Create_SNP_Set

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.*;

List tmp_end = new ArrayList();
List tmp_start = new ArrayList();
width = Integer.parseInt(in1.get(0));
int value_end=0;
int value_start=0;
int out_end=0;
int out_start=0;
for(int i=0; i < end_in.size(); i++) {
           value_end = Integer.parseInt(end_in.get(i));
	   value_start = Integer.parseInt(start_in.get(i));
if (value_start < value_end ) {
 		out_end = value_end + width;
		out_start = value_start - width;	
 	}
else {
		out_start = value_start + width;
		out_end = value_end - width;	
}
		
    tmp_end.add(out_end);
    tmp_start.add(out_start);
 }

end_out = tmp_end;
start_out = tmp_start;
chr_out = chr_in;

Script

out1="hsa:"+in1;

Wsdl

Wsdl Operation

Script

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);

Script

import java.util.List;
import java.util.ArrayList;

List tmp = new ArrayList();


for(int i=0; i < in2.size(); i++) {
  if(!in2.get(i).toString().equals("")) {
    tmp.add(in2.get(i).toString() + "\t" + in1);
    
    
  }
}
result = tmp;

Script

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);

Script

File f = File.createTempFile("taverna", ".tmp");

BufferedWriter writer = new BufferedWriter(new FileWriter(f));
writer.write(content);
writer.close();

filepath = f.getCanonicalPath();

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);
	}

String NEWLINE = System.getProperty("line.separator");

boolean displayResults = false;
if (displayresults != void) {
	displayResults = Boolean.valueOf(displayresults).booleanValue();
}

StringBuffer sb = new StringBuffer(2000);

if (outputfile == void) {
	throw new RuntimeException("The 'outputfile' parameter cannot be null");
}

if (filelist == null) {
	throw new RuntimeException("The 'filelist' parameter cannot be null");
}

String str = null;

Writer writer = new FileWriter(outputfile);
for (int i = 0; i < filelist.size(); i++) {
	BufferedReader reader = getReader(filelist.get(i));
	while ((str = reader.readLine()) != null) {
		writer.write(str);
		writer.write(NEWLINE);

		if (displayResults) {
			sb.append(str);
			sb.append(NEWLINE);
		}
	}

	reader.close();

}
writer.flush();
writer.close();

if (displayResults) {
	results= sb.toString();
}