package com.github.lindenb.jvarkit.tools.batchpicts;
import htsjdk.samtools.util.CloserUtil;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.Graphics2D;
import java.awt.GridLayout;
import java.awt.RenderingHints;
import java.awt.Toolkit;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.awt.image.BufferedImage;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.PrintWriter;
import java.io.Reader;
import java.io.StringReader;
import java.io.StringWriter;
import java.net.URL;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.List;
import java.util.Set;
import java.util.TreeSet;
import java.util.prefs.Preferences;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
import javax.imageio.ImageIO;
import javax.swing.AbstractAction;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JFileChooser;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JSpinner;
import javax.swing.JTextArea;
import javax.swing.JTextField;
import javax.swing.SpinnerNumberModel;
import javax.swing.SwingUtilities;
import javax.swing.border.EmptyBorder;
import javax.swing.border.TitledBorder;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.event.DocumentEvent;
import javax.swing.event.DocumentListener;
import javax.swing.text.BadLocationException;
import javax.xml.namespace.QName;
import javax.xml.stream.XMLEventFactory;
import javax.xml.stream.XMLEventReader;
import javax.xml.stream.XMLEventWriter;
import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLOutputFactory;
import javax.xml.stream.XMLStreamWriter;
import javax.xml.stream.events.Attribute;
import javax.xml.stream.events.Namespace;
import javax.xml.stream.events.StartElement;
import javax.xml.stream.events.XMLEvent;
import com.github.lindenb.jvarkit.io.IOUtils;
import com.github.lindenb.jvarkit.io.NullOuputStream;
import com.github.lindenb.jvarkit.util.htsjdk.HtsjdkVersion;
import com.github.lindenb.jvarkit.util.igv.IgvSocket;
import com.github.lindenb.jvarkit.util.jcommander.Launcher;
import com.github.lindenb.jvarkit.util.jcommander.Program;
import com.github.lindenb.jvarkit.util.log.Logger;
/*
BEGIN_DOC
## Motivation
Takes IGV pictures in batch. Save as HTML+png images or OpenOffice/ODP.
## Screenshot
END_DOC
*/
@SuppressWarnings("serial")
@Program(name="batchigvpictures",
description="Takes IGV pictures in batch. Save as HTML+png image",
keywords={"gui","igv","visualization"}
)
class BatchIGVPicturesFrame extends JFrame
{
private static final String PREF_EXTEND="snp.extend";
private static final String PREF_IGV_PORT="igv.port";
private static final String PREF_IGV_HOST="igv.host";
private static final String PREF_SAVE_AS_FILE="save.as.file";
private static final String PREF_IMG_WIDTH="img.width";
private static final String PREF_LOAD_VCF_FILE="load.vcf.file";
private static final String PREF_IGV_SLEEP="igv.sleep";
private static final String PREF_FORMAT="out.fmt";
private static final int FORMAT_HTML=0;
private static final int FORMAT_PPT=1;
String about="";
private Preferences preferences;
private AbstractSlave currentSlave=null;
private JTextArea snpArea;
private SpinnerNumberModel spinnerExtendSize;
private SpinnerNumberModel spinnerImageWidth;
private SpinnerNumberModel spinnerIgvWait;
private JTextField tfIgvHost;
private SpinnerNumberModel spinnerIgvPort;
private JLabel progressLbl=null;
private JComboBox<String> cboxFormat;
private static class Mutation
implements Comparable<Mutation>
{
String chrom;
int position;
@Override
public int compareTo(Mutation o) {
int i=chrom.compareTo(o.chrom);
if(i!=0) return i;
return position-o.position;
}
@Override
public boolean equals(Object obj) {
if(this==obj) return true;
return compareTo(Mutation.class.cast(obj))==0;
}
@Override
public int hashCode() {
return chrom.hashCode()*31+position;
}
@Override
public String toString() {
return chrom+":"+position;
}
}
private abstract class AbstractSlave
extends Thread
{
String pathOut;
int igvPort;
String igvHost;
int extend;
int imageWidth;
int waitMiliSecs;
Set<Mutation> mutations=new TreeSet<Mutation>();
protected void log(final String labelStr)
{
try {
SwingUtilities.invokeAndWait(new Runnable()
{
@Override
public void run() {
progressLbl.setText(labelStr);
}
});
}
catch (Exception e) {
}
}
protected IgvSocket createIgvSocket()
{
IgvSocket igvSocket=new IgvSocket();
igvSocket.setHost(this.igvHost);
igvSocket.setPort(this.igvPort);
return igvSocket;
}
protected BufferedImage scale(File pngFile)
throws IOException
{
BufferedImage src=ImageIO.read(pngFile);
if(src==null)
{
throw new IOException("Cannot read Image "+pngFile.getName());
}
BufferedImage dest=new BufferedImage(
this.imageWidth,
(int)((this.imageWidth/(double)src.getWidth())*src.getHeight()),
src.getType()
);
Graphics2D g=(Graphics2D)dest.getGraphics();
g.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY);
g.drawImage(src, 0, 0, dest.getWidth(), dest.getHeight(), null);
g.dispose();
return dest;
}
}
private class HtmlSlave
extends AbstractSlave
{
@Override
public void run()
{
File baseFile=new File(pathOut);
File resultFileOut=new File(pathOut+".html");
File pngFile=null;
PrintWriter out =null;
BufferedReader in =null;
XMLStreamWriter w=null;
FileOutputStream fout=null;
IgvSocket igvSocket=null;
PrintWriter igvLog=null;
try {
XMLOutputFactory xof=XMLOutputFactory.newFactory();
igvLog=new PrintWriter(new NullOuputStream());
fout=new FileOutputStream(resultFileOut);
w=xof.createXMLStreamWriter(fout, "UTF-8");
w.writeStartElement("html");
w.writeStartElement("body");
pngFile=File.createTempFile("igv_", ".png");
igvSocket=createIgvSocket();
out=igvSocket.getWriter();
in=igvSocket.getReader();
out.println("snapshotDirectory "+pngFile.getParentFile());
igvLog.println(in.readLine());
out.println("setSleepInterval "+(waitMiliSecs+1));
igvLog.println(in.readLine());
int index=0;
for(Mutation m:this.mutations)
{
if(this!=BatchIGVPicturesFrame.this.currentSlave) break;
log("Drawing "+(++index)+"/"+this.mutations.size()+" "+m);
int chromStart= Math.max(1,m.position - extend);
int chromEnd = m.position + extend;
out.println("goto "+m.chrom+":"+chromStart+"-"+chromEnd);
out.flush();
igvLog.println(in.readLine());
out.println("snapshot "+pngFile.getName());
out.flush();
igvLog.println(in.readLine());
BufferedImage dest=scale(pngFile);
String imgName=baseFile.getName()+"_"+m.chrom+"_"+m.position+".png";
w.writeStartElement("h3");
w.writeCharacters(m.toString());
w.writeEndElement();
w.writeEmptyElement("img");
w.writeAttribute("src",imgName);
w.writeAttribute("alt",m.toString());
w.writeAttribute("width",String.valueOf(dest.getWidth()));
w.writeAttribute("height",String.valueOf(dest.getHeight()));
File destScaledImage=new File(baseFile.getParentFile(),imgName);
ImageIO.write(dest, "png",destScaledImage);
dest=null;
log("Sleep "+waitMiliSecs+" millisecs...");
Thread.sleep(waitMiliSecs);
}
log("Done.");
w.writeEmptyElement("hr");
w.writeStartElement("div");
w.writeCharacters(about);
w.writeEndElement();//div
w.writeEndElement();//body
w.writeEndElement();//html
w.flush();
fout.flush();
}
catch (Exception e)
{
e.printStackTrace();
log("Error "+e.getMessage());
}
finally
{
CloserUtil.close(igvSocket);
CloserUtil.close(out);
CloserUtil.close(in);
CloserUtil.close(w);
CloserUtil.close(fout);
CloserUtil.close(igvLog);
pngFile.delete();
}
}
}
/** save image as OpenOffice Presentation */
private class PPTSlave
extends AbstractSlave
{
private class PictAndMut
{
Mutation mut;
String file;
Dimension dim;
}
private InputStream openODPResource(String filename)
throws IOException
{
filename="META-INF/opendocument/odp/"+filename;//no head '/'
Enumeration<URL> resources = getClass().getClassLoader()
.getResources(filename);
while (resources.hasMoreElements())
{
URL url=resources.nextElement();
InputStream in=url.openStream();
if(in!=null) return in;
}
throw new IOException("Cannot open resource:"+filename);
}
private void copyODPResource(
ZipOutputStream zout,
String filename,
String outname)
throws IOException
{
ZipEntry zentry=new ZipEntry(outname);
zout.putNextEntry(zentry);
InputStream is=openODPResource(filename);
IOUtils.copyTo(is, zout);
zout.flush();
is.close();
zout.closeEntry();
}
private void copyODPResource(
ZipOutputStream zout,
String filename)
throws IOException
{
copyODPResource(zout,filename,filename);
}
private String odpns(String localname)
{
return "urn:oasis:names:tc:opendocument:xmlns:"+localname+":1.0";
}
@Override
public void run()
{
File resultFileOut=new File(pathOut+".odp");
File pngFile=null;
PrintWriter igvout =null;
BufferedReader igvin =null;
FileOutputStream fout=null;
ZipOutputStream zout=null;
IgvSocket igvSocket=null;
PrintWriter igvLog=null;
List<PictAndMut> pictures=new ArrayList<PictAndMut>(this.mutations.size());
try {
igvLog=new PrintWriter(new NullOuputStream());
fout=new FileOutputStream(resultFileOut);
zout=new ZipOutputStream(fout);
pngFile=File.createTempFile("igv_", ".png");
igvSocket=createIgvSocket();
igvout=igvSocket.getWriter();
igvin=igvSocket.getReader();
igvout.println("snapshotDirectory "+pngFile.getParentFile());
igvLog.println(igvin.readLine());
igvout.println("setSleepInterval "+(waitMiliSecs+1));
igvLog.println(igvin.readLine());
copyODPResource(zout,"mimetype");
copyODPResource(zout,"meta.xml");
copyODPResource(zout,"settings.xml");
int index=0;
for(Mutation m:this.mutations)
{
if(this!=BatchIGVPicturesFrame.this.currentSlave) break;
log("Drawing "+(++index)+"/"+this.mutations.size()+" "+m);
int chromStart= Math.max(1,m.position - extend);
int chromEnd = m.position + extend;
igvout.println("goto "+m.chrom+":"+chromStart+"-"+chromEnd);
igvout.flush();
igvLog.println(igvin.readLine());
igvout.println("snapshot "+pngFile.getName());
igvout.flush();
igvLog.println(igvin.readLine());
BufferedImage dest=scale(pngFile);
String entryName="Pictures/"+m.chrom+"_"+m.position+".png";
PictAndMut pam=new PictAndMut();
pam.dim=new Dimension(dest.getWidth(), dest.getHeight());
pam.mut=m;
pam.file=entryName;
pictures.add(pam);
ZipEntry zentry=new ZipEntry(entryName);
zout.putNextEntry(zentry);
ImageIO.write(dest, "png",zout);
zout.closeEntry();
dest=null;
dest=null;
log("Sleep "+waitMiliSecs+" millisecs...");
Thread.sleep(waitMiliSecs);
}
CloserUtil.close(igvout);igvout=null;
CloserUtil.close(igvin);igvin=null;
CloserUtil.close(igvSocket);igvSocket=null;
{
/* content.xml */
ZipEntry zentry=new ZipEntry("content.xml");
zout.putNextEntry(zentry);
InputStream is=openODPResource("content.xml");
XMLOutputFactory xof=XMLOutputFactory.newFactory();
XMLInputFactory xif=XMLInputFactory.newFactory();
XMLEventReader xi=xif.createXMLEventReader(is);
XMLEventWriter xw=xof.createXMLEventWriter(zout);
while(xi.hasNext())
{
XMLEvent evt=xi.nextEvent();
xw.add(evt);
if(evt.isStartElement())
{
StartElement SE=evt.asStartElement();
QName qName=SE.getName();
if(qName.getLocalPart().equals("presentation") &&
qName.getNamespaceURI().equals(odpns("office")))
{
XMLEventFactory xef=XMLEventFactory.newFactory();
ArrayList<Attribute> attributes;
ArrayList<Namespace> namespaces;
for(PictAndMut pam:pictures)
{
final String XLINK="http://www.w3.org/1999/xlink";
attributes=new ArrayList<Attribute>();
namespaces=new ArrayList<Namespace>();
attributes.add(xef.createAttribute("draw",odpns("drawing"),"master-page-name",""));
evt=xef.createStartElement("draw",odpns("drawing"),"page",attributes.iterator(),namespaces.iterator());
xw.add(evt);
attributes=new ArrayList<Attribute>();
namespaces=new ArrayList<Namespace>();
attributes.add(xef.createAttribute("presentation",odpns("presentation"),"style-name",""));
double width_cm=20.0;
double height_cm= (width_cm/pam.dim.width)*pam.dim.getHeight();
attributes.add(xef.createAttribute("svg",odpns("svg-compatible"),"width",""+width_cm+"cm"));
attributes.add(xef.createAttribute("svg",odpns("svg-compatible"),"height",""+height_cm+"cm"));
attributes.add(xef.createAttribute("svg",odpns("svg-compatible"),"x","0cm"));
attributes.add(xef.createAttribute("svg",odpns("svg-compatible"),"y","0cm"));
attributes.add(xef.createAttribute("presentation",odpns("presentation"),"class","title"));
evt=xef.createStartElement("draw",odpns("drawing"),"frame",attributes.iterator(),namespaces.iterator());
xw.add(evt);
attributes=new ArrayList<Attribute>();
namespaces=new ArrayList<Namespace>();
attributes.add(xef.createAttribute("xlink",XLINK,"type","simple"));
attributes.add(xef.createAttribute("xlink",XLINK,"show","embed"));
attributes.add(xef.createAttribute("xlink",XLINK,"actuate","onLoad"));
attributes.add(xef.createAttribute("xlink",XLINK,"href",pam.file));
evt=xef.createStartElement("draw",odpns("drawing"),"image",attributes.iterator(),namespaces.iterator());
xw.add(evt);
attributes=new ArrayList<Attribute>();
namespaces=new ArrayList<Namespace>();
evt=xef.createStartElement("text",odpns("text"),"p",attributes.iterator(),namespaces.iterator());
xw.add(evt);
xw.add(xef.createCharacters(pam.mut.toString()));
evt=xef.createEndElement("text",odpns("text"),"p");
xw.add(evt);
evt=xef.createEndElement("draw",odpns("drawing"),"image");
xw.add(evt);
evt=xef.createEndElement("draw",odpns("drawing"),"frame");
xw.add(evt);
evt=xef.createEndElement("draw",odpns("drawing"),"page");
xw.add(evt);
}
}
}
}
xw.flush();
xi.close();
is.close();
zout.closeEntry();
}
copyODPResource(zout,"thumbnail.png","Thumbnails/thumbnail.png");
copyODPResource(zout,"styles.xml");
//copyODPResource(zout,"manifest.xml","META-INF/manifest.xml");
{
/* content.xml */
ZipEntry zentry=new ZipEntry("META-INF/manifest.xml");
zout.putNextEntry(zentry);
PrintWriter pw=new PrintWriter(zout);
pw.println(
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>"+
"<manifest:manifest xmlns:manifest=\"urn:oasis:names:tc:opendocument:xmlns:manifest:1.0\" manifest:version=\"1.2\">\n"+
" <manifest:file-entry manifest:full-path=\"/\" manifest:version=\"1.2\" manifest:media-type=\"application/vnd.oasis.opendocument.presentation\"/>\n"+
" <manifest:file-entry manifest:full-path=\"meta.xml\" manifest:media-type=\"text/xml\"/>\n");
for(PictAndMut pam:pictures)
{
pw.println(" <manifest:file-entry manifest:full-path=\""+
pam.file+
"\" manifest:media-type=\"image/png\"/>\n");
}
pw.print(
" <manifest:file-entry manifest:full-path=\"settings.xml\" manifest:media-type=\"text/xml\"/>\n"+
" <manifest:file-entry manifest:full-path=\"content.xml\" manifest:media-type=\"text/xml\"/>\n"+
" <manifest:file-entry manifest:full-path=\"Thumbnails/thumbnail.png\" manifest:media-type=\"image/png\"/>\n"+
" <manifest:file-entry manifest:full-path=\"Configurations2/accelerator/current.xml\" manifest:media-type=\"\"/>\n"+
" <manifest:file-entry manifest:full-path=\"Configurations2/\" manifest:media-type=\"application/vnd.sun.xml.ui.configuration\"/>\n"+
" <manifest:file-entry manifest:full-path=\"styles.xml\" manifest:media-type=\"text/xml\"/>\n"+
"</manifest:manifest>");
pw.flush();
/*
InputStream is=openODPResource("manifest.xml");
XMLOutputFactory xof=XMLOutputFactory.newFactory();
XMLInputFactory xif=XMLInputFactory.newFactory();
XMLEventReader xi=xif.createXMLEventReader(is);
XMLEventWriter xw=xof.createXMLEventWriter(zout);
boolean seen=false;
while(xi.hasNext())
{
XMLEvent evt=xi.nextEvent();
xw.add(evt);
if(!seen && evt.isStartElement())
{
StartElement SE=evt.asStartElement();
QName qName=SE.getName();
if(qName.getLocalPart().equals("file-entry") &&
qName.getNamespaceURI().equals(odpns("manifest")))
{
seen=true;
XMLEventFactory xef=XMLEventFactory.newFactory();
ArrayList<Attribute> attributes;
ArrayList<Namespace> namespaces;
for(PictAndMut pam:pictures)
{
attributes=new ArrayList<Attribute>();
namespaces=new ArrayList<Namespace>();
attributes.add(xef.createAttribute("manifest",odpns("manifest"),"full-path",pam.file));
attributes.add(xef.createAttribute("manifest",odpns("manifest"),"media-type","image/png"));
evt=xef.createStartElement("manifest",odpns("manifest"),"file-entry",attributes.iterator(),namespaces.iterator());
xw.add(evt);
evt=xef.createEndElement("manifest",odpns("manifest"),"file-entry");
xw.add(evt);
}
}
}
}
xw.flush();
xi.close();
is.close();
*/
zout.closeEntry();
}
log("Done.");
zout.flush();
zout.finish();
}
catch (Exception e)
{
e.printStackTrace();
log("Error "+e.getMessage());
}
finally
{
CloserUtil.close(igvSocket);
CloserUtil.close(igvout);
CloserUtil.close(igvin);
CloserUtil.close(zout);
CloserUtil.close(fout);
CloserUtil.close(igvLog);
pngFile.delete();
}
}
}
BatchIGVPicturesFrame()
{
setDefaultCloseOperation(DO_NOTHING_ON_CLOSE);
try {
this.preferences=Preferences.userNodeForPackage(BatchIGVPictures.class);
}
catch (Exception e) {
}
addWindowListener(new WindowAdapter()
{
@Override
public void windowClosing(WindowEvent e) {
doMenuClose();
}
});
JMenuBar menubar=new JMenuBar();
setJMenuBar(menubar);
JMenu menu=new JMenu("File");
menubar.add(menu);
menu.add(new AbstractAction("Quit")
{
@Override
public void actionPerformed(ActionEvent e) {
doMenuClose();
}
});
menu=new JMenu("Help");
menubar.add(menu);
menu.add(new AbstractAction("About")
{
@Override
public void actionPerformed(ActionEvent e) {
JOptionPane.showMessageDialog(BatchIGVPicturesFrame.this, about);
}
});
JPanel contentPane=new JPanel(new BorderLayout(5, 5));
contentPane.setBorder(new EmptyBorder(5, 5, 5, 5));
setContentPane(contentPane);
JPanel top0=new JPanel(new GridLayout(0,1,5,5));
contentPane.add(top0,BorderLayout.NORTH);
JPanel top=new JPanel(new FlowLayout(FlowLayout.LEADING));
top0.add(top);
/* extend */
JLabel lbl=new JLabel("Position Extend:",JLabel.RIGHT);
top.add(lbl);
JSpinner spin=new JSpinner(this.spinnerExtendSize=new SpinnerNumberModel(
preferences.getInt(PREF_EXTEND, 10), 1, 100, 1));
lbl.setLabelFor(spin);
top.add(spin);
this.spinnerExtendSize.addChangeListener(new ChangeListener()
{
@Override
public void stateChanged(ChangeEvent e) {
preferences.putInt(PREF_EXTEND,SpinnerNumberModel.class.cast(e.getSource()).getNumber().intValue());
}
});
/* image width */
lbl=new JLabel("Image Width:",JLabel.RIGHT);
top.add(lbl);
spin=new JSpinner(this.spinnerImageWidth=new SpinnerNumberModel(
preferences.getInt(PREF_IMG_WIDTH, 640), 1, 2000, 1));
lbl.setLabelFor(spin);
top.add(spin);
this.spinnerImageWidth.addChangeListener(new ChangeListener()
{
@Override
public void stateChanged(ChangeEvent e) {
preferences.putInt(PREF_IMG_WIDTH,SpinnerNumberModel.class.cast(e.getSource()).getNumber().intValue());
}
});
/* image width */
lbl=new JLabel("Wait ms:",JLabel.RIGHT);
top.add(lbl);
spin=new JSpinner(this.spinnerIgvWait=new SpinnerNumberModel(
preferences.getInt(PREF_IGV_SLEEP, 100), 1, 10000, 1));
lbl.setLabelFor(spin);
top.add(spin);
this.spinnerIgvWait.addChangeListener(new ChangeListener()
{
@Override
public void stateChanged(ChangeEvent e) {
preferences.putInt(PREF_IMG_WIDTH,SpinnerNumberModel.class.cast(e.getSource()).getNumber().intValue());
}
});
/* IGV Host */
lbl=new JLabel("IGV Host:",JLabel.RIGHT);
top.add(lbl);
this.tfIgvHost = new JTextField(
preferences.get(PREF_IGV_HOST,IgvSocket.DEFAULT_HOST),8);
top.add(this.tfIgvHost);
this.tfIgvHost.getDocument().addDocumentListener(new DocumentListener()
{
@Override
public void removeUpdate(DocumentEvent e) {
changedUpdate(e);
}
@Override
public void insertUpdate(DocumentEvent e) {
changedUpdate(e);
}
@Override
public void changedUpdate(DocumentEvent e) {
String s;
try {
s = e.getDocument().getText(0, e.getDocument().getLength()).trim();
preferences.put(PREF_IGV_HOST,s);
} catch (BadLocationException e1) {
e1.printStackTrace();
}
}
});
/* IGV port */
lbl=new JLabel("IGV PORT:",JLabel.RIGHT);
top.add(lbl);
spin=new JSpinner(this.spinnerIgvPort=new SpinnerNumberModel(
preferences.getInt(PREF_IGV_PORT, IgvSocket.DEFAULT_PORT), 1, 1000000, 1));
lbl.setLabelFor(spin);
top.add(spin);
this.spinnerIgvPort.addChangeListener(new ChangeListener()
{
@Override
public void stateChanged(ChangeEvent e) {
preferences.putInt(PREF_IGV_PORT,SpinnerNumberModel.class.cast(e.getSource()).getNumber().intValue());
}
});
top=new JPanel(new FlowLayout(FlowLayout.LEADING));
top0.add(top);
/* FORMAT */
lbl=new JLabel("Format:",JLabel.RIGHT);
top.add(lbl);
this.cboxFormat =new JComboBox<String>(new String[]{"HTML","PPT/ODP"});
this.cboxFormat.setSelectedIndex(preferences.getInt(PREF_FORMAT, FORMAT_HTML));
lbl.setLabelFor(this.cboxFormat);
top.add(this.cboxFormat);
this.cboxFormat.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e) {
preferences.putInt(PREF_FORMAT,Math.max(cboxFormat.getSelectedIndex(),0));
}
});
/* paint */
JButton but=new JButton(new AbstractAction("Load Mutation File")
{
@Override
public void actionPerformed(ActionEvent e) {
loadVCF();
}
});
top.add(but);
but=new JButton(new AbstractAction("Stop")
{
@Override
public void actionPerformed(ActionEvent e) {
stopPaint();
}
});
but.setFont(new Font("Dialog",Font.BOLD,18));
but.setBackground(Color.RED);
but.setForeground(Color.WHITE);
top.add(but);
but=new JButton(new AbstractAction("Draw")
{
@Override
public void actionPerformed(ActionEvent e) {
doMenuPaint();
}
});
but.setFont(new Font("Dialog",Font.BOLD,18));
but.setBackground(Color.GREEN);
but.setForeground(Color.WHITE);
top.add(but);
JPanel pane2=new JPanel(new BorderLayout(5,5));
contentPane.add(pane2,BorderLayout.CENTER);
pane2.add(new JScrollPane(this.snpArea=new JTextArea(10,80)),BorderLayout.CENTER);
pane2.setBorder(new TitledBorder("SNP: CHROM(tab)POSITION"));
/*
this.snpArea.setText(
"chr6\t85356177\n"+
"chr6\t85356228\n"+
"chr6\t85356328\n"
);
*/
this.progressLbl=new JLabel("");
contentPane.add(this.progressLbl,BorderLayout.SOUTH);
}
private void stopPaint()
{
if(this.currentSlave!=null)
{
try {
this.currentSlave.interrupt();
}
catch (Exception e) {
}
}
this.currentSlave=null;
this.progressLbl.setText("");
}
private void doMenuClose()
{
stopPaint();
try
{
this.preferences.flush();
}
catch(Exception err)
{
}
this.setVisible(false);
this.dispose();
}
private void loadVCF()
{
String prevFile=this.preferences.get(PREF_LOAD_VCF_FILE, null);
File selFile=prevFile==null?null:new File(prevFile);
JFileChooser fc=new JFileChooser();
if(selFile!=null)
{
fc.setSelectedFile(selFile);
}
if(fc.showOpenDialog(this)!=JFileChooser.APPROVE_OPTION)
{
return ;
}
BufferedReader r=null;
try
{
r=IOUtils.openFileForBufferedReading(fc.getSelectedFile());
Set<Mutation> mutations=this.loadMutations(r);
StringWriter sw=new StringWriter();
for(Mutation m:mutations)
{
sw.write(m.chrom+"\t"+m.position+"\n");
}
this.snpArea.setText(sw.toString());
this.snpArea.setCaretPosition(0);
this.preferences.put(PREF_LOAD_VCF_FILE, fc.getSelectedFile().getPath());
}
catch(Exception err)
{
JOptionPane.showMessageDialog(this,
"Cannot pars data in "+fc.getSelectedFile()+" "+err.getMessage());
}
finally
{
CloserUtil.close(r);
}
}
private Set<Mutation> loadMutations(Reader reader)
throws IOException
{
Set<Mutation> mutations=new TreeSet<Mutation>();
BufferedReader in=new BufferedReader(reader);
String line;
while(((line=in.readLine()))!=null)
{
if(line.isEmpty() || line.startsWith("#")) continue;
String tokens[]=line.split("[\t]",3);
if(tokens.length<2) throw new IOException("Bad line "+line);
Mutation m=new Mutation();
m.chrom=tokens[0].trim();
if(!m.chrom.matches("[A-Z0-9a-z_\\.]+"))
{
throw new IOException("Bad chrom in "+line);
}
try {
m.position=Integer.parseInt(tokens[1].replace(",", "").replace(".", ""));
} catch (Exception e) {
throw new IOException("Bad Position in in "+line);
}
if(m.position<0) throw new IOException("Bad Position in in "+line);
mutations.add(m);
}
return mutations;
}
private void doMenuPaint()
{
stopPaint();
int fotmat=Math.max(this.cboxFormat.getSelectedIndex(),0);
this.currentSlave=null;
if(fotmat==FORMAT_HTML)
{
this.currentSlave=new HtmlSlave();
}
else
{
this.currentSlave=new PPTSlave();
}
this.currentSlave.igvHost= this.tfIgvHost.getText().trim();
this.currentSlave.igvPort= this.spinnerIgvPort.getNumber().intValue();
this.currentSlave.extend= this.spinnerExtendSize.getNumber().intValue();
this.currentSlave.imageWidth=this.spinnerImageWidth.getNumber().intValue();
this.currentSlave.waitMiliSecs=this.spinnerIgvWait.getNumber().intValue();
try {
this.currentSlave.mutations=loadMutations(new StringReader(this.snpArea.getText()));
}
catch (Exception e) {
JOptionPane.showMessageDialog(this,"Cannot parse SNPs area:"+e.getMessage());
stopPaint();
return;
}
if(this.currentSlave.mutations.isEmpty())
{
stopPaint();
return;
}
File file=null;
String fileStr=this.preferences.get(PREF_SAVE_AS_FILE, null);
if(fileStr!=null)
{
file=new File(fileStr);
}
JFileChooser chooser=new JFileChooser(file!=null?file.getParentFile():null);
if(file!=null )
{
chooser.setSelectedFile(file);
}
if(chooser.showSaveDialog(this)!=JFileChooser.APPROVE_OPTION)
{
return;
}
File selectedFile=chooser.getSelectedFile();
this.currentSlave.pathOut=selectedFile.getPath();
this.preferences.put(PREF_SAVE_AS_FILE, selectedFile.getPath());
if(fotmat==FORMAT_HTML)
{
if(this.currentSlave.pathOut.endsWith(".html"))
{
this.currentSlave.pathOut=this.currentSlave.pathOut.substring(0,this.currentSlave.pathOut.length()-5);
}
else if(this.currentSlave.pathOut.endsWith(".htm"))
{
this.currentSlave.pathOut=this.currentSlave.pathOut.substring(0,this.currentSlave.pathOut.length()-4);
}
selectedFile=new File(this.currentSlave.pathOut+".html");
}
else if(fotmat==FORMAT_PPT)
{
if(this.currentSlave.pathOut.endsWith(".odp"))
{
this.currentSlave.pathOut=this.currentSlave.pathOut.substring(0,this.currentSlave.pathOut.length()-4);
}
selectedFile=new File(this.currentSlave.pathOut+".odp");
}
else
{
throw new IllegalStateException();
}
if(selectedFile!=null && selectedFile.exists() &&
JOptionPane.showConfirmDialog(this, selectedFile.toString()+" already exists. Overwrite ?", "Overwrite", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE, null)!=JOptionPane.OK_OPTION
)
{
stopPaint();
return;
}
this.currentSlave.start();
}
}
public class BatchIGVPictures extends Launcher
{
private static final Logger LOG=Logger.build(BatchIGVPictures.class).make();
@Override
public int doWork(final List<String> args) {
final BatchIGVPicturesFrame app=new BatchIGVPicturesFrame();
app.about=" Author: Pierre Lindenbaum "+
" Version:"+getVersion()+
" Htsjdk.version:"+HtsjdkVersion.getVersion()+
" Date:"+getCompileDate()
;
try
{
SwingUtilities.invokeAndWait(new Runnable() {
@Override
public void run()
{
Dimension win=Toolkit.getDefaultToolkit().getScreenSize();
app.setTitle(getProgramName());
app.pack();
Dimension ps=app.getPreferredSize();
app.setLocation(
(win.width-ps.width)/2,
(win.height-ps.height)/2
);
app.setVisible(true);
}
});
return RETURN_OK;
}
catch(Exception err)
{
LOG.error(err);
return -1;
}
finally
{
}
}
public static void main(String[] args) {
new BatchIGVPictures().instanceMain(args);
}
}