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java.lang.Objectorg.biojava.bio.seq.io.SeqAlignReadWrite
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
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 |
public static final int FASTADNA
public static final int FASTAPROTEIN
public static final int EMBL
public static final int GENBANK
public static final int SWISSPROT
public static final int GENPEPT
public static final int MSFDNA
public static final int FASTA
public static final int FASTAALIGN
public static final int MSFPROTEIN
Constructor Detail |
public SeqAlignReadWrite()
Method Detail |
public static int guessFileType(java.lang.String fileName) throws java.lang.Exception
java.lang.Exception
public static java.lang.Object fileToBiojava(int fileType, java.io.BufferedReader br) throws java.lang.Exception
java.lang.Exception
public static void biojavaToFile(int fileType, java.io.OutputStream os, java.lang.Object biojava) throws java.lang.Exception
java.lang.Exception
public static void main(java.lang.String[] args) throws java.lang.Exception
java.lang.Exception
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