UniProt to Gene Ontology

Script

String [] lines = parsed_uniprot.split("\n");
List list = new ArrayList();


for (String line: lines)
{
	if (line.startsWith(identifier_name))
	{
		list.add(line.substring(identifier_name.length()+1,line.length()).trim());
	}
}

out1 = list;

Script

String input = in1;

String pat = ">[^<]+";

java.util.regex.Pattern p = java.util.regex.Pattern.compile(pat);
java.util.regex.Matcher matcher = p.matcher(input);

String output = "";
int counter =1;
while(matcher.find())
{
	output += input.substring(matcher.start()+1, matcher.end());
	if (counter%2==0)
	{
		output+="\n";
	}
	else
	{
		output +="\t";
	}
	counter++;
}

out1 = output;

Value

Script

String seperatorString = "\n";
if (seperator != void) {
	seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
Iterator j = go_defs.iterator();
for (Iterator i = go_ids.iterator(); i.hasNext();) {
	String id = (String) i.next();
	String def = (String) j.next();
	sb.append(id + seperatorString + def);
	if (i.hasNext()) {
		sb.append(seperatorString);
	}
}
concatenated = sb.toString();