[Biojava-l] Error while reading byte data for creating a Trace.

[abhinav]

Richard Holland wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> I suspect the byte array itself may contain inaccurate data.
>
> Internally, both the URL and File constructors read the data into a byte
> array and then pass it to the same method as is used by the byte[]
> constructor.
>
> So, something must be different between the byte array you have, and the
> byte array obtained by reading the file in.
>
> The File constructor uses the following code to read the file:
>
>     byte[] bytes = null;
>     ByteArrayOutputStream baos = new ByteArrayOutputStream();
>     FileInputStream fis = new FileInputStream(ABIFile);
>     BufferedInputStream bis = new BufferedInputStream(fis);
>     int b;
>     while ((b = bis.read()) >= 0)
>     {
>       baos.write(b);
>     }
>     bis.close(); fis.close(); baos.close();
>     bytes = baos.toByteArray();
>
> If the above code produces different results to your byte array when
> reading data from the same file as your code, then something has gone
> wrong with the construction of your byte array.
>
> Lastly, a full stack trace would help us pinpoint the line that is
> breaking, and hopefully provide a hint as to what is wrong with the
> contents of the byte array. If you could provide one that would be very
> helpful.
>
> cheers,
> Richard
>
>
> abhi232 at cc.gatech.edu wrote:
>   
>> Hi all,
>> I am having a byte array which is having the data from an .ab1 file.The
>> biojava library provides a class called as ABITrace which takes as input
>> either a byte[] array , a file or a url.If i use the later parameters (the
>> file or the url )the program works but if I pass the byte array to the
>> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is there a
>> problem with the ABITrace class or how can I bypass this particular error.
>> I am printing the length of the byte array and it comes to 144930...Can
>> that cause a problem in my code?
>>
>> Thanks in advance.
>> Abhinav
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>     
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.2.2 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iD8DBQFHMD7P4C5LeMEKA/QRAmGIAJ9a/V6nZqMROz3H4u69ECQ+9iTgMgCeNZvr
> oe52S3khmTvi5BFCL1W4KHM=
> =5JAO
> -----END PGP SIGNATURE-----
>   

Yes I looked at the file ABITrace and found out that the first three 
characters must be ABI or the 128-130 characters must be ABI.But I 
cannot find that in the file that I am having.Also If this is not the 
case then there should be an illegal format exception whereas I am 
arrayIndexOutOfBound Exception which is also weird.
I am getting the following stack trace.
The bytes that i want are:0
The bytes that i want are:11
The bytes that i want are:0
The size of the byte array generated is:144930
Byte array also recieved
java.lang.ArrayIndexOutOfBoundsException: 128
    at org.biojava.bio.program.abi.ABITrace.isABI(ABITrace.java:552)
    at org.biojava.bio.program.abi.ABITrace.initData(ABITrace.java:289)
    at org.biojava.bio.program.abi.ABITrace.<init>(ABITrace.java:136)
    at Trace.init(Trace.java:138)
    at sun.applet.AppletPanel.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
The bytes I want are the first three bytes that I want to check if my 
file is ABI or not.I checked the isABI function as well it returns true 
or false value and not arrayIndexOutOfBouond . Also the number 128 does 
it hve any significance in this case?
Thanks in advance
Abhinav