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genopri-shcs/project/PPPClient/src/io/Reader.java
5595a8d46022ms_access_migration

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Reader.java
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package io;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.sql.Date;
import java.sql.SQLException;
import database.DBconnector_client;
public class Reader {
private File input_f;
private BufferedReader br;
private DBconnector_client conn_mu;
public Reader(){
conn_mu = new DBconnector_client();
}
public void readBIM(String path) throws IOException, SQLException{
//check extension file
String[] pathCheck = path.split("\\.");
if(!pathCheck[pathCheck.length-1].equalsIgnoreCase("bim")) {
throw new IOException("Wrong Format File");
}
input_f = new File(path);
br = new BufferedReader(new FileReader(input_f));
String newline;
while((newline = br.readLine()) != null ){
String[] tokens = newline.split("\t");
conn_mu.insertMarker(tokens[1], tokens[4], tokens[5], Integer.parseInt(tokens[3]), -1, tokens[0]);
}
}
public void readFAM(String path) throws IOException, SQLException{
String[] pathCheck = path.split("\\.");
if(!pathCheck[pathCheck.length-1].equalsIgnoreCase("fam")) {
throw new IOException("Wrong Format File");
}
input_f = new File(path);
br = new BufferedReader(new FileReader(input_f));
String newline;
while((newline = br.readLine()) != null){
String[] tokens = newline.split(" ");
int pat_id;
try{
pat_id = Integer.parseInt(tokens[0]);
}
catch(Exception e){
String[] subtokens = tokens[0].split("_");
pat_id = Integer.parseInt(subtokens[1]);
}
conn_mu.insertPatient(pat_id, null, null, null, new Date(System.currentTimeMillis()));
}
}
/**
* @param args
*/
public static void main(String[] args) {
Reader r = new Reader();
try {
// r.readBIM("C:\\Users\\raisaro\\Dropbox\\EPFL\\Genomic Privacy\\CHUV\\dataSet\\SHCS693.samples.26-04-13.HLA.bim");
System.out.println("BIM file complete");
r.readFAM("C:\\Users\\raisaro\\Dropbox\\EPFL\\Genomic Privacy\\CHUV\\dataSet\\SHCS693.samples.26-04-13.HLA.fam");
// FIXME: hardcoded link
System.out.println("FAM file complete");
} catch (IOException | SQLException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
}
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