Send data to arduino from PC in java over Serial (RXTXlib)

I belive that you solved this by now, but still:

The type returned by Serial.read() is an int which is an decimal equivalent of a character - character '1' is 49. You must thus convert that int to a char to check the condition like that:

int led = 13 ;
char charRead;
void setup() {
      Serial.begin(9600);
      pinMode(led, OUTPUT);           
}
void loop() {
     if(Serial.available()>0) {
            delay(100);
            while(Serial.available()>0){
              charRead = char(Serial.read());
              if(charRead=='1'){
                digitalWrite(led,1);
              }
             }
          }
         delay(1000);
}

You could also just check the int if you do not want to convert to a char

int intRead = Serial.read();
if(intRead==49){...}