String array error, not understandable

Question

I get this error:
Exception in thread "AWT-EventQueue-0" java.lang.StringIndexOutOfBoundsException: String index out of range: -1
i cant understand its reason because it comes only when a string of length more than 12 is entered.Moreover it doesnt comes for all the strings of more than 12,instead for some strings it doesnt come while in others it does.
Please help im stuck in this for 3 days already
Following is my code and error:
Code:
public ArrayList SecondaryStructure(Sequence s){
ArrayList result=new ArrayList();
if ( ! validateSeq(s) )
JOptionPane.showMessageDialog(null,"Invalid Sequence","Error",JOptionPane.ERROR_MESSAGE);
else
String AA_seq=convert(s);
result=secondaryStructure.predictSecondaryStructure(AA_seq);
return result;
return null;
public boolean validateSeq(Sequence s){
boolean found=false;
String temp=s.getSeq();
if(s.getType().equals("AA"))
String tempArray[]=new String[temp.length()];
int j=0;
for(int aI=0;aI<temp.length();aI++)
Character c=temp.charAt(aI);
tempArray[aI]=c.toString();
System.out.println("show:"+tempArray[aI]);
for(int i=0;i<tempArray.length;i++)
try
if (tempArray.equals("F") || tempArray[i].equals("L") || tempArray[i].equals("I") || tempArray[i].equals("M") || tempArray[i].equals("V") || tempArray[i].equals("S") || tempArray[i].equals("P") || tempArray[i].equals("T") || tempArray[i].equals("A") || tempArray[i].equals("Y") || tempArray[i].equals("H") || tempArray[i].equals("Q") || tempArray[i].equals("N") || tempArray[i].equals("K") || tempArray[i].equals("D") || tempArray[i].equals("E") || tempArray[i].equals("C") || tempArray[i].equals("W") || tempArray[i].equals("R") || tempArray[i].equals("G") || tempArray[i].equals("Stop") || tempArray[i].equals("*"))
found=true;
else if(tempArray[i].equals("Phe") || tempArray[i].equals("Leu") || tempArray[i].equals("Ile") || tempArray[i].equals("Met") || tempArray[i].equals("Val") || tempArray[i].equals("Ser") || tempArray[i].equals("Pro") || tempArray[i].equals("Thr") || tempArray[i].equals("Ala") || tempArray[i].equals("Thr") || tempArray[i].equals("His") || tempArray[i].equals("Gln") || tempArray[i].equals("Asn") || tempArray[i].equals("Lys") || tempArray[i].equals("Asp") || tempArray[i].equals("Glu") || tempArray[i].equals("Cys") || tempArray[i].equals("Trp") || tempArray[i].equals("Arg") || tempArray[i].equals("Gly") || tempArray[i].equals("Stop") || tempArray[i].equals("*"))
found=true;
else
found=false;
}catch(Exception e){System.out.println("Error: "+ e.toString());}
return found;
Input: ATGCWYKWTTAAA
Error:
show:A
show:T
show:G
show:C
Exception in thread "AWT-EventQueue-0" java.lang.StringIndexOutOfBoundsException: String index out of range: -1
show:W
show:Y
at java.lang.String.substring(String.java:1938)
at Helix.predictHelix(Helix.java:87)
show:K
show:W
show:T
show:T
show:A
show:A
show:A

Answer 1

eman-e-maryam wrote:
I get this error:
Exception in thread "AWT-EventQueue-0" java.lang.StringIndexOutOfBoundsException: String index out of range: -1
i cant understand its reason because it comes only when a string of length more than 12 is entered.Moreover it doesnt comes for all the strings of more than 12,instead for some strings it doesnt come while in others it does.The error is telling you exactly what's wrong. You are trying to access a character at position -1 in a String. No string has a character there. They can only be in the range 0..Integer.MAX_VALUE. If you look more closely at the message, you'll see it's even telling you exactly WHERE the problem is happening.
Use a debugger or add print statements so you can see what your code is doing, rather than asking others to debug it for you. After that, once you track down where it's becoming -1, if you still can't figure out what's wrong or how to fix it, post again.
As already requested, use [code] and [/code] tags around your code, or the CODE button so that your code will be readable.
And don't post all the code you've ever written. Post just enough to demonstrate the problem. An SSCCE.