jebl.evolution.io
Class FastaImporter
java.lang.Object
jebl.evolution.io.FastaImporter
- All Implemented Interfaces:
- ImmediateSequenceImporter, SequenceImporter
public class FastaImporter
- extends java.lang.Object
- implements SequenceImporter, ImmediateSequenceImporter
Class for importing Fasta sequential file format.
- Version:
- $Id: FastaImporter.java 857 2007-12-14 02:49:27Z twobeers $
- Author:
- Andrew Rambaut, Alexei Drummond, Joseph Heled
Field Summary |
static java.lang.String |
descriptionPropertyName
Name of Jebl sequence property which stores sequence description (i.e. |
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
descriptionPropertyName
public static final java.lang.String descriptionPropertyName
- Name of Jebl sequence property which stores sequence description (i.e. anything after sequence name in fasta
file), so this data is available and an export to fasta can preserves the original data.
This is stored some attribute of the sequence and of the taxon for backwards compatibility.
Generally, attributes on taxon should not be used, as they are unsafe
when dealing with objects that share the same taxon.
- See Also:
- Constant Field Values
FastaImporter
public FastaImporter(java.io.File file,
SequenceType sequenceType)
throws java.io.FileNotFoundException
- Use this constructor if you are reading from a file. The advantage over the
other constructor is that a) the input size is known, so read() can report
meaningful progress, and b) the file is closed at the end.
WARNING: You cannot reuse the FastaImporter thus constructed to import sequences
from the same file again.
- Parameters:
file
- sequenceType
-
- Throws:
java.io.FileNotFoundException
FastaImporter
public FastaImporter(java.io.Reader reader,
SequenceType sequenceType)
- This constuctor takes a reader.
AR notes - this constructor was depeciated with the explanation below. I
disagree that we can predict that we want to import from a file, and a
reader is more flexible (it may be from the network or the clipboard).
-- This constructor should normally never be needed because usually we
want to import from a file. Then, the constructor expecting a file
should be used.
- Parameters:
reader
- holds sequences datasequenceType
- pre specified sequences type. We should try and guess them some day.
setIllegalCharacterPolicy
public void setIllegalCharacterPolicy(IllegalCharacterPolicy newPolicy)
importSequences
public final java.util.List<Sequence> importSequences()
throws java.io.IOException,
ImportException
- Description copied from interface:
SequenceImporter
- importSequences.
- Specified by:
importSequences
in interface SequenceImporter
- Returns:
- sequences from file.
- Throws:
java.io.IOException
ImportException
importSequences
public void importSequences(ImmediateSequenceImporter.Callback callback,
ProgressListener progressListener)
throws java.io.IOException,
ImportException
- Specified by:
importSequences
in interface ImmediateSequenceImporter
- Throws:
java.io.IOException
ImportException
http://code.google.com/p/jebl2/