger/artemis/components/BasePlot.java
index 9d595b25bd9fb27d6e2bfbc9066dfe5e759880bf..1d46bfb497a598e6c9c28144bd353318685422a3 100644
--- a/uk/ac/sanger/artemis/components/BasePlot.java
+++ b/uk/ac/sanger/artemis/components/BasePlot.java
@@ -722,6 +722,13 @@ public class BasePlot extends Plot
**/
public int drawMultiValueGraph(Graphics g, LineAttributes[] lines)
{
+ if( getAlgorithm() instanceof UserDataAlgorithm &&
+ ((UserDataAlgorithm)getAlgorithm()).FORMAT == UserDataAlgorithm.TABIX_INDEXED_FORMAT)
+ {
+ ((UserDataAlgorithm) getAlgorithm()).readIndexValues(
+ entryGroup.getSequenceEntry(), getStart(), getEnd());
+ }
+
if(recalculate_flag)
recalculateValues();
@@ -735,11 +742,9 @@ public class BasePlot extends Plot
final int window_size = getWindowSize();
// the number of values to plot at each x position
- final int get_values_return_count =
+ final int nvalues =
getBaseAlgorithm().getValueCount();
- final int number_of_values = value_array_array[0].length;
-
boolean isWiggle = false;
boolean isBlast = false;
if(getAlgorithm() instanceof UserDataAlgorithm)
@@ -753,17 +758,16 @@ public class BasePlot extends Plot
isBlast = true;
}
- if(number_of_values > 1 && !isWiggle)
+ if(value_array_array[0].length > 1 && !isWiggle)
drawGlobalAverage(g, min_value, max_value);
Stroke stroke = ((Graphics2D)g).getStroke();
- for(int value_index = 0; value_index < get_values_return_count;
- ++value_index)
+ for(int i = 0; i < nvalues; ++i)
{
- if(value_index < lines.length)
+ if(i < lines.length)
{
- g.setColor(lines[value_index].getLineColour());
- ((Graphics2D)g).setStroke(lines[value_index].getStroke());
+ g.setColor(lines[i].getLineColour());
+ ((Graphics2D)g).setStroke(lines[i].getStroke());
}
else
g.setColor(Color.black);
@@ -778,8 +782,8 @@ public class BasePlot extends Plot
drawPoints(g, min_value, max_value, step_size, window_size,
getWidthInBases(),
offset,
- value_array_array[value_index], value_index,
- get_values_return_count, isWiggle, isBlast);
+ value_array_array[i], i,
+ nvalues, isWiggle, isBlast);
}
((Graphics2D)g).setStroke(stroke);
@@ -870,7 +874,7 @@ public class BasePlot extends Plot
}
}
- return get_values_return_count;
+ return nvalues;
}
diff --git a/uk/ac/sanger/artemis/components/BioJavaEntrySource.java b/uk/ac/sanger/artemis/components/BioJavaEntrySource.java
index 8f9a64ce7cbf0db3e1d8d4d89c45440407d63214..ca1c454014268b0febef7f0557ed724138c7d1c7 100644
--- a/uk/ac/sanger/artemis/components/BioJavaEntrySource.java
+++ b/uk/ac/sanger/artemis/components/BioJavaEntrySource.java
@@ -25,29 +25,12 @@
package uk.ac.sanger.artemis.components;
-import java.net.*;
import java.io.*;
-import java.util.*;
-import java.lang.RuntimeException;
-import org.biojava.bio.program.das.*;
-import org.biojava.bio.BioException;
-import org.biojava.bio.seq.io.SequenceBuilderFactory;
-import org.biojava.bio.seq.io.EmblProcessor;
-import org.biojava.bio.seq.io.SmartSequenceBuilder;
-import org.biojava.bio.seq.io.SymbolTokenization;
-import org.biojava.bio.seq.io.StreamReader;
-import org.biojava.bio.seq.io.SequenceFormat;
import org.biojava.bio.seq.io.EmblLikeFormat;
-import org.biojava.bio.seq.SequenceIterator;
-import org.biojava.bio.symbol.Alphabet;
-import org.biojava.bio.seq.DNATools;
import uk.ac.sanger.artemis.util.*;
import uk.ac.sanger.artemis.io.BioJavaEntry;
-import uk.ac.sanger.artemis.io.EntryInformation;
-import uk.ac.sanger.artemis.io.SimpleEntryInformation;
-
import uk.ac.sanger.artemis.*;
import uk.ac.sanger.artemis.sequence.*;
@@ -145,50 +128,6 @@ public class BioJavaEntrySource implements EntrySource
public Entry getEntry (final boolean show_progress)
throws OutOfRangeException, NoSequenceException, IOException
{
-// DASSequence dasSeq = null;
-
-// try {
-// final URL dbURL =
-// new URL("http://genome.ornl.gov/das/das.cgi/ecoli");
-// // new URL("http://genome.cse.ucsc.edu:80/cgi-bin/das/cb1");
-// // new URL("http://servlet.sanger.ac.uk:8080/das/ens1131cds/");
-// final DASSequenceDB dasDB = new DASSequenceDB (dbURL);
-
-// final Set ids = dasDB.ids();
-
-// for (Iterator i = ids.iterator(); i.hasNext(); ) {
-// System.out.println(i.next().toString());
-// }
-
-// // dasSeq = (DASSequence) dasDB.getSequence((String) ids.iterator().next());
-
-// SequenceIterator si = dasDB.sequenceIterator();
-
-// if (si.hasNext()) {
-// dasSeq = (DASSequence) si.nextSequence();
-
-// System.err.println("Got: " + dasSeq);
-
-// final BioJavaEntry bioJavaEntry = new BioJavaEntry (dasSeq);
-
-// return new Entry (bioJavaEntry);
-// } else {
-// System.err.println("No more sequences...");
-// }
-
-
-// // final BioJavaEntry emblEntry =
-// // new BioJavaEntry (document, new EmblLikeFormat ());
-
-// // return new Entry (emblEntry);
-// } catch (MalformedURLException mue) {
-// mue.printStackTrace();
-// } catch (BioException be) {
-// be.printStackTrace();
-// }
-
-// return null;
-
final String fileName = "/nfs/team81/kmr/pow/java2/AE002734.game";
final FileDocument document = new FileDocument (new File (fileName));
@@ -196,14 +135,6 @@ public class BioJavaEntrySource implements EntrySource
new BioJavaEntry (document, new EmblLikeFormat ());
return new Entry (emblEntry);
-
-// final String fileName = "/nfs/team81/kmr/pow/java2/AB000095.embl";
-// final FileDocument document = new FileDocument (new File (fileName));
-
-// final BioJavaEntry emblEntry =
-// new BioJavaEntry (document, new EmblLikeFormat ());
-
-// return new Entry (emblEntry);
}
/**
diff --git a/uk/ac/sanger/artemis/components/FeatureDisplay.java b/uk/ac/sanger/artemis/components/FeatureDisplay.java
index 8c279573a1c5a75526dad041e9ebdf18d7d97d00..bc6cb235cc3856f9fcd2c9b5ac22cd50078475dd 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/FeaturePlot.java b/uk/ac/sanger/artemis/components/FeaturePlot.java
index 646f45c368a9789ed1a739fe710bb5d12dd82a7e..6d3425b093317139eac5c5016b5d38432f9e922c 100644
--- a/uk/ac/sanger/artemis/components/FeaturePlot.java
+++ b/uk/ac/sanger/artemis/components/FeaturePlot.java
@@ -25,24 +25,30 @@
package uk.ac.sanger.artemis.components;
-import uk.ac.sanger.artemis.sequence.*;
-import uk.ac.sanger.artemis.util.OutOfRangeException;
-import uk.ac.sanger.artemis.util.ReadOnlyException;
-import uk.ac.sanger.artemis.*;
-import uk.ac.sanger.artemis.io.EntryInformationException;
-import uk.ac.sanger.artemis.plot.*;
-import java.awt.*;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Graphics;
+
+import uk.ac.sanger.artemis.Feature;
+import uk.ac.sanger.artemis.FeatureChangeEvent;
+import uk.ac.sanger.artemis.FeatureChangeListener;
+import uk.ac.sanger.artemis.Options;
+import uk.ac.sanger.artemis.plot.FeatureAlgorithm;
+import uk.ac.sanger.artemis.plot.LineAttributes;
+import uk.ac.sanger.artemis.sequence.AminoAcidSequence;
+
/**
* The components of this class display a plot of a FeatureAlgorithm for a
* particular feature.
- *
* @author Kim Rutherford
- * @version $Id: FeaturePlot.java,v 1.11 2009-07-20 15:11:17 tjc Exp $
**/
public class FeaturePlot extends Plot
implements DisplayAdjustmentListener, FeatureChangeListener {
+
+ private static final long serialVersionUID = 1L;
+
/**
* Create a new FeatureDisplay object.
* @param algorithm The object that will generate the values we plot in
@@ -102,10 +108,9 @@ public class FeaturePlot extends Plot
public void displayAdjustmentValueChanged (DisplayAdjustmentEvent event) {
start_base = event.getStart ();
end_base = event.getEnd ();
- width_in_bases = event.getWidthInBases ();
+ //width_in_bases = event.getWidthInBases ();
recalculate_flag = true;
-
repaint();
}
@@ -138,13 +143,6 @@ public class FeaturePlot extends Plot
return end_base;
}
- /**
- * Return the width in bases of the display, from the last event.
- **/
- private int getWidthInBases () {
- return width_in_bases;
- }
-
/**
* This array is used by drawGraph (). It is reallocated when the scale
* changes.
@@ -386,12 +384,6 @@ public class FeaturePlot extends Plot
**/
private int end_base;
- /**
- * The width in bases of the display, as obtained from the
- * DisplayAdjustmentEvent.
- **/
- private int width_in_bases;
-
protected void calculateFeatures(boolean fromPeak)
{
// TODO Auto-generated method stub
diff --git a/uk/ac/sanger/artemis/components/MultiComparator.java b/uk/ac/sanger/artemis/components/MultiComparator.java
index b9a64b897040179a9cc5739a90d08ab8ad26dd26..06a393fb88061a2b83333f2d734681cb74525b34 100644
--- a/uk/ac/sanger/artemis/components/MultiComparator.java
+++ b/uk/ac/sanger/artemis/components/MultiComparator.java
@@ -39,8 +39,20 @@ import uk.ac.sanger.artemis.io.EntryInformationException;
import uk.ac.sanger.artemis.io.DocumentEntryFactory;
import uk.ac.sanger.artemis.io.DocumentEntry;
-import java.awt.*;
-import java.awt.event.*;
+import java.awt.Cursor;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Image;
+import java.awt.MediaTracker;
+import java.awt.Point;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
import java.io.IOException;
import java.io.File;
import java.net.URL;
@@ -58,9 +70,7 @@ import javax.swing.JPanel;
* This JFrame component contains an arbitrary number of AlignmentViewer
* components and FeatureDisplay components along with ComparatorGlue objects
* to keep them synchronized.
- *
- * @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: MultiComparator.java,v 1.22 2008-09-03 10:58:33 tjc Exp $
+ * @author Kim Rutherford
**/
public class MultiComparator extends JFrame
@@ -132,9 +142,6 @@ public class MultiComparator extends JFrame
/** Used to show the progress of loading file. */
private InputStreamProgressListener progress_listener;
- /** current group used for drag and drop */
- private int current_group = -1;
-
/**
* Initialise entry_group_array and comparison_data_array and create all
* the FeatureDisplay and AlignmentViewer components.
@@ -162,16 +169,10 @@ public class MultiComparator extends JFrame
this.progress_listener = progress_listener;
this.entry_sources = Utilities.getEntrySources(this, null);
- final StringBuffer title_buffer = new StringBuffer();
-
- title_buffer.append("ACT: ");
-
+ final StringBuffer title_buffer = new StringBuffer("ACT: ");
for(int i = 0; i < entry_group_array.length - 1; ++i)
- {
- final String sequence_name =
- entry_group_array[i].getDefaultEntry().getName();
- title_buffer.append(sequence_name).append(" vs ");
- }
+ title_buffer.append(
+ entry_group_array[i].getDefaultEntry().getName()).append(" vs ");
final EntryGroup last_entry_group =
entry_group_array[entry_group_array.length - 1];
@@ -206,7 +207,6 @@ public class MultiComparator extends JFrame
getGotoEventSourceArray()[i]);
final int scroll_bar_position;
-
if(i == getEntryGroupArray().length - 1 &&
getEntryGroupArray().length == 2)
{
@@ -255,17 +255,11 @@ public class MultiComparator extends JFrame
getAlignmentViewerArray()[i]);
}
- final Font default_font = getDefaultFont();
-
- setFont(default_font);
-
+ setFont(getDefaultFont());
makeMenus();
-
- GridBagLayout gridbag = new GridBagLayout();
- getContentPane().setLayout(gridbag);
+ getContentPane().setLayout(new GridBagLayout());
GridBagConstraints c = new GridBagConstraints();
-
c.gridwidth = GridBagConstraints.REMAINDER;
c.fill = GridBagConstraints.BOTH;
c.anchor = GridBagConstraints.NORTH;
@@ -598,7 +592,7 @@ public class MultiComparator extends JFrame
**/
private void makeMenus()
{
- final Font default_font = getDefaultFont();
+ //final Font default_font = getDefaultFont();
final JMenuBar menu_bar = new JMenuBar();
setJMenuBar(menu_bar);
diff --git a/uk/ac/sanger/artemis/components/Plot.java b/uk/ac/sanger/artemis/components/Plot.java
index 9fcc723afc22fc2d14351ac2cb072652b0873014..5a24f1de1757616800c3ed93e3537d071b716282 100644
--- a/uk/ac/sanger/artemis/components/Plot.java
+++ b/uk/ac/sanger/artemis/components/Plot.java
@@ -29,8 +29,15 @@ import uk.ac.sanger.artemis.Options;
import uk.ac.sanger.artemis.circular.TextFieldFloat;
import uk.ac.sanger.artemis.plot.*;
-import java.awt.*;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.GridLayout;
+import java.awt.Image;
+import java.awt.Scrollbar;
import java.awt.event.*;
+import java.util.Vector;
import javax.swing.JMenu;
import javax.swing.JPanel;
@@ -44,15 +51,16 @@ 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
- * @version $Id: Plot.java,v 1.26 2009-08-18 09:01:44 tjc Exp $
**/
public abstract class Plot extends JPanel
{
+ private static final long serialVersionUID = 1L;
/** scroll bar for changing the window size. */
private JScrollBar window_changer = null;
@@ -73,12 +81,16 @@ public abstract class Plot extends JPanel
* drawScaleLine() is called.
**/
private boolean draw_scale;
+
+ private final int SCROLL_NOB_SIZE = 10;
/**
* Set to true if drawMultiValueGraph() should call recalculateValues().
* It is reset to false by recalculateValues().
**/
protected boolean recalculate_flag = true;
+
+ private boolean showAverage = true;
/**
* The x position of the last click or -1 if the user hasn't clicked
@@ -95,7 +107,7 @@ public abstract class Plot extends JPanel
/**
* A vector of those objects listening for PlotMouse events.
**/
- final private java.util.Vector listener_list = new java.util.Vector();
+ final private Vector<PlotMouseListener> listener_list = new Vector<PlotMouseListener>();
/**
* Recalculate the values all the state that is used for drawing the plot
@@ -116,10 +128,12 @@ public abstract class Plot extends JPanel
/** number of graph lines to be drawn */
private int numPlots;
- /** colour array for graph drawing */
protected LineAttributes lines[];
private int lastPaintHeight = getHeight();
+
+ /** the minimum distance in pixels between the labels */
+ private final static int MINIMUM_LABEL_SPACING = 50;
/**
* Create a new plot component.
@@ -130,34 +144,27 @@ public abstract class Plot extends JPanel
**/
public Plot(Algorithm algorithm, boolean draw_scale)
{
- super();
+ super(new BorderLayout());
this.algorithm = algorithm;
this.draw_scale = draw_scale;
- final Font font = Options.getOptions().getFont();
-
- setFont(font);
- FontMetrics fm = getFontMetrics(font);
+ setFont(Options.getOptions().getFont());
+ FontMetrics fm = getFontMetrics(getFont());
font_height = fm.getHeight();
- setLayout(new BorderLayout());
-
final int MAX_WINDOW;
-
if(getAlgorithm().getDefaultMaxWindowSize() != null)
MAX_WINDOW = getAlgorithm().getDefaultMaxWindowSize().intValue();
else
MAX_WINDOW = 500;
final int MIN_WINDOW;
-
if(getAlgorithm().getDefaultMinWindowSize() != null)
MIN_WINDOW = getAlgorithm().getDefaultMinWindowSize().intValue();
else
MIN_WINDOW = 5;
final int START_WINDOW;
-
if(getAlgorithm().getDefaultWindowSize() == null)
START_WINDOW = 10;
else
@@ -189,17 +196,11 @@ public abstract class Plot extends JPanel
}
});
-
-// setBackground(Color.white);
add(window_changer, "East");
-
addMouseListener(mouse_listener);
addMouseMotionListener(mouse_motion_listener);
-
}
- final int SCROLL_NOB_SIZE = 10;
-
/**
* Return the algorithm that was passed to the constructor.
**/
@@ -220,8 +221,7 @@ public abstract class Plot extends JPanel
final MouseListener mouse_listener = new MouseAdapter()
{
/**
- * Listen for mouse press events so that we can do a popup menu and a
- * crosshair.
+ * Listen for mouse press popup menu and crosshair events.
**/
public void mousePressed(MouseEvent event)
{
@@ -296,10 +296,9 @@ public abstract class Plot extends JPanel
});
popup.add(setScale);
- final JCheckBoxMenuItem scaling_toggle =
- new JCheckBoxMenuItem("Scaling");
- scaling_toggle.setState(getAlgorithm().scalingFlag());
+ final JCheckBoxMenuItem scaling_toggle =
+ new JCheckBoxMenuItem("Scaling",getAlgorithm().scalingFlag());
scaling_toggle.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent _)
@@ -309,10 +308,19 @@ public abstract class Plot extends JPanel
repaint();
}
});
-
popup.add(scaling_toggle);
-
-
+
+ final JCheckBoxMenuItem showAverageLn = new JCheckBoxMenuItem("Show average", showAverage);
+ showAverageLn.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent _)
+ {
+ showAverage = showAverageLn.isSelected();
+ repaint();
+ }
+ });
+ popup.add(showAverageLn);
+
if(Plot.this instanceof BasePlot)
{
final JMenuItem showMinMaxValues =
@@ -351,13 +359,11 @@ public abstract class Plot extends JPanel
}
});
}
-
-
+
popup.addSeparator();
final JMenu max_window_size =
new JMenu("Maximum Window Size");
-
popup.add(max_window_size);
final int[] window_sizes =
@@ -366,9 +372,7 @@ public abstract class Plot extends JPanel
200000, 500000, 1000000
};
-
JMenuItem window_size_item;
-
for(int i = 0 ; i < window_sizes.length ; ++i)
{
final int size = i;
@@ -440,7 +444,6 @@ public abstract class Plot extends JPanel
}
final JSplitPane splitPane = getJSplitPane();
-
if(splitPane == null)
{
popup.addSeparator();
@@ -458,8 +461,7 @@ public abstract class Plot extends JPanel
{
public void actionPerformed(ActionEvent e)
{
- Dimension d = getSize();
- rescale((int) (d.height * 0.9f));
+ rescale((int) (getSize().height * 0.9f));
}
});
@@ -467,8 +469,7 @@ public abstract class Plot extends JPanel
{
public void actionPerformed(ActionEvent e)
{
- Dimension d = getSize();
- rescale((int) (d.height * 1.1f));
+ rescale((int) (getSize().height * 1.1f));
}
});
@@ -486,12 +487,10 @@ public abstract class Plot extends JPanel
if(select == 1)
return;
-
try
{
- final int value = Integer
- .parseInt(newGraphHgt.getText().trim());
- rescale(value);
+ rescale(Integer.parseInt(
+ newGraphHgt.getText().trim()));
}
catch(NumberFormatException nfe)
{
@@ -611,7 +610,7 @@ public abstract class Plot extends JPanel
PlotMouseListener listener;
for(int i = 0; i < listener_list.size(); ++i)
{
- listener = (PlotMouseListener)listener_list.elementAt(i);
+ listener = listener_list.elementAt(i);
listener.mouseClick(getPointPosition(cross_hair_position));
}
}
@@ -625,7 +624,7 @@ public abstract class Plot extends JPanel
PlotMouseListener listener;
for(int i = 0; i < listener_list.size(); ++i)
{
- listener = (PlotMouseListener)listener_list.elementAt(i);
+ listener = listener_list.elementAt(i);
listener.mouseDrag(getPointPosition(drag_start_position),
getPointPosition(cross_hair_position));
}
@@ -640,7 +639,7 @@ public abstract class Plot extends JPanel
PlotMouseListener listener;
for(int i = 0; i < listener_list.size(); ++i)
{
- listener = (PlotMouseListener)listener_list.elementAt(i);
+ listener = listener_list.elementAt(i);
listener.mouseDoubleClick(getPointPosition(cross_hair_position));
}
}
@@ -685,11 +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.
@@ -706,8 +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;
}
@@ -737,31 +746,19 @@ public abstract class Plot extends JPanel
drag_start_position = -1;
}
- // the minimum distance in pixels between the labels
- private final static int MINIMUM_LABEL_SPACING = 50;
-
/**
- * Draw the scale line at the bottom of the graph.
+ * Draw the scale line at the bottom of the graph (used by FeaturePlot).
* @param start The base on the left
* @param end The base on the right
**/
protected void drawScaleLine(final Graphics g,
final int start, final int end)
{
- final int width = getWidth() - window_changer.getWidth();
- final int height = getHeight();
-
- final int scale_number_y_pos = height - 1;
-
+ final int hgt = getHeight();
+ final int scale_number_y_pos = hgt - 1;
final float bases_per_pixel = 1.0F;
- // set the spacing so that the labels are at multiples of 10
- final int base_label_spacing = MINIMUM_LABEL_SPACING;
-
- final int label_spacing = (int)(base_label_spacing / bases_per_pixel);
-
- final int possible_index_of_first_label = start / base_label_spacing;
-
+ final int possible_index_of_first_label = start / MINIMUM_LABEL_SPACING;
final int index_of_first_label;
if(possible_index_of_first_label == 0)
@@ -769,22 +766,18 @@ public abstract class Plot extends JPanel
else
index_of_first_label = possible_index_of_first_label;
- final int index_of_last_label = end / base_label_spacing;
-
- String label_string;
+ final int index_of_last_label = end / MINIMUM_LABEL_SPACING;
for(int i = index_of_first_label; i <= index_of_last_label; i++)
{
- label_string = String.valueOf((int)(i * base_label_spacing));
-
final int scale_number_x_pos =
- (int)((i * base_label_spacing - start) / bases_per_pixel);
+ (int)((i * MINIMUM_LABEL_SPACING - start) / bases_per_pixel);
- g.drawString(label_string,
+ g.drawString(String.valueOf((int)(i * MINIMUM_LABEL_SPACING)),
scale_number_x_pos + 2,
scale_number_y_pos);
- g.drawLine(scale_number_x_pos, height - getScaleHeight() / 2,
- scale_number_x_pos, height - getScaleHeight());
+ g.drawLine(scale_number_x_pos, hgt - getScaleHeight() / 2,
+ scale_number_x_pos, hgt - getScaleHeight());
}
}
@@ -977,7 +970,8 @@ public abstract class Plot extends JPanel
final float max_value)
{
// if a heatmap do not show the average
- if(lines != null && lines[0].getPlotType().equals(LineAttributes.PLOT_TYPES[2]))
+ if(!showAverage || (
+ lines != null && lines[0].getPlotType().equals(LineAttributes.PLOT_TYPES[2])))
return;
final Float average = getAlgorithm().getAverage();
@@ -1129,22 +1123,6 @@ public abstract class Plot extends JPanel
{
return font_height;
}
-
- /**
- * Used to get the X coordinate for the tooltip text.
- * @param total_unit_count The maximum number of residues/bases we can
- * show. This is used to draw the scale line and to calculate the
- * distance (in pixels) between plot points.
- * @param start_position The distance from the edge of the canvas (measured
- * in residues/bases) to start drawing the plot.
- * @param xpos The mouse position on the canvas.
- **/
- protected int getXCoordinate(final int total_unit_count,
- final int start_position,
- final int xpos)
- {
- return (xpos * total_unit_count)/getSize().width + start_position;
- }
/**
* Used to get the Y coordinate for the tooltip text.
@@ -1162,7 +1140,6 @@ public abstract class Plot extends JPanel
final float plot_values[], int base_pos)
{
int ypos = (int)((base_pos - start_position - (window_size/2))/step_size);
-
if(ypos < 0)
ypos = 0;
else if(ypos > plot_values.length-1)
@@ -1170,5 +1147,4 @@ public abstract class Plot extends JPanel
return plot_values[ypos];
}
-
}
diff --git a/uk/ac/sanger/artemis/components/PrintACT.java b/uk/ac/sanger/artemis/components/PrintACT.java
index 0c3403f5ce10d36bea209722515b04262073ad47..5928f777c2463d516a4dfcba0ff7d2e0b6093c9d 100644
--- a/uk/ac/sanger/artemis/components/PrintACT.java
+++ b/uk/ac/sanger/artemis/components/PrintACT.java
@@ -32,7 +32,12 @@ import java.awt.print.Printable;
import java.awt.print.PrinterException;
import java.awt.print.PrinterJob;
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.Box;
import javax.swing.JCheckBox;
@@ -50,12 +55,18 @@ import javax.swing.JScrollPane;
import javax.swing.JSeparator;
import javax.swing.KeyStroke;
+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;
/**
-*
* Use to print images from ACT
-*
*/
public class PrintACT extends ScrollPanel implements Printable
{
@@ -274,18 +285,15 @@ public class PrintACT extends ScrollPanel implements Printable
}
/**
- *
* Print to a jpeg or png file
- *
*/
public void print()
{
// file chooser
- String cwd = System.getProperty("user.dir");
- JFileChooser fc = new JFileChooser(cwd);
- File fselect = new File(cwd+
- System.getProperty("file.separator")+
- "act.png");
+ final StickyFileChooser fc = new StickyFileChooser();
+ File fselect = new File(fc.getCurrentDirectory()+
+ System.getProperty("file.separator")+
+ "act.png");
fc.setSelectedFile(fselect);
// file name prefix
@@ -296,8 +304,27 @@ public class PrintACT extends ScrollPanel implements Printable
YBox.add(labFormat);
Box bacross = Box.createHorizontalBox();
- JComboBox formatSelect =
- new JComboBox(javax.imageio.ImageIO.getWriterFormatNames());
+ final JComboBox formatSelect = new JComboBox(PrintArtemis.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[] = PrintArtemis.getImageFormats();
+ for(int i=0; i<fmts.length; i++)
+ selected = selected.replaceAll("."+fmts[i]+"$", "");
+ }
+ else
+ selected = "act";
+
+ fc.setSelectedFile(new File(selected+"."+
+ formatSelect.getSelectedItem()));
+ }
+ });
formatSelect.setSelectedItem("png");
Dimension d = formatSelect.getPreferredSize();
@@ -319,6 +346,12 @@ public class PrintACT 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") )
@@ -345,12 +378,46 @@ public class PrintACT 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 ACT with Batik SVG Generator");
+ final SVGGraphics2D svgG = new SVGGraphics2D(ctx, true);
+ svgG.setFont(Options.getOptions().getFont());
+ svgG.setSVGCanvasSize( getImageSize() );
+ 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;
+ }
+
/**
- *
* Returns a generated image
* @param pageIndex page number
* @return image
- *
*/
private RenderedImage createImage()
{
diff --git a/uk/ac/sanger/artemis/components/PrintArtemis.java b/uk/ac/sanger/artemis/components/PrintArtemis.java
index f72fef4d423ef4f2a13579c2d7b5b8707ddcdf41..5c37fd88450813938b079ccc60009130b29de40a 100644
--- a/uk/ac/sanger/artemis/components/PrintArtemis.java
+++ b/uk/ac/sanger/artemis/components/PrintArtemis.java
@@ -29,9 +29,26 @@ 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 java.util.Arrays;
+import java.util.HashSet;
+
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 +83,45 @@ 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 +175,9 @@ 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 +185,7 @@ 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 +217,14 @@ 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 +428,21 @@ public class PrintArtemis extends ScrollPanel implements Printable
f.setVisible(true);
}
+ public static String[] getImageFormats()
+ {
+ final String fmts[] = javax.imageio.ImageIO.getWriterFormatNames();
+ final HashSet<String> list = new HashSet<String>();
+ for(int i=0; i<fmts.length; i++)
+ list.add(fmts[i].toLowerCase());
+
+ final String tmpFmts[] = new String[list.size()+1];
+ System.arraycopy(list.toArray(), 0, tmpFmts, 0, list.size());
+ tmpFmts[tmpFmts.length-1] = "svg";
+ Arrays.sort(tmpFmts);
+
+ return tmpFmts;
+ }
+
/**
*
* Print to a jpeg or png file
@@ -399,7 +451,7 @@ 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 +465,27 @@ 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 +558,13 @@ 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 +591,45 @@ 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 +691,7 @@ 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
diff --git a/uk/ac/sanger/artemis/components/variant/TabixReader.java b/uk/ac/sanger/artemis/components/variant/TabixReader.java
index a42cdf5431db2708dfed279fcdd60e5883cfd429..102d718982e3eb8575a1deac9b15040eaf33d2f7 100644
--- a/uk/ac/sanger/artemis/components/variant/TabixReader.java
+++ b/uk/ac/sanger/artemis/components/variant/TabixReader.java
@@ -413,8 +413,28 @@ public class TabixReader extends AbstractVCFReader
return mSeq;
}
- protected String getFileName()
+ public int getStartColumn()
+ {
+ return mBc;
+ }
+
+ public int getEndColumn()
+ {
+ return mEc;
+ }
+
+ public int getSeqColumn()
+ {
+ return mSc;
+ }
+
+ public String getFileName()
{
return mFn;
}
+
+ public char getCommentChar()
+ {
+ return (char)mMeta;
+ }
}
diff --git a/uk/ac/sanger/artemis/plot/Algorithm.java b/uk/ac/sanger/artemis/plot/Algorithm.java
index 434d20230f527492e21cc714beb43b37426415e0..1ffeb9e5ce2170ccc6d16978a6defdd4b3245f76 100644
--- a/uk/ac/sanger/artemis/plot/Algorithm.java
+++ b/uk/ac/sanger/artemis/plot/Algorithm.java
@@ -143,6 +143,14 @@ public abstract class Algorithm {
{
return algorithm_name;
}
+
+ /**
+ * Return the name of this algorithm.
+ **/
+ public void setAlgorithmName (String algorithm_name)
+ {
+ this.algorithm_name = algorithm_name;
+ }
/**
* Return the short (one word) name of this algorithm, as passed tp the
diff --git a/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java b/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
index 84c6561ab82e46ec20e7cbb4b0dbe5d3ddc011fd..0a69f718add3b0acc61c65572245071d91b9a580 100644
--- a/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
+++ b/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
@@ -1,10 +1,7 @@
/* UserDataAlgorithm.java
- *
- * created: Wed May 10 2000
- *
* This file is part of Artemis
*
- * Copyright (C) 2000 Genome Research Limited
+ * Copyright (C) 2000-2012 Genome Research Limited
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
@@ -19,52 +16,57 @@
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- *
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java,v 1.14 2009-07-22 12:51:54 tjc Exp $
*/
package uk.ac.sanger.artemis.plot;
-import uk.ac.sanger.artemis.sequence.*;
-
-import uk.ac.sanger.artemis.util.*;
+import uk.ac.sanger.artemis.Entry;
+import uk.ac.sanger.artemis.sequence.Bases;
+import uk.ac.sanger.artemis.sequence.Strand;
+import uk.ac.sanger.artemis.util.Document;
+import uk.ac.sanger.artemis.util.FileDocument;
+import uk.ac.sanger.artemis.util.LinePushBackReader;
+import uk.ac.sanger.artemis.util.StringVector;
+import uk.ac.sanger.artemis.components.variant.TabixReader;
+import uk.ac.sanger.artemis.io.IndexFastaStream;
import uk.ac.sanger.artemis.io.ReadFormatException;
-
import java.awt.Color;
import java.awt.GridLayout;
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.Reader;
+import java.io.StringReader;
+import java.util.Arrays;
import java.util.HashMap;
import java.util.regex.Pattern;
-
import javax.swing.ButtonGroup;
import javax.swing.JCheckBox;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
+import net.sf.samtools.util.BlockCompressedInputStream;
+
/**
* Objects of this class have one useful method - getValues (), which takes a
* range of bases and returns a single floating point number. The number is
* calculated by averaging the values from a data file. The Strand to use is
* set in the constructor.
- *
- * @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: UserDataAlgorithm.java,v 1.14 2009-07-22 12:51:54 tjc Exp $
+ * @author Kim Rutherford
**/
public class UserDataAlgorithm extends BaseAlgorithm
{
/** A base per line file format */
public static int BASE_PER_LINE_FORMAT = 1;
-
/** Base position is specified in the first column file format */
public static int BASE_SPECIFIED_FORMAT = 2;
-
/** Wiggle format */
public static int WIGGLE_VARIABLE_STEP_FORMAT = 3;
- public static int WIGGLE_FIXED_STEP_FORMAT = 4;
-
- public static int BLAST_FORMAT = 5;
- public static int MSPCRUNCH_BLAST_FORMAT = 6;
+ public static int WIGGLE_FIXED_STEP_FORMAT = 4;
+ public static int BLAST_FORMAT = 5;
+ public static int MSPCRUNCH_BLAST_FORMAT = 6;
+ public static int TABIX_INDEXED_FORMAT = 7;
/** The data read by the constructor - for BASE_PER_LINE_FORMAT */
private float data[][] = null;
@@ -76,7 +78,6 @@ public class UserDataAlgorithm extends BaseAlgorithm
/** The maximum value in the data array. */
private float data_max = Float.MIN_VALUE;
-
/** The minimum value in the data array. */
private float data_min = Float.MAX_VALUE;
@@ -95,8 +96,10 @@ public class UserDataAlgorithm extends BaseAlgorithm
public int FORMAT = BASE_PER_LINE_FORMAT;
private LineAttributes lines[];
-
- public Wiggle wiggle[];
+ private Wiggle wiggle[];
+ private TabixIdxGraph idxReader;
+ private static org.apache.log4j.Logger logger4j =
+ org.apache.log4j.Logger.getLogger(UserDataAlgorithm.class);
/**
* Create a new UserDataAlgorithm object. This reads a file
@@ -109,51 +112,63 @@ public class UserDataAlgorithm extends BaseAlgorithm
* @param logTransform true if the log transformation is to be
* shown.
**/
- public UserDataAlgorithm (final Strand strand, final Document document,
+ public UserDataAlgorithm (final Strand strand, final Document doc,
final boolean logTransform)
throws IOException
{
- super (strand, "User algorithm from " + document.getName (), "user");
-
+ super (strand,
+ (logTransform ? "User log plot " + doc.getName () :
+ "User plot " + doc.getName ()), "user");
this.logTransform = logTransform;
- final Reader document_reader = document.getReader ();
- LinePushBackReader pushback_reader = new LinePushBackReader (document_reader);
- String first_line = pushback_reader.readLine ();
+ if(isIndexed(doc) && doc.getInputStream() instanceof BlockCompressedInputStream)
+ {
+ setAlgorithmName(
+ (logTransform ? "Indexed log plot " + doc.getName () :
+ "Indexed plot " + doc.getName ()));
+ FORMAT = TABIX_INDEXED_FORMAT;
+ idxReader = new TabixIdxGraph(
+ ((FileDocument) doc).getFile().getAbsolutePath());
+ number_of_values = idxReader.getNumberOfValues();
+ return;
+ }
+
+ final Reader doc_reader = doc.getReader ();
+ final LinePushBackReader pushback_reader = new LinePushBackReader (doc_reader);
+ String firstLn = pushback_reader.readLine ();
- Pattern dataPattern = Pattern.compile("^\\s*([\\d\\.-]+\\s*)+$");
- Pattern blastPattern = Pattern.compile(
+ final Pattern dataPattern = Pattern.compile("^\\s*([\\d\\.-]+\\s*)+$");
+ final Pattern blastPattern = Pattern.compile(
"^(\\S+\\t+){2}[\\d\\.]+\\t+(\\d+\\t+){7}\\S+\\t+(\\s*\\d+)$");
- Pattern mspCrunchPattern = Pattern.compile(
+ final Pattern mspCrunchPattern = Pattern.compile(
"^\\d+\\s[\\d\\.]+(\\s\\d+){2}\\s\\D\\S+(\\s\\d+){2}\\s\\D\\S+.*");
- if(dataPattern.matcher(first_line).matches())
+ if(dataPattern.matcher(firstLn).matches())
FORMAT = BASE_PER_LINE_FORMAT;
- else if(blastPattern.matcher(first_line).matches())
+ else if(blastPattern.matcher(firstLn).matches())
FORMAT = BLAST_FORMAT;
- else if(mspCrunchPattern.matcher(first_line).matches())
+ else if(mspCrunchPattern.matcher(firstLn).matches())
FORMAT = MSPCRUNCH_BLAST_FORMAT;
else
{
- StringBuffer header = new StringBuffer(first_line+"\n");
-
- while(!dataPattern.matcher(first_line).matches())
+ StringBuffer header = new StringBuffer(firstLn+"\n");
+ while(!dataPattern.matcher(firstLn).matches())
{
- first_line = pushback_reader.readLine ().trim();
- header.append(first_line+"\n");
+ firstLn = pushback_reader.readLine ().trim();
+ header.append(firstLn+"\n");
}
FORMAT = parseHeader(header);
}
final Pattern patt = Pattern.compile("\\s+");
- String tokens[] = patt.split(first_line);
+ String tokens[] = patt.split(firstLn);
if (tokens.length < 1)
throw new ReadFormatException ("unknown file type");
this.number_of_values = tokens.length;
- pushback_reader.pushBack (first_line);
+ pushback_reader.pushBack (firstLn);
if(FORMAT == BASE_PER_LINE_FORMAT)
data = new float [strand.getSequenceLength ()][tokens.length];
@@ -167,7 +182,20 @@ public class UserDataAlgorithm extends BaseAlgorithm
else
readWiggle(pushback_reader);
pushback_reader.close();
- document_reader.close();
+ doc_reader.close();
+ }
+
+ /**
+ * Test if the tabix (.tbi) index is present.
+ * @param doc
+ * @return
+ */
+ private static boolean isIndexed(Document doc)
+ {
+ if(doc instanceof FileDocument)
+ return (new File(
+ ((FileDocument)doc).getFile().getAbsolutePath() + ".tbi")).exists();
+ return false;
}
/**
@@ -373,8 +401,7 @@ public class UserDataAlgorithm extends BaseAlgorithm
coordIndexStart = 2;
coordIndexEnd = 3;
}
-
-
+
while ((line = pushback_reader.readLine ()) != null)
{
String tokens[] = patt.split(line.trim());
@@ -488,7 +515,6 @@ public class UserDataAlgorithm extends BaseAlgorithm
public void getValues (int start, int end, final float [] values)
{
final int value_count = getValueCount ();
-
if(getStrand ().getDirection() == Bases.REVERSE)
{
int tstart = start;
@@ -521,6 +547,8 @@ public class UserDataAlgorithm extends BaseAlgorithm
values[i] = values[i]/count;
}
}
+ else if(FORMAT == TABIX_INDEXED_FORMAT)
+ idxReader.getValues(start, end, values);
else
{
for (int i = 0 ; i < value_count ; ++i)
@@ -542,7 +570,6 @@ public class UserDataAlgorithm extends BaseAlgorithm
private int parseHeader(StringBuffer headerText) throws ReadFormatException
{
FORMAT = BASE_SPECIFIED_FORMAT;
-
BufferedReader reader = new BufferedReader(
new StringReader(headerText.toString()));
@@ -604,7 +631,7 @@ public class UserDataAlgorithm extends BaseAlgorithm
*
* @param trackLine
*/
- private void parseTrackLine(String trackLine)
+ private void parseTrackLine(final String trackLine)
{
String colour = "0,0,0";
int beginIndex = trackLine.indexOf(" color=");
@@ -618,9 +645,9 @@ public class UserDataAlgorithm extends BaseAlgorithm
incrementLines(LineAttributes.parse(colour));
}
- private void incrementLines(Color colour)
+ private void incrementLines(final Color c)
{
- LineAttributes line = new LineAttributes(colour);
+ LineAttributes line = new LineAttributes(c);
if(lines == null)
lines = new LineAttributes[1];
@@ -800,7 +827,7 @@ public class UserDataAlgorithm extends BaseAlgorithm
return wiggle[index].span;
}
- public boolean isWiggleFormat()
+ protected boolean isWiggleFormat()
{
if(FORMAT == WIGGLE_VARIABLE_STEP_FORMAT ||
FORMAT == WIGGLE_FIXED_STEP_FORMAT)
@@ -808,10 +835,171 @@ public class UserDataAlgorithm extends BaseAlgorithm
return false;
}
+ public void readIndexValues(Entry seqEntry, int start, int end)
+ {
+ if(start<1)
+ start = 1;
+ idxReader.readValuesForRange(seqEntry, start, end);
+ }
+
class Wiggle
{
int start;
int step;
int span = 0;
}
+
+ class TabixIdxGraph
+ {
+ private TabixReader reader;
+ /** number of columns with values */
+ private int nValues = 1;
+ private float[][] rvalues;
+ private boolean startColIsEndCol = true;
+ private int sbeg, send;
+
+ TabixIdxGraph(final String fName) throws IOException
+ {
+ this.reader = new TabixReader(fName);
+ if(getStartColumn() != getEndColumn())
+ startColIsEndCol = false;
+
+ final StringBuffer headerBuffer = new StringBuffer();
+ String metaChar = String.valueOf(reader.getCommentChar());
+ String hdr;
+ while( (hdr = reader.readLine() ) != null && hdr.startsWith(metaChar) )
+ headerBuffer.append(hdr + "\n");
+ //System.out.println("Header "+headerBuffer.toString());
+
+ // assume base end column is last column before columns of values
+ nValues = reader.readLine().split("\\t").length - getEndColumn();
+ }
+
+ /**
+ * Return the values between a pair of bases
+ * @param start
+ * @param end
+ * @param values
+ */
+ private void getValues(int start, int end, final float[] values)
+ {
+ for (int i = 0 ; i < getNumberOfValues() ; ++i)
+ {
+ values [i] = 0;
+ for (int base = start ; base <= end ; ++base)
+ values [i] += rvalues[base - this.sbeg][i] / (end - start + 1);
+ }
+ }
+
+ /**
+ * Get the sequence name
+ * @param seqEntry - sequence entry
+ * @return
+ */
+ private String getReferenceName(Entry seqEntry)
+ {
+ String refStr = null;
+ if(seqEntry.getEMBLEntry().getSequence() instanceof IndexFastaStream)
+ refStr =
+ ((IndexFastaStream)seqEntry.getEMBLEntry().getSequence()).getContig();
+ else if(seqEntry.getHeaderText() != null)
+ {
+ final String hdr = seqEntry.getHeaderText();
+ int idx = hdr.indexOf("ID ");
+ if (idx == -1)
+ {
+ idx = hdr.indexOf("LOCUS "); // genbank
+ if (idx > -1)
+ refStr = hdr.substring(idx + 12).split("[;\\s]")[0];
+ }
+ else
+ refStr = hdr.substring(idx + 5).split("[;\\s]")[0];
+ }
+
+ final String seqNames[] = reader.getSeqNames();
+ if(refStr == null || !Arrays.asList(seqNames).contains(refStr))
+ {
+ logger4j.debug(refStr+" NOT FOUND IN "+reader.getFileName()+
+ " SET TO DEFAULT "+seqNames[0]);
+ refStr = reader.getSeqNames()[0];
+ }
+ return refStr;
+ }
+
+ /**
+ * Read the values in a range
+ * @param seqEntry - sequence entry
+ * @param start - start base
+ * @param end - end base
+ */
+ private void readValuesForRange(Entry seqEntry, int start, int end)
+ {
+ if(end <= start || (start == this.sbeg && end == this.send))
+ return;
+
+ this.sbeg = start;
+ this.send = end;
+ rvalues = new float[end-start+1][getNumberOfValues()];
+ final String r = getReferenceName(seqEntry)+":"+start+"-"+end;
+ try
+ {
+ final TabixReader.Iterator tbxIt = reader.query(r);
+ String ln;
+ while( tbxIt != null && (ln = tbxIt.next()) != null )
+ {
+ StringVector parts = StringVector.getStrings(ln, "\t", true);
+ final int base;
+ if(startColIsEndCol)
+ base = Integer.parseInt((String)parts.get(getStartColumn()-1)) - start;
+ else
+ {
+ int b = Integer.parseInt((String)parts.get(getStartColumn()-1));
+ int e = Integer.parseInt((String)parts.get(getEndColumn()-1));
+ base = b + ((b - e)/2) - start;
+ }
+ for(int i=0; i<rvalues[base].length; i++)
+ {
+ float val = Float.parseFloat( (String) parts.get(i+getEndColumn()) );
+ if(logTransform)
+ val = (float) Math.log(val+1);
+
+ if (val > data_max)
+ data_max = val;
+ if (val < data_min)
+ data_min = val;
+ rvalues[base][i] = val;
+ }
+ }
+ }
+ catch (IOException e)
+ {
+ logger4j.debug("IOException READING RANGE "+r+" FROM "+reader.getFileName());
+ e.printStackTrace();
+ }
+ catch (NumberFormatException e)
+ {
+ logger4j.debug("NumberFormatException READING RANGE "+r+" FROM "+reader.getFileName());
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Number of columns with values
+ * @return
+ */
+ private int getNumberOfValues()
+ {
+ return nValues;
+ }
+
+ private int getStartColumn()
+ {
+ return reader.getStartColumn();
+ }
+
+ private int getEndColumn()
+ {
+ return reader.getEndColumn();
+ }
+ }
}