Saturday, December 24, 2011

C/C++ map



map { string,info> mymap;
map {string,info>::iterator it;


// insert into map

it = mymap.find(chrmName);
if ( it !=mymap.end() ) // found id{
            it->second.fnc();
 }else // not found{
            mymap.insert(  pair( chrmName, info()  )  ) ;
 }

// iterate over map
cout << "map size:" << mymap.size() << endl;

 map::iterator it3;
 int count=0;
 int tot = 0;
  
 for ( it3=mymap.begin() ; it3 != mymap.end(); it3++ ){

        count++;
        cout << it3->first.c_str() << "=>" ;
        cout<< it3->second.getCount() << endl;
        tot = tot+ it3->second.getCount();

    }


C/C++ vector



void fnc() {
     vector nameV;

      nameV.push_back("ab");
      nameV.push_back("cd");


      int sz = nameV.size();
      cout<< " Size of Vector:" << sz << endl;

      for(int i=0;i
      {
          cout<<  nameV[i] << endl;
      }



}

Wednesday, December 21, 2011

JAVA uniform random number [0 , 1]


import java.util.Random;

 Random myrand = new Random();
double zeroToOne = myrand.nextDouble();

JAVA file operation

 FileInputStream fstream = new FileInputStream("allUpper.seq");
 DataInputStream in = new DataInputStream(fstream);
  BufferedReader br = new BufferedReader(new InputStreamReader(in));

BufferedWriter out = new BufferedWriter(new FileWriter("kMer.txt")); // for write

while ((seqLine = br.readLine()) != null) {
               out.write(seqLine);
               out.write("\n");
  }
br.close();
 in.close();
 fstream.close();
  out.close();

Sunday, December 18, 2011

linux sshfs mount remote folder in local disk


sshfs   alamt@kw2237.rc:/home/KAUST/alamt  /home/tanviralam/kaustmachine/
ssh -X  alamt@kw2237.rc

run matlab
/mnt/kaustapps/MATLAB-faculty/matlab.R2011b



http://www.go2linux.org/sshfs-mount-remote-filesystem-using-ssh

Installation of sshfs
Get the packages
  • For Debian:
    apt-get install fuse-utils sshfs
  • For Ubuntu:
    sudo apt-get install fuse-utils sshfs
  • For Fedora and Centos:
    yum install fuse-utils sshfs
  • For Mandriva: urpmi:
    urpmi fuse-utils sshfs
Next step is to mount the fuse module[localuser: tanviralam remoteuser: alamt]

1. modprobe fuse

2. Next create the mount point
mkdir /home/tanviralam/remote

chown [local-user]:[your-group] /mnt/remote-fs/

chown tanvialam:777 /home/tanviralam/remote

3. Add yourself to the fuse group

adduser [local-user] fuse
adduser tanviralam fuse

4. Untill here all the command should be issued as root, now switch to your users and mount the remote filesystem.

sshfs remote-user@remote.server:/remote/directory /home/tanviralam/remote/