if (counter7[i].trim().startsWith("CA"))
{
StringTokenizer a2 = new StringTokenizer(counter7[i],"\t");
int amino2=0;
while(a2.hasMoreTokens())
{
String aa2 = a2.nextToken();
amino2++;
if (amino2 == 2)
{
if(aa2.trim().startsWith("ALA"))
store2 [z2] = "A";
It is the tokenizing part. Amino is just the name for my token.