edu.upenn.gloDB.io
Interface SequenceFile

All Superinterfaces:
DataFile
All Known Implementing Classes:
FASTASequence

public interface SequenceFile
extends DataFile

Interface for files that contain Sequences (ie. FASTA).

Version:
$Id: SequenceFile.java,v 1.1.2.5 2005/01/07 19:56:59 fisher Exp $

Method Summary
 Sequence load(java.lang.String filename)
          Load the first sequence in the data file and return the resulting Sequence object.
 Sequence load(java.lang.String filename, java.lang.String id)
          Load the first sequence in the data file and return the resulting Sequence object.
 Sequence load(java.lang.String filename, java.lang.String id, FASTAParser parser)
          Load the first Sequence in the data file and return the resulting Sequence object.
 java.util.HashSet loadAll(java.lang.String filename)
          Load all Sequences in the data file and return a HashSet containing the resulting Sequence objects.
 java.util.HashSet loadAll(java.lang.String filename, FASTAParser parser)
          Load all Sequences in the data file and return a HashSet containing the resulting Sequence objects.
 void save(java.lang.String id)
          Save the Sequence object to a file based on it's ID.
 void save(java.lang.String id, java.lang.String filename, boolean overwrite)
          Save the Sequence object data.
 
Methods inherited from interface edu.upenn.gloDB.io.DataFile
getDesc, getExt, getFileFilter, getID
 

Method Detail

load

Sequence load(java.lang.String filename)
Load the first sequence in the data file and return the resulting Sequence object.


load

Sequence load(java.lang.String filename,
              java.lang.String id)
Load the first sequence in the data file and return the resulting Sequence object.


load

Sequence load(java.lang.String filename,
              java.lang.String id,
              FASTAParser parser)
Load the first Sequence in the data file and return the resulting Sequence object.


loadAll

java.util.HashSet loadAll(java.lang.String filename)
Load all Sequences in the data file and return a HashSet containing the resulting Sequence objects.


loadAll

java.util.HashSet loadAll(java.lang.String filename,
                          FASTAParser parser)
Load all Sequences in the data file and return a HashSet containing the resulting Sequence objects.


save

void save(java.lang.String id)
Save the Sequence object to a file based on it's ID. This should use the ID as the filename and set the overwrite flag to 'true'.


save

void save(java.lang.String id,
          java.lang.String filename,
          boolean overwrite)
Save the Sequence object data.




Copyright 2012 Stephen Fisher and Junhyong Kim, University of Pennsylvania. All Rights Reserved.