Script

String encoded = java.net.URLEncoder.encode(contents_file, "UTF-8");

String url_string = "http://cypher001.ncl.ac.uk:8080/examples/servlets/servlet/HelloWorldExample?contents="+encoded;

Script

String encoded = java.net.URLEncoder.encode(contents_file, "UTF-8");

String url_string = "http://cypher001.ncl.ac.uk:8080/examples/servlets/servlet/HelloWorldExample?contents="+encoded;

Script

String [] lines = in1.split("\n");
List list = new ArrayList();

for (int i =0;i

Script

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


for (String line: lines)
{
	if (line.startsWith(identifier_name))
	{
		list.add(line.substring(3,line.length()).trim());
	}
}

out1 = list;

Value

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;

Value

Wsdl

Wsdl Operation

Value

Value

Value

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 = "";
List list = new ArrayList();

while(matcher.find())
{
	String match = input.substring(matcher.start()+1, matcher.end());
	if (match.contains("abstractText") || match.contains("fullName")
		|| match.contains("title") || match.contains("dx.doi.org")
		|| match.contains("yearOfPublication") || match.contains("volume")
		|| match.contains("pageInfo"))
	{
		list.add(match);
	}
}
String authors = "";
String abstractText ="";
String year = "";
String volume ="";
String pageInfo ="";
String link ="";
String journal = "";
String title = "";

for (Object o: list)
{
	String word = o.toString();
	int length = word.length();
	if (word.contains("abstractText"))
	{
		abstractText = word.substring(13, length);
	}
	else if (word.contains("fullName"))
	{
		authors += word.substring(9) +", ";
	}
	else if (word.contains("dx.doi.org"))
	{
		link = word.substring(4);
	}
	else if (word.contains("yearOfPublication"))
	{
		year = word.substring(18);
	}
	else if (word.contains("volume"))
	{
		volume = word.substring(7);
	}
	else if (word.contains("pageInfo"))
	{
		pageInfo = word.substring(9);
	}
	else if (word.contains("title") && journal.equals(""))
	{
		journal = word.substring(6);
	}
	else if (word.contains("title"))
	{
		title = word.substring(6);
	}

}


output = authors.substring(0,authors.length()-2) + " ("+year+"). "+title+". "+journal+", "+volume+ " :" + pageInfo+ ". "+link;

out1 = output;

Script

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

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

String seperatorString = "\n";
if (seperator != void) {
	seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	sb.append(item);
	if (i.hasNext()) {
		sb.append(seperatorString);
	}
}
concatenated = sb.toString();

Script

path = root + gi_num + ".faa";

Script

//Title:


BufferedWriter out = new BufferedWriter(new FileWriter(outPutFile));

//////////////////////////////////////////////////////////////////
out.write("  ");

out.write("
"+Title+"
");




//Design Document Intro
//Beanshell Script:


String[] lines = Intro.split("\n");
String output = "";
for (String line: lines)
{
	output += "
"+line+"
";
}

out.write(output);


//Target Proteome IDs:
//Beanshell script:



lines = Tid.split("\n");
output = "
Target species:
";
for (String line: lines)
{
	output+= "
    "+line+"
";
}

out.write(output);



//Source Proteome IDs:
//Beanshell script:



lines = Sid.split("\n");
output = "
Source species:
";
for (String line: lines)
{
	output+= "
    "+line+"
";
}

out.write(output);



//Similarity Measure:
//Beanshell script:



lines = Sim_M.split("\n");
 output = "";
for (String line: lines)
{
	output+= "
"+line+"
";
}

out.write(output);


//Total List of Identified Proteins:
//Beanshell script:



lines = TotalID_d.split("\n");
output = "
Identified proteins:
";
for (String line: lines)
{
	output+= "
    "+line.split("\t")[0]+"
";
}

out.write(output);
//////////////////////////////////////////////////////////////////
out.close();
outputFile = output;

Script

path = root +"-output.html";

Value

Script

out1 = "The two proteomes have an average identity of "+threshold+" percent.";

Value

Script

BufferedWriter out = new BufferedWriter(new FileWriter(input,true));

if (Title == void)
{Title = "";}
if (Tid == void)
{Tid = "";}
if (TSpecies == void)
{TSpecies = "";}
if (KPI == void)
{KPI = "";}
if (KDiagram == void)
{KDiagram = "";}
if (GO == void)
{GO = "";}
if (InterPro == void)
{InterPro = "";}
if (PubMed == void)
{PubMed = "";}
if (OC_R == void)
{OC_R = "";}
if (OS == void)
{OS = "";}

///////////////////////////////////////////////////////
out.write("
"+Title+"
");

String [] lines = Tid.split("\n");
String output ="";
out.write(output);

if (TSpecies != void)
{
	String [] lines = TSpecies.split("\n");
	String output ="";

	for (String line: lines)
	{	
		output += "";
	}
	out.write(output);
}

if (Sid != void)
{
	String [] lines = Sid.split("\n");
	String output ="";
	out.write(output);
}

if (SSpecies != void)
{
	String [] lines = SSpecies.split("\n");
	String output ="";
	
	for (String line: lines)
	{
		output += "";
	}
	out.write(output);
}

String [] lines = KPI.split("\n");
String output ="";

for (String line: lines)
{
	output += "";
}
out.write(output);


String [] lines = KDiagram.split("\n");
String output ="";

for (String line: lines)
{
	output += "";
}
out.write(output);


String [] lines = GO.split("\n");
String output ="";
out.write(output);

String [] lines = InterPro.split("\n");
String output ="";
out.write(output);

String [] lines = PubMed.split("\n");
String output ="";
out.write(output);


String [] lines = OC_R.split("\n");
String output ="";
out.write(output);



String [] lines = OS.split("\n");
String output ="";

for (String line: lines)
{
	output += "";
}
output+="
Target Protein IDs
";

for (String line: lines)
{
	output += line+ "
";
}
output += "
Target Species
" + line+ "
Source Protein IDs
";

	for (String line: lines)
	{
		output += line+ "
";
	}
	output+= "
Source Species
" + line+ "
KEGG Pathway Information
" + line+ "
KEGG Diagram
Gene Ontology Annotations
";

for (String line: lines)
{
	output += line+ "
";
}
output+= "
InterPro
";

for (String line: lines)
{
	output += line+ "
";
}
output+= "
Publications
";

for (String line: lines)
{
	output += line+ "
";
}
output+= "
New ONDEX Concepts and Relations
";

for (String line: lines)
{
	output += line+ "
";
}
output+= "
ONDEX Screenshots
";
out.write(output);



////////////////////////////////////////////

out.close();
output1 = output;

Script

String seperatorString = "\n";
if (seperator != void) {
	seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	sb.append(item);
	if (i.hasNext()) {
		sb.append(seperatorString);
	}
}
concatenated = sb.toString();

Script

String file = filename;

List output = new ArrayList();

for (Object o : uniprot)
{
	output.add(file);
}

uniprot_ids = uniprot;
filenames = output;

Script

path = root + gi_num + ".faa";

Script

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

Script

path = root + source_gi_num + target_gi_num+ ".blast";

Script

String seperatorString = "\n";
if (seperator != void) {
	seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	sb.append(item);
	if (i.hasNext()) {
		sb.append(seperatorString);
	}
}
concatenated = sb.toString();