[Biojava-l] Need help for resolving the issue args[0]

[mark.schreiber at novartis.com]

Can you post the stack trace?



biojava-l-bounces at lists.open-bio.org wrote on 06/19/2009 02:52:38 PM:

>  Hello Support,
> I am a new developer of biojava, I have a good knowledge about java and 
bio,
> but this is new tool for me, I have some problem while working in this
> tools, below I have write down the code for reading the Gen Bank file 
and
> then convert into "DNA", "RNA" or "Protein". I have already add the 
biojava
> library into my source code. When I have read this code I have come to 
know
> from your arguments portion for the execution of this code, I have need
> three argument, one for the filename, second for the file type and third 
is
> the alphabet.
> Now the problem is that how I will pass these three parameter values 
into
> source code for args[0], args[1] and args[2]. When I have passed these
> values by using the string pattern then this code generte a errors, 
"illegel
> statement". Please help me out how I can fixed this problem, I will be 
very
> thankful to you if you will reply me soon
> 
> 
> package biojava;
> import java.io.*;
> 
> import org.biojava.bio.*;
> import org.biojava.bio.seq.*;
> import org.biojava.bio.seq.io.*;
> 
> public class ReadFasta2 {
> 
>  /**
>   * This program will read any file supported by SeqIOTools it takes 
three
>   * arguments, the first is the file name the second is the name of
>   * a file format supported by SeqIOTools. eg fasta, genbank etc.
>   * The third argument is the alphabet (eg dna, rna, protein).
>   *
>   * Both the format and alphabet names are case insensitive.
>   *
>   */
>  public static void main(String[] args) {
>    try {
>      //prepare a BufferedReader for file io
>      BufferedReader br = new BufferedReader(new FileReader(args[0]));
> 
>      String format = args[1];
>      String alphabet = args[2];
> 
>      /*
>       * get a Sequence Iterator over all the sequences in the file.
>       * SeqIOTools.fileToBiojava() returns an Object. If the file read
>       * is an alignment format like MSF and Alignment object is returned
>       * otherwise a SequenceIterator is returned.
>       */
>      SequenceIterator iter =
>          (SequenceIterator)SeqIOTools.fileToBiojava(format,alphabet, 
br);
>    }
>    catch (FileNotFoundException ex) {
>      //can't find file specified by args[0]
>      ex.printStackTrace();
>    }catch (BioException ex) {
>      //error parsing requested format
>      ex.printStackTrace();
>    }
>  }
> }
> --
> 
> 
> 
> 
> -- 
> Abdul Qaddus
> www.futurelinkers.com
> Cell No:- +92-3336540863
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

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