User:Lindenb/Notebook/UMR915/20110104

20110103        Top        20110105       

Eclipse!

too cloudy...

hg19

  cat chr1.fa chr2.fa chr3.fa chr4.fa chr5.fa chr6.fa  chr7.fa  chr8.fa chr9.fa chr10.fa chr11.fa\
  chr12.fa chr13.fa chr14.fa chr15.fa chr16.fa chr17.fa chr18.fa chr19.fa chr20.fa chr21.fa chr22.fa chrX.fa chrY.fa chrM.fa > hg19.fa
  
  bwa-0.5.9rc1/bwa index hg19.fa
  (....)
  Segmentation fault
  
  bwa-0.5.9rc1/bwa  index   -a bwtsw hg19.fa

source

import java.awt.Color;
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import java.awt.image.BufferedImage;
import java.io.ByteArrayOutputStream;
import java.io.IOException;

import javax.imageio.ImageIO;



public class HelloAxisService
	{
	private BufferedImage bamImage(
			String filePath,
			String refSeq,
			int chromStart,
			int chromEnd,
			int highlight
			) throws Exception
			{
			BufferedImage img= new BufferedImage(100,100, BufferedImage.TYPE_INT_ARGB);
			Graphics2D g=img.createGraphics();
			g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
			g.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING	, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
			g.setColor(Color.WHITE);
			g.fillRect(0, 0, img.getWidth()-1, img.getHeight()-1);
			g.setColor(Color.BLACK);
			g.drawLine(0, 0, 50, 50);
			g.drawRect(0, 0, img.getWidth()-1, img.getHeight()-1);
			g.dispose();
			return img;
			}
	
	public byte[] getBamImage(
		String filePath,
		String refSeq,
		int chromStart,
		int chromEnd,
		int highlight
		) throws IOException
		{
		try
		{
		BufferedImage img= bamImage(filePath, refSeq, chromStart, chromEnd, highlight);
		ByteArrayOutputStream baos=new ByteArrayOutputStream();
		ImageIO.write(img, "PNG", baos);
		return baos.toByteArray();
		} catch(Throwable err)
		{
			throw new IOException(err);
		}
		}
	
	
	}

import java.awt.image.BufferedImage;
import java.io.InputStream;

import javax.imageio.ImageIO;
import javax.swing.ImageIcon;
import javax.swing.JLabel;
import javax.swing.JOptionPane;

import generated.HelloAxisServiceStub;


public class HelloAxisClient {
public static void main(String[] args)
	{
	try {
		HelloAxisServiceStub app=new HelloAxisServiceStub("http://localhost:8080/axis2/services/HelloAxisService");
		HelloAxisServiceStub.GetBamImage param=new HelloAxisServiceStub.GetBamImage();
		param.setArgs0("");
		param.setArgs1("");
		param.setArgs2(1);
		param.setArgs3(1);
		param.setArgs4(1);
		HelloAxisServiceStub.GetBamImageResponse res=app.getBamImage(param);
		//System.err.println(res.getClass()+" "+res.get_return()+" "+res);
		InputStream in=res.get_return().getInputStream();
		BufferedImage img=ImageIO.read(in);
		in.close();
		JOptionPane.showMessageDialog(null, new JLabel(new ImageIcon(img)));
		}
	catch (Exception e)
		{
		e.printStackTrace();
		}
	}
}

axis.lib=/home/lindenb/package/axis2-1.5.1/lib
axis.jar=$(axis.lib)/*

axis:
	rm -rf myaxisservice myaxisclient
	mkdir myaxisservice myaxisclient
	mkdir myaxisservice/META-INF
	cp services.xml myaxisservice/META-INF
	javac -d myaxisservice -sourcepath src src/HelloAxisService.java
	jar cvf /home/lindenb/srv/apache-tomcat-7.0.4/webapps/axis2/WEB-INF/services/myaxisservice.aar -C myaxisservice .
	rm -rf myaxisservice
	sleep 1
	 ~/package/axis2-1.5.1/bin/wsdl2java.sh -uri "http://localhost:8080/axis2/services/HelloAxisService?wsdl" -o . -d adb -p generated
	javac  -cp '/home/lindenb/package/axis2-1.5.1/lib/*' -d myaxisclient  -sourcepath src src/HelloAxisClient.java
	java -cp '/home/lindenb/package/axis2-1.5.1/lib/*':myaxisclient HelloAxisClient
	rm -rf myaxisclient