/**
* Connect to ftp server
*
* @param server the host you connect
* @param user the user account to login [anonymous as default]
* @param passwd the password according to you account, and if the account is anonymous "" as
* default
*/
public void initConnection(String server, String user, String passwd) {
ftp = new FTPClient();
try {
ftp.connect(server);
ftp.login(user, passwd);
int reply = ftp.getReplyCode();
if (!FTPReply.isPositiveCompletion(reply)) {
ftp.disconnect();
LogUtils.log("disconnect after login");
}
LogUtils.log("Connected to " + server + " with name [" + user + "]");
} catch (SocketException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
}
/**
* download file from remote host and display the downloaded percentage
*
* @param folder remote directory
* @param fileName the file you want to download
* @param destfolder the destination folder you will store the file
*/
public void downloadFileInProgress(String folder, String fileName, String destfolder) {
try {
ftp.enterLocalPassiveMode();
ftp.changeWorkingDirectory(folder);
LogUtils.log("Changing to directory:[" + folder + "]");
String realFile = destfolder + File.separator + fileName;
File localFile = new File(realFile);
FileOutputStream fos = new FileOutputStream(localFile);
LogUtils.log("Start downloading..");
FTPFile[] fs = ftp.listFiles();
DecimalFormat df = new DecimalFormat("#.00%");
for (FTPFile f : fs) {
if (f.getName().equals(fileName)) {
InputStream is = ftp.retrieveFileStream(f.getName());
BufferedReader br = new BufferedReader(new InputStreamReader(is));
String line = br.readLine();
long transfered = 0, total = f.getSize();
double ratio = 0.0;
while (line != null) {
byte[] buff = line.getBytes();
transfered += buff.length;
if (transfered * 1.0 / total - ratio >= 0.01) {
ratio = transfered * 1.0 / total;
LogUtils.log("Download size : " + df.format(ratio));
}
fos.write(buff);
line = br.readLine();
}
is.close();
ftp.logout();
ftp.disconnect();
LogUtils.log("Download done!");
}
}
fos.close();
} catch (IOException e) {
e.printStackTrace();
}
}
/**
* The actual calculation function
*
* @param dataIn
* @param fileName
*/
public void simCalculation(HashMap<String, Double> dataIn, String fileName) {
Object[] objs = pathways.keySet().toArray();
int npaths = objs.length;
NetworkOutput.open(fileName);
for (int i = 0; i < npaths - 1; i++) {
HashSet<String> source = pathwayOverlap(pathways.get(objs[i].toString()), geneSet);
for (int j = i + 1; j < npaths; j++) {
HashSet<String> target = pathwayOverlap(pathways.get(objs[j].toString()), geneSet);
// 相似性计算
double sim = geneSetSim(source, target, dataIn);
// p值计算
// double pval = permutePval(pathways.get(objs[i].toString())
// .size(), pathways.get(objs[j].toString()).size(),
// nperms, sim, dataIn);
// pval calculation
HashSet<String> union =
unionGenes(pathways.get(objs[i].toString()), pathways.get(objs[j].toString()));
double pval =
pValuePermuteLabel(
pathways.get(objs[i].toString()).size(),
pathways.get(objs[j].toString()).size(),
union,
nperms,
sim,
dataIn);
// 存储数据到csv文件中
String[] contents = {
objs[i].toString(), objs[j].toString(), String.valueOf(sim), String.valueOf(pval)
};
NetworkOutput.writeRecord(contents);
LogUtils.log(
objs[i].toString()
+ "["
+ i
+ "]"
+ objs[j].toString()
+ "["
+ j
+ "] ["
+ npaths
+ "]["
+ pval
+ "]");
}
}
NetworkOutput.close();
}
/**
* calculate the similarity of pathways entrance
*
* @param type This indicate the category of network[norm,tumor,semantic]
* @param fileName The name of file to store the pathway similarity and pvals
*/
public void similarityCalculation(String type, String fileName, double threshold) {
if (type.equalsIgnoreCase("norm")) {
HashMap<String, Double> normNet = GeneInteractionNet.geneNetFilter("normnet.out", threshold);
simCalculation(normNet, fileName);
} else if (type.equalsIgnoreCase("tumor")) {
HashMap<String, Double> tumorNet = GeneInteractionNet.geneNetFilter("tumnet.out", threshold);
simCalculation(tumorNet, fileName);
} else if (type.equalsIgnoreCase("semantic")) {
HashMap<String, Double> semNet = GeneInteractionNet.geneNetFilter("semnet.out", threshold);
simCalculation(semNet, fileName);
} else {
LogUtils.log("Type error:[type should be in [norm,tumor,semantic] ], but given:" + type);
}
}
/**
* download file from remote host without progress percentage display
*
* @param folder remote directory
* @param fileName the file you want to download
* @param destfolder the destination folder you will store the file
*/
public void downloadFile(String folder, String fileName, String destfolder) {
try {
ftp.enterLocalPassiveMode();
ftp.changeWorkingDirectory(folder);
LogUtils.log("Changing to directory:[" + folder + "]");
String realFile = destfolder + File.separator + fileName;
File localFile = new File(realFile);
FileOutputStream fos = new FileOutputStream(localFile);
FileInputStream fis = new FileInputStream(localFile);
LogUtils.log("Start downloading..");
FTPFile[] fs = ftp.listFiles();
for (FTPFile f : fs) {
if (f.getName().equals(fileName)) {
ftp.retrieveFile(f.getName(), fos);
LogUtils.log("Download done!");
break;
}
}
fos.close();
} catch (IOException e) {
e.printStackTrace();
}
}