public class FastaImporter extends java.lang.Object implements SequenceImporter, ImmediateSequenceImporter
ImmediateSequenceImporter.Callback
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
descriptionPropertyName
Name of Jebl sequence property which stores sequence description (i.e.
|
Constructor and Description |
---|
FastaImporter(java.io.File file,
SequenceType sequenceType)
Use this constructor if you are reading from a file.
|
FastaImporter(java.io.Reader reader,
SequenceType sequenceType)
This constuctor takes a reader.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<Sequence> |
importSequences()
importSequences.
|
void |
importSequences(ImmediateSequenceImporter.Callback callback,
ProgressListener progressListener) |
void |
setIllegalCharacterPolicy(IllegalCharacterPolicy newPolicy) |
public static final java.lang.String descriptionPropertyName
public FastaImporter(java.io.File file, SequenceType sequenceType) throws java.io.FileNotFoundException
file
- sequenceType
- java.io.FileNotFoundException
public FastaImporter(java.io.Reader reader, SequenceType sequenceType)
reader
- holds sequences datasequenceType
- pre specified sequences type. We should try and guess them some day.public void setIllegalCharacterPolicy(IllegalCharacterPolicy newPolicy)
public final java.util.List<Sequence> importSequences() throws java.io.IOException, ImportException
SequenceImporter
importSequences
in interface SequenceImporter
java.io.IOException
ImportException
public void importSequences(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener) throws java.io.IOException, ImportException
importSequences
in interface ImmediateSequenceImporter
java.io.IOException
ImportException
http://code.google.com/p/jebl2/