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:[EMAIL PROTECTED]]
>> Sent: Thursday, February 28, 2002 4:31 PM
>> To: [EMAIL PROTECTED]
>> 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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>>
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