[Biojava-l] A problem in reading remote AB1 files

[Hüseyin Kaya]

Hi BioJava Community,

I have a little problem in reading AB1 files residing on a
remote webserver.

I have two different AB1 files; ok.ab1 and failed.ab1.
They were both generated from the same sequencer.

Here is a quick summary:

Reading ok.ab1     from a local directory   is OK
Reading failed.ab1 from a local directory   is OK
Reading ok.ab1     from a remote webserver  is OK
Reading failed.ab1 from a remote webserver  is not OK

The exception is:
java.lang.ArrayIndexOutOfBoundsException
   at java.lang.System.arraycopy(Native Method)
   at
org.biojava.utils.io.CachingInputStream.read(CachingInputStream.java:101)
   at java.io.DataInputStream.readFully(Unknown Source)
   at java.io.DataInputStream.readFully(Unknown Source)
   at
org.biojava.bio.program.abi.ABIFParser$DataStream.readFully(ABIFParser.java:376)
   at
org.biojava.bio.program.abi.ABIFParser.readDataRecords(ABIFParser.java:129)
   at org.biojava.bio.program.abi.ABIFParser.<init>(ABIFParser.java:100)
   at org.biojava.bio.program.abi.ABIFParser.<init>(ABIFParser.java:89)
   at
org.biojava.bio.program.abi.ABIFChromatogram$Parser.<init>(ABIFChromatogram.java:117)
   at
org.biojava.bio.program.abi.ABIFChromatogram.load(ABIFChromatogram.java:101)
   at
org.biojava.bio.program.abi.ABIFChromatogram.create(ABIFChromatogram.java:89)
   at
org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:119)
   at BugTest.readChromatogram(BugTest.java:34)
   at BugTest.main(BugTest.java:22)


I will be glad if you help me in resolving this problem.
Sincerely
Huseyin Kaya

BugTest.java

import java.net.URL;
import org.biojava.bio.chromatogram.AbstractChromatogram;
import org.biojava.bio.chromatogram.ChromatogramFactory;

public class BugTest
{
 public static final String URL_REMOTE_FAILED = "
http://dna.iontek.com.tr/files/failed.ab1";
 public static final String URL_REMOTE_OK     = "
http://dna.iontek.com.tr/files/ok.ab1";

 public static final String URL_LOCAL_FAILED  = "file:///C:/failed.ab1";
 public static final String URL_LOCAL_OK    = "file:///C:/ok.ab1";

 public static void main(String[] args) throws Exception
 {
  readChromatogram("Reading ok.ab1     from local directory",URL_LOCAL_OK);
  readChromatogram("Reading failed.ab1 from local
directory",URL_LOCAL_FAILED);
  readChromatogram("Reading ok.ab1   from webserver      ",URL_REMOTE_OK);
  // This one is failed
  readChromatogram("Reading failed.ab1 from webserver
",URL_REMOTE_FAILED);
 }

 private static void readChromatogram(String message, String urlstr)
 {
  System.out.println(message + "["+urlstr+"]");
  AbstractChromatogram ch = null ;
  URL url;
  try
  {
   url = new URL(urlstr);
   ch = (AbstractChromatogram)ChromatogramFactory.create(url.openStream());

  } catch (Exception e)
  {
   e.printStackTrace();
  }
  if (ch != null)
   System.out.println("Trace length is "+ch.getTraceLength());

 }
}