compbio.data.sequence
Class ClustalAlignmentUtil

java.lang.Object
  compbio.data.sequence.ClustalAlignmentUtil

public final class ClustalAlignmentUtil
extends java.lang.Object

Tools to read and write clustal formated files

Version:

1.0 September 2009

Author:

Petr Troshin based on jimp class

Field Summary

static char

gapchar Dash char to be used as gap char in the alignments

Constructor Summary

ClustalAlignmentUtil()

Method Summary

static boolean	isValidClustalFile(java.io.InputStream input) Please note this method closes the input stream provided as a parameter
static Alignment	readClustalFile(java.io.File file)
static Alignment	readClustalFile(java.io.InputStream instream) Read Clustal formatted alignment.
static void	writeClustalAlignment(java.io.Writer out, Alignment alignment) Write Clustal formatted alignment Limitations: does not record the consensus.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

gapchar

public static final char gapchar

Dash char to be used as gap char in the alignments

See Also:

Constant Field Values

Constructor Detail

ClustalAlignmentUtil

public ClustalAlignmentUtil()

Method Detail

readClustalFile

public static Alignment readClustalFile(java.io.InputStream instream)
                                 throws java.io.IOException,
                                        UnknownFileFormatException

Read Clustal formatted alignment. Limitations: Does not read consensus Sequence names as well as the sequences are not guaranteed to be unique!

Throws:

{@link - IOException}

{@link - UnknownFileFormatException}

java.io.IOException

UnknownFileFormatException

isValidClustalFile

public static boolean isValidClustalFile(java.io.InputStream input)

Please note this method closes the input stream provided as a parameter

Parameters:

input -

Returns:

true if the file is recognised as Clustal formatted alignment, false otherwise

writeClustalAlignment

public static void writeClustalAlignment(java.io.Writer out,
                                         Alignment alignment)
                                  throws java.io.IOException

Write Clustal formatted alignment Limitations: does not record the consensus. Potential bug - records 60 chars length alignment where Clustal would have recorded 50 chars.

Parameters:

out -

alignment -

Throws:

java.io.IOException

readClustalFile

public static Alignment readClustalFile(java.io.File file)
                                 throws UnknownFileFormatException,
                                        java.io.IOException

Throws:

UnknownFileFormatException

java.io.IOException