Compare two genomes for similarity

Value

Script

string = new String(bytes);

Script

List split = new ArrayList();
if (!string.equals("")) {
	String regexString = ",";
	if (regex != void) {
		regexString = regex;
	}
	String[] result = string.split(regexString);
	for (int i = 0; i < result.length; i++) {
		split.add(result[i]);
	}
}

Value

Script

import java.util.regex.*;

filteredlist = new ArrayList();
Pattern thePat = Pattern.compile(regex);
int theGroup = Integer.parseInt(group);

for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	Matcher matcher = thePat.matcher(item);

	if (matcher.find()) {
		filteredlist.add(matcher.group(theGroup));
	}
}

Value

Script

import java.lang.Double;

double seqSimDbl = Double.valueOf(seqSim.trim()).doubleValue();
double minSimDbl = Double.valueOf(minSim.trim()).doubleValue();

int i = Double.compare(seqSimDbl,minSimDbl);

if (i >= 0)
{
	simBln = 1;
} else
{
	simBln = 0;
}

Script

import javax.swing.JOptionPane;

answer = JOptionPane.showInputDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.QUESTION_MESSAGE);

Value

Value

Script

if (command == null || command.equals("")) {
	throw new RuntimeException("The 'command' port cannot be null.");
}
Process proc = null;
Runtime rt = Runtime.getRuntime();

String osName = System.getProperty("os.name");
String[] cmdArray = null;
if (osName.equals("Windows NT") || osName.equals("Windows XP")) {
	cmdArray = new String[] { "cmd.exe", "/c", command };
} else if (osName.equals("Windows 95")) {
	cmdArray = new String[] { "command.exe", "/c", command };
} else {// TODO: investigate if this will work in Linux and OSX
	cmdArray = new String[] { command };
}

// concatenate the arrays
if ((args == null)) {
	args = new ArrayList();
}

int argSize = cmdArray.length + args.size();
ArrayList appArray = new ArrayList(argSize);
for (int i = 0; i < cmdArray.length; i++) {
	appArray.add(cmdArray[i]);
}

for (int i = 0; i < args.size(); i++) {
	appArray.add(args.get(i));
}

String[] applist = new String[argSize];
appArray.toArray(applist);
proc = rt.exec(applist);

// Get the input stream and read from it
InputStream in = proc.getInputStream();

int c;
StringBuffer sb = new StringBuffer();
while ((c = in.read()) != -1) {
	sb.append((char) c);
}
in.close();
result = sb.toString();

Value

Script

List cmdArgsList = new ArrayList();
cmdArgsList.add("-i");
cmdArgsList.add(fastAFileName);
cmdArgsList.add("-p");
cmdArgsList.add("F");
cmdArgsList.add("-n");
cmdArgsList.add("ensemblBlastDB");

Script

List cmdArgsList = new ArrayList();
cmdArgsList.add("-p");
cmdArgsList.add("blastn");
cmdArgsList.add("-d");
cmdArgsList.add("./ensemblBlastDB");
cmdArgsList.add("-i");
cmdArgsList.add(sequenceFileName);
cmdArgsList.add("-o");
cmdArgsList.add("blast.out");

Script

if (command == void || command.equals("")) {
	throw new RuntimeException("The 'command' port cannot be null.");
}
Process proc = null;
Runtime rt = Runtime.getRuntime();

String osName = System.getProperty("os.name");
String[] cmdArray = null;
if (osName.equals("Windows NT") || osName.equals("Windows XP")) {
	cmdArray = new String[] { "cmd.exe", "/c", command };
} else if (osName.equals("Windows 95")) {
	cmdArray = new String[] { "command.exe", "/c", command };
} else {// TODO: investigate if this will work in Linux and OSX
	cmdArray = new String[] { command };
}

// concatenate the arrays
if ((args == void) || (args == null)) {
	args = new ArrayList();
}

int argSize = cmdArray.length + args.size();
ArrayList appArray = new ArrayList(argSize);
for (int i = 0; i < cmdArray.length; i++) {
	appArray.add(cmdArray[i]);
}

for (int i = 0; i < args.size(); i++) {
	appArray.add(args.get(i));
}

String[] applist = new String[argSize];
appArray.toArray(applist);
proc = rt.exec(applist);

// Get the input stream and read from it
InputStream in = proc.getInputStream();

int c;
StringBuffer sb = new StringBuffer();
while ((c = in.read()) != -1) {
	sb.append((char) c);
}
in.close();
result = sb.toString();