Sorry, I can't replicate your error. When I run your code, a class cast exception is generated where SymbolList list is assigned, but no null pointer exception. Anyone else want to take a swing?
Greg > -----Original Message----- > From: Guoneng Zhong [mailto:[EMAIL PROTECTED]] > Sent: Friday, March 01, 2002 9:05 AM > To: Cox, Greg > Cc: [EMAIL PROTECTED] > Subject: Re: [Biojava-l] exception with no stacktrace > > > 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) > >> > >> _______________________________________________ > >> Biojava-l mailing list - [EMAIL PROTECTED] > >> http://biojava.org/mailman/listinfo/biojava-l > >> > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
