Tutorial 1 Workflow

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]);
	}
}

Xpath Expression

/default:msms_pipeline_analysis/default:msms_run_summary/default:spectrum_query/default:search_result/default:search_hit/@protein

Script

out1 = new ArrayList();
counts = new HashMap();

for (i=0; i

Script

String delims = "[ \t|]+";
String[] tokens;
out1 = new ArrayList();
counts = new Hashtable();

for (i=0; i

Script

String delims = "[ \t]+";
String[] tokens;
out1 = new ArrayList();
dict = new Hashtable();

for (i=0; i1) dict{tokens[1] + "_at"} = tokens[0]; 
}

for (i=0; i1)  out1.add( tokens[0] + "\t" + dict{tokens[0]} + "\t" + tokens[1]); 
}

Value

Value

Script

if ((url == void) || (url == null)) {
	throw new RuntimeException("The url must be specified");
}

URL inputURL = null;
if (base != void) {
  inputURL = new URL(new URL(base), url);
}
else {
  inputURL = new URL(url);
}
URLConnection con = inputURL.openConnection();
InputStream in = con.getInputStream();

StringBuffer result = new StringBuffer();
BufferedReader reader;

String encoding = con.getContentEncoding();
if (encoding == null) {
  reader = new BufferedReader(new InputStreamReader(in));
} else {
  reader = new BufferedReader(new InputStreamReader(in, encoding));
}
String line = null;
String NEWLINE = System.getProperty("line.separator");
while ((line = reader.readLine()) != null) {
	result.append(line);
	result.append(NEWLINE);
}

reader.close();
contents = result.toString();

Script

combined_data<-in1;

A<-matrix(unlist(strsplit(combined_data,"\t")), nrow = length(combined_data), ncol = 4, byrow = TRUE);

genes<-as.numeric(A[,3]);

proteins<-as.numeric(A[,4]);

png(filename="comparison.png", height=400, width=400, bg="white");
plot(genes, proteins, xlab="gene expression", ylab="protein spectral count");
dev.off();

R Server