Compare two genomes for similarity

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 == null) {
	String args = new String();
}


int argSize = cmdArray.length + 1;
ArrayList appArray = new ArrayList(argSize);
for (int i = 0; i < cmdArray.length; i++) {
	appArray.add(cmdArray[i]);
}
appArray.add(args);

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

File f = new File("D:/blastdb/");
proc = rt.exec(applist,null,f);

// 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();

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Script

BufferedReader getReader (String fileUrl) throws IOException {
		InputStreamReader reader;
		try {
			reader = new FileReader(fileUrl);
		}
		catch (FileNotFoundException e) {
			// try a real URL instead
			URL url = new URL(fileUrl);
			reader = new InputStreamReader (url.openStream());
		}
		return new BufferedReader(reader);
	}



StringBuffer sb = new StringBuffer(4000);

BufferedReader in = getReader(fileurl);
String str;
String lineEnding = System.getProperty("line.separator");

while ((str = in.readLine()) != null) {
	sb.append(str);
	sb.append(lineEnding);
}
in.close();
filecontents = sb.toString();
  

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 thePat1 = Pattern.compile(regex1);
Pattern thePat2 = Pattern.compile(regex2);
int theGroup = Integer.parseInt(group);

for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	
	Matcher matcher1 = thePat1.matcher(item);
	Matcher matcher2 = thePat2.matcher(item);

	if (matcher1.find()) {
		filteredlist.add("file=" + file + "\r");
	} else if (matcher2.find()) {
		filteredlist.add("file1=" + file2 + "\r");
	} else {
		filteredlist.add(item);
	}
}

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Script

BufferedWriter out = new BufferedWriter(new FileWriter(outputFile));
out.write(filecontents);
out.close();
outputFile = filecontents;

Script

String output = new String();
output = stringlist.get(0);
for (i = 1; i < stringlist.size(); i++)
{
	output = output + "\n" + stringlist.get(i);
}

Value

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Script

String fileUrl1 = new String();
fileUrl1 = fileurl + "/output/mgcat.log";
BufferedReader getReader (String fileUrl) throws IOException {
		InputStreamReader reader;
		try {
			reader = new FileReader(fileUrl1);
		}
		catch (FileNotFoundException e) {
			// try a real URL instead
			URL url = new URL(fileUrl1);
			reader = new InputStreamReader (url.openStream());
		}
		return new BufferedReader(reader);
	}



StringBuffer sb = new StringBuffer(4000);

BufferedReader in = getReader(fileUrl1);
String str;
String lineEnding = System.getProperty("line.separator");

while ((str = in.readLine()) != null) {
	sb.append(str);
	sb.append(lineEnding);
}
in.close();
filecontents = sb.toString();
  

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()) {
		String t = new String();
		t = matcher.group(theGroup);
		t = t.trim();
		filteredlist.add(t);
	}
}

Value

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Script

double a = Double.valueOf(seqSim);
double b = Double.valueOf(reqSim);

if (a >= b)
{
	cont = 1;
}
else
{
	cont = 0;
}

Script

import javax.swing.JOptionPane;

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

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