Package ubic.gemma.core.analysis.sequence

Class SequenceWriter

java.lang.Object

ubic.gemma.core.analysis.sequence.SequenceWriter

public class SequenceWriter
extends Object

Tools for writing biosequences to files so they can be analyzed by external tools, and then read back into Gemma.

Author:

paul

Field Summary

Fields

Modifier and Type	Field	Description
static final String	SPACE_REPLACEMENT	Spaces in the sequence name will cause problems when converting back from some formats (e.g.

Constructor Summary

Constructors

Constructor	Description
SequenceWriter()

Method Summary

Modifier and Type	Method	Description
static String	getIdentifier(BioSequence b)	Modify the identifier for the purposes of using in temporary Fasta files.
static int	writeSequencesToFile(Collection<BioSequence> sequences, File outputFile)	Write a collection of sequences in FASTA format

Methods inherited from class java.lang.Object

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

Field Details

SPACE_REPLACEMENT

public static final String SPACE_REPLACEMENT

Spaces in the sequence name will cause problems when converting back from some formats (e.g. PSL), so they are replaced.

See Also:

• Constant Field Values

Constructor Details

SequenceWriter

public SequenceWriter()

Method Details

writeSequencesToFile

public static int writeSequencesToFile(Collection<BioSequence> sequences,
 File outputFile)
                                throws IOException

Write a collection of sequences in FASTA format

Parameters:

sequences - sequences

outputFile - file

Returns:

number of sequences written, excluding blanks and duplicates.

Throws:

IOException - io problems

getIdentifier

public static String getIdentifier(BioSequence b)

Modify the identifier for the purposes of using in temporary Fasta files. WARNING There is a faint possibility that this could cause problems in identifying the sequences later.

Parameters:

b - b

Returns:

string