KEGG:Pathway Scheme

Wsdl

Wsdl Operation

Wsdl

Wsdl Operation

Script

import java.util.regex.Matcher;
import java.util.regex.Pattern;


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

List tmp = new ArrayList();


for(int i=0; i < in1.size(); i++) {
  
    tmp.add(in1.get(i).toString().replace("hsa:",""));
    
    
  
}
result = tmp;

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();
}

Script

import java.util.regex.Matcher;
import java.util.regex.Pattern;


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

List tmp = new ArrayList();


for(int i=0; i < in1.size(); i++) {
   if( in1.get(i).toString().equals("path:ko00010") || in1.get(i).toString().equals("path:ko00020") || in1.get(i).toString().equals("path:ko00030") || in1.get(i).toString().equals("path:ko00040") || in1.get(i).toString().equals("path:ko00051") || in1.get(i).toString().equals("path:ko00052") || in1.get(i).toString().equals("path:ko00053") || in1.get(i).toString().equals("path:ko00500") || in1.get(i).toString().equals("path:ko00520") || in1.get(i).toString().equals("path:ko00620") 
|| in1.get(i).toString().equals("path:ko00630") || in1.get(i).toString().equals("path:ko00640") || in1.get(i).toString().equals("path:ko00650") || in1.get(i).toString().equals("path:ko00660") || in1.get(i).toString().equals("path:ko00562") || in1.get(i).toString().equals("path:ko00190") || in1.get(i).toString().equals("path:ko00195") || in1.get(i).toString().equals("path:ko00196") || in1.get(i).toString().equals("path:ko00710") || in1.get(i).toString().equals("path:ko00720") 
|| in1.get(i).toString().equals("path:ko00680") || in1.get(i).toString().equals("path:ko00910") || in1.get(i).toString().equals("path:ko00920") || in1.get(i).toString().equals("path:ko00061") || in1.get(i).toString().equals("path:ko00062") || in1.get(i).toString().equals("path:ko00071") || in1.get(i).toString().equals("path:ko00072") || in1.get(i).toString().equals("path:ko00073") || in1.get(i).toString().equals("path:ko00100") || in1.get(i).toString().equals("path:ko00120") 
|| in1.get(i).toString().equals("path:ko00121") || in1.get(i).toString().equals("path:ko00140") || in1.get(i).toString().equals("path:ko00561") || in1.get(i).toString().equals("path:ko00564") || in1.get(i).toString().equals("path:ko00565") 
|| in1.get(i).toString().equals("path:ko00600") || in1.get(i).toString().equals("path:ko00590") || in1.get(i).toString().equals("path:ko00591") || in1.get(i).toString().equals("path:ko00592") || in1.get(i).toString().equals("path:ko01040") || in1.get(i).toString().equals("path:ko00230") || in1.get(i).toString().equals("path:ko00240") || in1.get(i).toString().equals("path:ko00250") || in1.get(i).toString().equals("path:ko00260") || in1.get(i).toString().equals("path:ko00270") 
|| in1.get(i).toString().equals("path:ko00280") || in1.get(i).toString().equals("path:ko00290") || in1.get(i).toString().equals("path:ko00300") || in1.get(i).toString().equals("path:ko00310") || in1.get(i).toString().equals("path:ko00330") || in1.get(i).toString().equals("path:ko00340") || in1.get(i).toString().equals("path:ko00350") || in1.get(i).toString().equals("path:ko00360") || in1.get(i).toString().equals("path:ko00380") || in1.get(i).toString().equals("path:ko00400") 
|| in1.get(i).toString().equals("path:ko00410") || in1.get(i).toString().equals("path:ko00430") || in1.get(i).toString().equals("path:ko00440") || in1.get(i).toString().equals("path:ko00450") || in1.get(i).toString().equals("path:ko00460") || in1.get(i).toString().equals("path:ko00471") || in1.get(i).toString().equals("path:ko00472") || in1.get(i).toString().equals("path:ko00473") || in1.get(i).toString().equals("path:ko00480") || in1.get(i).toString().equals("path:ko00510") 
|| in1.get(i).toString().equals("path:ko00513") || in1.get(i).toString().equals("path:ko00512") || in1.get(i).toString().equals("path:ko00514") || in1.get(i).toString().equals("path:ko00532") || in1.get(i).toString().equals("path:ko00534") || in1.get(i).toString().equals("path:ko00533") || in1.get(i).toString().equals("path:ko00531") || in1.get(i).toString().equals("path:ko00563") || in1.get(i).toString().equals("path:ko00601") || in1.get(i).toString().equals("path:ko00603") 
|| in1.get(i).toString().equals("path:ko00604") || in1.get(i).toString().equals("path:ko00540") || in1.get(i).toString().equals("path:ko00550") || in1.get(i).toString().equals("path:ko00511") || in1.get(i).toString().equals("path:ko00730") || in1.get(i).toString().equals("path:ko00740") || in1.get(i).toString().equals("path:ko00750") || in1.get(i).toString().equals("path:ko00760") || in1.get(i).toString().equals("path:ko00770") || in1.get(i).toString().equals("path:ko00780") 
|| in1.get(i).toString().equals("path:ko00785") || in1.get(i).toString().equals("path:ko00790") || in1.get(i).toString().equals("path:ko00670") || in1.get(i).toString().equals("path:ko00830") || in1.get(i).toString().equals("path:ko00860") || in1.get(i).toString().equals("path:ko00130") || in1.get(i).toString().equals("path:ko00900") || in1.get(i).toString().equals("path:ko00902") || in1.get(i).toString().equals("path:ko00909") || in1.get(i).toString().equals("path:ko00904") 
|| in1.get(i).toString().equals("path:ko00906") || in1.get(i).toString().equals("path:ko00905") || in1.get(i).toString().equals("path:ko00981") || in1.get(i).toString().equals("path:ko00908") || in1.get(i).toString().equals("path:ko00903") || in1.get(i).toString().equals("path:ko00281") || in1.get(i).toString().equals("path:ko01052") || in1.get(i).toString().equals("path:ko00522") || in1.get(i).toString().equals("path:ko01051") || in1.get(i).toString().equals("path:ko01056") 
|| in1.get(i).toString().equals("path:ko01057") || in1.get(i).toString().equals("path:ko00253") || in1.get(i).toString().equals("path:ko00523") || in1.get(i).toString().equals("path:ko01054") || in1.get(i).toString().equals("path:ko01053") || in1.get(i).toString().equals("path:ko01055") || in1.get(i).toString().equals("path:ko00940") || in1.get(i).toString().equals("path:ko00945") || in1.get(i).toString().equals("path:ko00941") || in1.get(i).toString().equals("path:ko00944") 
|| in1.get(i).toString().equals("path:ko00942") || in1.get(i).toString().equals("path:ko00943") || in1.get(i).toString().equals("path:ko00901") || in1.get(i).toString().equals("path:ko00950") || in1.get(i).toString().equals("path:ko00960") || in1.get(i).toString().equals("path:ko01058") || in1.get(i).toString().equals("path:ko00232") || in1.get(i).toString().equals("path:ko00965") || in1.get(i).toString().equals("path:ko00966") || in1.get(i).toString().equals("path:ko00402") 
|| in1.get(i).toString().equals("path:ko00311") || in1.get(i).toString().equals("path:ko00312") || in1.get(i).toString().equals("path:ko00521") || in1.get(i).toString().equals("path:ko00524") || in1.get(i).toString().equals("path:ko00331") || in1.get(i).toString().equals("path:ko00231") || in1.get(i).toString().equals("path:ko00401") || in1.get(i).toString().equals("path:ko00362") || in1.get(i).toString().equals("path:ko00627") || in1.get(i).toString().equals("path:ko00364") 
|| in1.get(i).toString().equals("path:ko00625") || in1.get(i).toString().equals("path:ko00361") || in1.get(i).toString().equals("path:ko00623") || in1.get(i).toString().equals("path:ko00622") || in1.get(i).toString().equals("path:ko00633") || in1.get(i).toString().equals("path:ko00642") || in1.get(i).toString().equals("path:ko00643") || in1.get(i).toString().equals("path:ko00791") || in1.get(i).toString().equals("path:ko00930") || in1.get(i).toString().equals("path:ko00351") 
|| in1.get(i).toString().equals("path:ko00363") || in1.get(i).toString().equals("path:ko00621") || in1.get(i).toString().equals("path:ko00626") || in1.get(i).toString().equals("path:ko00624") || in1.get(i).toString().equals("path:ko00980") || in1.get(i).toString().equals("path:ko00982") || in1.get(i).toString().equals("path:ko00983")
) {
    tmp.add(in1.get(i).toString().replace("ko","hsa"));
    
   } 
  
}
out1 = tmp;

Script

List strippedlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	if (strippedlist.contains(item) == false) {
		strippedlist.add(item);
	}
}

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);