[Biojava-l] exception with no stacktrace

[Guoneng Zhong]

This is the function that has the code I included:

     private static void readFile() throws Exception{
         String file = "[some path]";
         AlignmentFormat format = new MSFAlignmentFormat();
         BufferedReader reader = new BufferedReader(new FileReader(file));
         if(false){
             String line = null;
             while((line=reader.readLine()) != null){
                 System.out.println(line);
             }
	return;
         }
         Alignment alignment = format.read(reader);
         List labels = alignment.getLabels();
         System.out.println("Retrieved "+labels.size()+" labels");
         for(int i=0;i<labels.size();i++){
             SymbolList list = (SymbolList)labels.get(i);
             System.out.println(list.seqString());
         }
         reader.close();
     }

The if statement on false is my way of testing and to show you that when 
I switch it to true, the buffered reader works.  So there's nothing 
wrong with the reader.  But when I switch that block to false, and let 
the alignment parser use the reader, I get this null pointer exception 
that is not at all informative of where the problem is.  It could be 
that the output I have has a missing part, but the exception does not 
tell me anything.

Is there any other way I can debug this without downloading the source 
code and incorporate it into my IDE and step through with my debugger?

Thanks,
Guoneng

On Thursday, February 28, 2002, at 04:54 PM, Cox, Greg wrote:

> I'd need to see all your code to be sure, but it looks like your file 
> isn't
> initialized, and that's what's causing the null pointer exception.  
> Whenere
> is 'file' coming from in creating the bufferedReader?  If you're sure 
> it's
> valid, I'd recommed breaking that line up into sub lines to track down 
> which
> statement is causing problems.
>
> Greg
>
>> -----Original Message-----
>> From: Guoneng Zhong [mailto:Guoneng.Zhong@med.nyu.edu]
>> Sent: Thursday, February 28, 2002 4:31 PM
>> To: biojava-l@biojava.org
>> Subject: [Biojava-l] exception with no stacktrace
>>
>>
>> Hi,
>> I tried the following lines and got the following exception.
>> Problem is
>> that I don't know what the problem is.  What line and what the
>> underlying cause.  There is no stacktrace beyond my own...
>>
>> Thanks ahead for all the help!
>>
>> G
>>
>>          AlignmentFormat format = new MSFAlignmentFormat();
>>          Alignment alignment = format.read(new BufferedReader(new
>> FileReader(file)));
>>          List labels = alignment.getLabels();
>>          System.out.println("Retrieved "+labels.size()+" labels");
>>          for(int i=0;i<labels.size();i++){
>>              SymbolList list = (SymbolList)labels.get(i);
>>              System.out.println(list.seqString());
>>          }
>>
>> MSFFormatReader null
>> Exception in thread "main" java.lang.NullPointerException
>> 	at test.TestClustalW.readFile(TestClustalW.java:27)
>> 	at test.TestClustalW.main(TestClustalW.java:20)
>>
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