[Biojava-l] biojava API - is it current?

[Schreiber, Mark]

Hi Haibo -
 
Unfortunately the API docs on the webpage have become seriously out of date. I think Thomas is going to fix this but he may have gotten busy :)
 
- Mark
 

	-----Original Message----- 
	From: hz5 at njit.edu [mailto:hz5 at njit.edu] 
	Sent: Sat 19/04/2003 3:48 a.m. 
	To: biojava-l at biojava.org 
	Cc: 
	Subject: [Biojava-l] biojava API - is it current?
	
	

	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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