<?xml version="1.0" encoding="UTF-8"?>
<s:scufl xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha" version="0.2" log="0">
  <s:workflowdescription lsid="urn:lsid:www.mygrid.org.uk:operation:P81DV9PQW02" author="" title="" />
  <s:processor name="options" boring="true">
    <s:stringconstant>swiss</s:stringconstant>
  </s:processor>
  <s:processor name="parse_swiss">
    <s:beanshell>
      <s:scriptvalue>String[] split = input.split("\n");
Vector nonEmpty = new Vector();

for (int i = 0; i &lt; split.length; i++) 
{		
	String trimmed = split[i].trim();
	String[] trimmedSplit = trimmed.split(":");
	System.out.println(trimmedSplit.length);
	if (trimmedSplit.length == 2){
	    nonEmpty.add(trimmedSplit[1].trim());	
	}
}

String output = "";

for (int i = 0; i &lt; nonEmpty.size(); i++)
{
	output = output + (String) (nonEmpty.elementAt(i) + "\n");
}


//String[] split2 = intermediate.split(":");
//Vector nonEmpty2 = new Vector();

//for (int i = 0; i &lt; split2.length; i++) 
//{		
//	String trimmed2 = split2[i].trim();
//	String[] trimmedSplit2 = trimmed2.split(":");	
//	nonEmpty2.add(trimmedSplit2[1].trim());	
//}

//String output = "";

//for (int i = 0; i &lt; nonEmpty2.size(); i++)
//{
//	output = output + (String) (nonEmpty2.elementAt(i) + "\n");
//}</s:scriptvalue>
      <s:beanshellinputlist>
        <s:beanshellinput s:syntactictype="'text/plain'">input</s:beanshellinput>
      </s:beanshellinputlist>
      <s:beanshelloutputlist>
        <s:beanshelloutput s:syntactictype="'text/plain'">output</s:beanshelloutput>
      </s:beanshelloutputlist>
    </s:beanshell>
  </s:processor>
  <s:processor name="parse_ddbj_gene_info">
    <s:description>extract information from geneGeneInfo processor at http://xml.nig.ac.jp/wsdl/Ensembl.wsdl</s:description>
    <s:soaplabwsdl>http://phoebus.cs.man.ac.uk:1977/axis/services/seq_analysis.parse_ddbj_gene_info</s:soaplabwsdl>
  </s:processor>
  <s:link source="gene_info" sink="parse_ddbj_gene_info:file_direct_data" />
  <s:link source="options:value" sink="parse_ddbj_gene_info:options" />
  <s:link source="parse_ddbj_gene_info:output" sink="parse_swiss:input" />
  <s:link source="parse_swiss:output" sink="swiss_ids" />
  <s:source name="gene_info" />
  <s:sink name="swiss_ids" />
</s:scufl>


