Clustering of Molecular Compounds with BioDICE Clustering Visualization Tool

Value

Script

warnings = new ArrayList();
File SMItmp = File.createTempFile("SMItmp", ".smi");
File SUBtmp = File.createTempFile("SUBtmp", ".sub");
File IDStmp = File.createTempFile("IDStmp", ".ids");
SMItmp.deleteOnExit();
SUBtmp.deleteOnExit();
IDStmp.deleteOnExit();

FileWriter fw = new FileWriter(SMItmp);

for (int i = 0; i < SMILES.size(); i++) {
	switch (SMILES.get(i).size()) {
		case 0: {
		warnings.add("Warning: search for '" + compounds_list.get(i) + "' didn't produce any result. This compound will be ignored");			
		break;
		}
		case 1: {
		fw.write(compounds_list.get(i) + "_" + CSID.get(i).get(0) + "," + focus.get(i) + "," + SMILES.get(i).get(0) + "\n");			
		break;
		}
		default:
		for (int j = 0; j < SMILES.get(i).size(); j++)
			fw.write(compounds_list.get(i) + "_" + CSID.get(i).get(j) + "," + focus.get(i) + "," + SMILES.get(i).get(j) + "\n");
	}
}
fw.close();

String[] args = new String[3];
args[0] = SMItmp.getPath();
args[1] = SUBtmp.getPath();
args[2] = IDStmp.getPath();
moss.Miner.main(args);

sub = args[1];
ids = args[2];

Script

BufferedReader getReader (String fileUrl, String encoding) throws IOException {
		InputStreamReader reader;
		try {
			if (encoding == null) {
				reader = new FileReader(fileUrl);
			} else {
				reader = new InputStreamReader(new FileInputStream(fileUrl),encoding); 
			}
		}
		catch (FileNotFoundException e) {
			// try a real URL instead
			URL url = new URL(fileUrl);
			if (encoding == null) {
				reader = new InputStreamReader (url.openStream());
			} else {
				reader = new InputStreamReader (url.openStream(), encoding);
			}
		}
		return new BufferedReader(reader);
	}



StringBuffer sb = new StringBuffer(4000);

if (encoding == void) {
	encoding = null;
}

BufferedReader in = getReader(fileurl, encoding);
String str;
String lineEnding = System.getProperty("line.separator");

while ((str = in.readLine()) != null) {
	sb.append(str);
	sb.append(lineEnding);
}
in.close();
filecontents = sb.toString();
  

Script

BufferedReader getReader (String fileUrl, String encoding) throws IOException {
		InputStreamReader reader;
		try {
			if (encoding == null) {
				reader = new FileReader(fileUrl);
			} else {
				reader = new InputStreamReader(new FileInputStream(fileUrl),encoding); 
			}
		}
		catch (FileNotFoundException e) {
			// try a real URL instead
			URL url = new URL(fileUrl);
			if (encoding == null) {
				reader = new InputStreamReader (url.openStream());
			} else {
				reader = new InputStreamReader (url.openStream(), encoding);
			}
		}
		return new BufferedReader(reader);
	}



StringBuffer sb = new StringBuffer(4000);

if (encoding == void) {
	encoding = null;
}

BufferedReader in = getReader(fileurl, encoding);
String str;
String lineEnding = System.getProperty("line.separator");

while ((str = in.readLine()) != null) {
	sb.append(str);
	sb.append(lineEnding);
}
in.close();
filecontents = sb.toString();
  

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

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

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

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);