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

abhinav abhi232 at cc.gatech.edu
Tue Nov 6 18:03:02 UTC 2007

Richard Holland wrote:
> Hash: SHA1
> I think that either the file is at fault, or the method you are using to
> read the file into Java is at fault.
> Could you provide us with the complete piece of code you are using from
> the point where you read the file into the array through to the point
> where you generate the output you quoted?  (Not as an attachment as the
> mailing list will strip those - simply paste it into the message body
> instead).
> cheers,
> Richard
> abhinav wrote:
>> Richard Holland wrote:
>> 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
>> 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
> Version: GnuPG v1.4.2.2 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
> T1Z8W0JhCe7+hx5rbKLGqVk=
> =qNcr
Ok Yes here is the code that i am using .I establish a connection with a 
php page which in turn reads the file and prints the content back to 
me.I am using DataOutputStream for sending data and BufferedReader for 
taking in the data.Then I am reading the data into a string and 
converting it to byte[] array . this the code where the connection is 
estableshed and the data is taken and displayed.

 private HttpURLConnection httpConn;
    private DataOutputStream out;
    private DataInputStream temp_stream;
    private BufferedReader in;
    private BufferedInputStream in_buff_stream;
    private String str ;
    private byte[] bytearray;
    Chromatogram abif_chromatogram;

    /** Creates a new instance of testPost */
    public testPost()

        httpConn = null;
        str = new String("");
        bytearray = new byte[144930];

    public byte[] create_and_write_Connection(String url,String 
            URL conn_url = new URL(url);
            httpConn = (HttpURLConnection)conn_url.openConnection();
            out=new DataOutputStream(httpConn.getOutputStream());
            System.out.println("Connection established successfully and 
data written");
            InputStreamReader in_stream = new 

                System.out.println("The character encoding used is:"+ 
            in = new BufferedReader(in_stream);

            System.out.println("Data acceptance started");

                str += in.readLine();
            System.out.println("The string to be returned is:"+str);
            bytearray = str.getBytes("ISO8859-1");
            String temp_string = new String(bytearray,"windows-1252");
           System.out.println("The encoded string is as follows:"+ 
            System.out.println("The size of byte array inside testpost 
is:"+ Array.getLength(bytearray));
             for(int i = 0 ; i < 3 ; i ++)
                System.out.println("The bytes that i want are:"+ 
            return bytearray;
        catch(Exception e)
        return bytearray;
Please guide me on this point

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