You may want to modify the code as follows:
FileInputStream fileIn = new FileInputStream("shapeFile.txt");
Scanner scan = new Scanner(fileIn);
int[] var1 = new int[3];
while(scan.hasNext()) {
String shape = scan.next();
if(shape.equals("Circle")) {
for(int i = 0; i < 3;i++) {
if(scan.hasNextInt()) {
var1[i] = scan.nextInt();
} else {
break;
}
}
myShapes.addShape(new Circle(var1[0], var1[1], var1[2], Color.RED));
}
}