org.biojava.bio.seq.io
Class SeqAlignReadWrite

java.lang.Object
  extended byorg.biojava.bio.seq.io.SeqAlignReadWrite

public class SeqAlignReadWrite
extends java.lang.Object

Title: File2Biojava Description: This project will take in a file of any common bioinformatics file formats and convert it to the appropriate Biojava object. It will also convert the Biojava object back into the corresponding file format. Copyright: Copyright (c) 2002 Company: Maxygen

Version:
1.0
Author:
Nimesh Singh

Field Summary
static int EMBL
           
static int FASTA
           
static int FASTAALIGN
           
static int FASTADNA
           
static int FASTAPROTEIN
           
static int GENBANK
           
static int GENPEPT
           
static int MSFDNA
           
static int MSFPROTEIN
           
static int SWISSPROT
           
 
Constructor Summary
SeqAlignReadWrite()
           
 
Method Summary
static void biojavaToFile(int fileType, java.io.OutputStream os, java.lang.Object biojava)
          Converts a Biojava object to the given filetype.
static java.lang.Object fileToBiojava(int fileType, java.io.BufferedReader br)
          Reads a file and returns the corresponding Biojava object.
static int guessFileType(java.lang.String fileName)
          Attempts to guess the filetype of a file given the name
static void main(java.lang.String[] args)
          Just for testing purposes.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

FASTADNA

public static final int FASTADNA
See Also:
Constant Field Values

FASTAPROTEIN

public static final int FASTAPROTEIN
See Also:
Constant Field Values

EMBL

public static final int EMBL
See Also:
Constant Field Values

GENBANK

public static final int GENBANK
See Also:
Constant Field Values

SWISSPROT

public static final int SWISSPROT
See Also:
Constant Field Values

GENPEPT

public static final int GENPEPT
See Also:
Constant Field Values

MSFDNA

public static final int MSFDNA
See Also:
Constant Field Values

FASTA

public static final int FASTA
See Also:
Constant Field Values

FASTAALIGN

public static final int FASTAALIGN
See Also:
Constant Field Values

MSFPROTEIN

public static final int MSFPROTEIN
See Also:
Constant Field Values
Constructor Detail

SeqAlignReadWrite

public SeqAlignReadWrite()
Method Detail

guessFileType

public static int guessFileType(java.lang.String fileName)
                         throws java.lang.Exception
Attempts to guess the filetype of a file given the name

Throws:
java.lang.Exception

fileToBiojava

public static java.lang.Object fileToBiojava(int fileType,
                                             java.io.BufferedReader br)
                                      throws java.lang.Exception
Reads a file and returns the corresponding Biojava object.

Throws:
java.lang.Exception

biojavaToFile

public static void biojavaToFile(int fileType,
                                 java.io.OutputStream os,
                                 java.lang.Object biojava)
                          throws java.lang.Exception
Converts a Biojava object to the given filetype.

Throws:
java.lang.Exception

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception
Just for testing purposes.

Throws:
java.lang.Exception