Java compile issue in installing pupil 2.0 at HPC

HPC submit nodes do not have enough memory to carry out JAVA VM, therefore we need to do:

SSH -Y TEST04

Start MySql with launchd.plist

1. Create a mysql plist file on /Library/LaunchDaemons/com.mysql.mysqld.plis

2. Start MySql Server
sudo launchctl load -w /Library/LaunchDaemons/com.mysql.mysqld.plist

3. Stop MySql Server
sudo launchctl unload -w /Library/LaunchDaemons/com.mysql.mysqld.plist

How to uninstall Mysql in MacOS

Do this command first:
vim /etc/hostconfig and removed the line MYSQLCOM=-YES-

Then do the following lines:
sudo rm /usr/local/mysql
sudo rm -rf /usr/local/mysql*
sudo rm -rf /Library/StartupItems/MySQLCOM
sudo rm -rf /Library/PreferencePanes/My*
sudo rm -rf /Library/Receipts/mysql*
sudo rm -rf /Library/Receipts/MySQL*
sudo rm -rf /var/db/receipts/com.mysql.*
sudo rm /etc/my.cnf
rm -rf ~/Library/PreferencePanes/My*

Do not forget to remove the my.cnf file.

Angry Eunice

Spots

import java.awt.*;

public class Spots extends java.applet.Applet{

final int MaxSpots = 10;
int[] xPositions = new int[10];
int[] yPositions = new int[10];
int currentSpots = 0;

public void init() {
setBackground(Color.black);
}

public boolean mouseDown(Event evt, int x, int y){
if (currentSpots < MaxSpots){
addSpots(x,y);
}
else
{System.out.println("Too Many Spots.....\n");}

return true;
}

void addSpots(int x, int y){
xPositions[currentSpots] = x;
yPositions[currentSpots] = y;
currentSpots++;
repaint();
}

public void paint(Graphics g){
g.setColor(Color.blue);

for(int i=0; i < currentSpots; i++)
{
g.fillOval(xPositions[i] -10, yPositions[i] -10,20,20);
}
}

}

Figure for Manuscript: Retinoic Acid Binding Site

PyMOL>show surface, 1CBS
PyMOL>color blue, 1CBS
PyMOL>select active, resn REA around 5.0
PyMOL>zoom active
PyMOL>select ligand, resn REA
PyMOL>show stick, ligand
PyMOL>set stick_radius = 0.15
PyMOL>set transparency = 0.3
PyMOL>center ligand
PyMOL>zoom center,9
PyMOL>ray 3000,3000

Color Swirl in Both background and foreground

import java.awt.Font;
import java.awt.Graphics;
import java.util.Date;
import java.awt.Color;

public class ColorSwirl extends java.applet.Applet implements Runnable {

Font swirlFont = new Font("Arial", Font.BOLD, 24 );
Color[] colors = new Color[50];
Thread runner;

public void start() {
if (runner == null) {
runner = new Thread(this);
runner.start();
}

}

public void stop() {
if (runner != null) {
runner.stop();
runner = null;
}

}

public void update(Graphics g){
paint(g);
}

public void run() {

// Initialize the color array
float c = 0;
for (int i=0; i < colors.length; i++){
colors[i] = Color.getHSBColor(c, (float) 1.0, (float) 1.0);
c = c + 0.02f;
}

// Cycle through the colors
int j = 0;
while (true) {
setBackground(colors[49-j]);
setForeground(colors[j]);
repaint();
j++;
try { Thread.sleep(100); }
catch (InterruptedException e) {}
if (j == colors.length) j = 0;

}
}

public void paint (Graphics g) {
g.setFont(swirlFont);
g.drawString("I love my dear DaXiongXiong", 15, 50);
}

}

Max OS Lion

How to create 4 dimensional Vector

import java.awt.Point;

class FourDPoint extends Point {

/**
* @param args
*/
int threeDimension, fourDimension;

FourDPoint(int x, int y, int threeD, int fourD){
super(x,y);
this.threeDimension = threeD;
this.fourDimension = fourD;
}


public static void main(String[] args) {
// TODO Auto-generated method stub
FourDPoint fourDimPoint = new FourDPoint(5, 10, 120, 600);

System.out.println("The First Dimension is: " + fourDimPoint.x);
System.out.println("The Second Dimension is: " + fourDimPoint.y);
System.out.println("The Third Dimension is: " + fourDimPoint.threeDimension);
System.out.println("The Fourth Dimension is: " + fourDimPoint.fourDimension);
}

}

java.util.StringTokenizer

import java.util.StringTokenizer;

class showToken {

/**
* @param args
*/
public static void main(String[] args) {
// TODO Auto-generated method stub
StringTokenizer stringOne;
String myBirthdayMonth, myBirthdayDate, myBirthdayYear;

String quoteOne = "01/22/2010/";
stringOne = new StringTokenizer(quoteOne, "/");
myBirthdayMonth = stringOne.nextToken();
myBirthdayDate = stringOne.nextToken();
myBirthdayYear = stringOne.nextToken();

System.out.println("My Birthday Month: " + myBirthdayMonth);
System.out.println("My Birthday Date: " + myBirthdayDate);
System.out.println("My Birthday Year: " + myBirthdayYear);

}

}

How to determine if an element exists in a Perl array

#!/usr/bin/perl

my @testArray = qw(apple apple1 apple2 banana);

my $testElement1 = "apple1";

my $testElement2 = "banana";

my $Counter = 0; my %testHash = {};

%testHash = map { $_ => $Counter++} @testArray;

print "Test element 1 exists!\n" if (exists $testHash{$testElement1});

print "Test element 2 exists!\n" if (exists $testHash{$testElement2});

Eunice in China 05/31/2011

My dear daughter

Mysql Issue

Yesterday I installed Mysql on my laptop. After running mysqld_safe it always gave me the same error information:

wipa-43-181:~ ZHENGFU$ mysqladmin version
/usr/local/mysql/bin/mysqladmin: connect to server at 'localhost' failed
error: 'Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)'
Check that mysqld is running and that the socket: '/tmp/mysql.sock' exists!

Seems like the mysql server did not start so the socket file was not created. Does anyone know how to figure it out?

Hello World! My First Blog!

public class HelloWord {

/**
* @param args
*/
public static void main(String[] args) {
// TODO Auto-generated method stub
System.out.println("Hello world! My First Blog!");
}

}