[Biojava-l] Re: Biojava-l Digest, Vol 4, Issue 14

[Vivek　Tyagi]

Hi, The code is not compiling as some deprecated methods may be in use in the code but worry not just recompile with             -deprecation and that should do it. 
Vivek Tyagi
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Today's Topics:

1. biojava API - is it current? (hz5 at njit.edu)


----------------------------------------------------------------------

Message: 1
Date: Fri, 18 Apr 2003 11:48:53 -0400 (EDT)
From: hz5 at njit.edu
Subject: [Biojava-l] biojava API - is it current?
To: biojava-l at biojava.org
Message-ID: <1050680933.3ea01e653aa7c at webmail.njit.edu>
Content-Type: text/plain; charset=ISO-8859-1

I got this code from Biojava in Anger(to create a customized Alphabets):
****************************************************************
import org.biojava.bio.symbol.*;
import org.biojava.bio.*;
import java.util.*;
public class Binary {
public static void main(String[] args) {
//make the "zero" Symbol with no annotation
Symbol zero =
AlphabetManager.createSymbol("A", Annotation.EMPTY_ANNOTATION);

//make the "one" Symbol
Symbol one =
AlphabetManager.createSymbol("B", Annotation.EMPTY_ANNOTATION);
//System.out.println(one.getToken());

//collect the Symbols in a Set
Set symbols = new HashSet();
symbols.add(zero); symbols.add(one);

//make the Binary Alphabet
FiniteAlphabet binary = new SimpleAlphabet(symbols, "Binary");

//iterate through the symbols to show everything works
for (Iterator i = binary.iterator(); i.hasNext(); ) {
Symbol sym = (Symbol)i.next();
System.out.println(sym.getName());
}

//it is usual to register newly creates Alphabets with the AlphabetManager
AlphabetManager.registerAlphabet(binary.getName(), binary);

/*
* The newly created Alphabet will have been registered with the
* AlphabetManager under the name "Binary". If you retreive an instance
* of it using this name it should be canonical with the previous instance
*/
Alphabet alpha = AlphabetManager.alphabetForName("Binary");

//check canonical status
System.out.println(alpha == binary);
}
}
****************************************************************
on line 6-8:
//make the "zero" Symbol with no annotation
Symbol zero =
AlphabetManager.createSymbol("A", Annotation.EMPTY_ANNOTATION);

however, by looking at the api at http://www.biojava.org/docs/api/, I can only 
see 3 createSymbol methods in AlphabetManager class, none of them taking 2 
arguments:
---static Symbol createSymbol(char token, Annotation annotation, java.util.List 
symList, Alphabet alpha)
---static Symbol createSymbol(char token, Annotation annotation, java.util.Set 
symSet, Alphabet alpha)
---static AtomicSymbol createSymbol(char token, java.lang.String name, 
Annotation annotation)

The wierd thing is that the program can compile, I am using:
biojava-1.3pre1.jar 13-Jan-2003 18:23 2.2M 
bytecode-0.91.jar 01-Sep-2002 09:37 59k 
jakarta-regexp.jar 02-Jul-2001 05:30 29k 
xerces.jar 14-Aug-2001 12:02 1.7M


Then I change the code and let it take 3 arguments as stated in the api:
---static AtomicSymbol createSymbol(char token, java.lang.String name, 
Annotation annotation)

//make the "zero" Symbol with no annotation
AtomicSymbol zero =
AlphabetManager.createSymbol('c', "A", Annotation.EMPTY_ANNOTATION);

It won't compile, says:
Note: D:\projects\Normalization Normenclature of Peptide Ligand\Binary.java 
uses or overrides a deprecated API.
Note: Recompile with -deprecation for details.

No idea why is this, does this mean that the api currently on the web is not 
for the versiion of biojave I am using, if so, how can I get a copy of biojava 
that go with the current api at http://www.biojava.org/docs/api/?

Thanks!
Haibo





=========================================================
Haibo Zhang, PhD student
Computational Biology, NJIT & Rutgers University
Center for Applied Genomics, PHRI
http://afs13.njit.edu/~hz5

------------------------------

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End of Biojava-l Digest, Vol 4, Issue 14
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