Package jebl.evolution.io
Class FastaImporter
java.lang.Object
jebl.evolution.io.FastaImporter
- All Implemented Interfaces:
ImmediateSequenceImporter
,SequenceImporter
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
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Nested Class Summary
Nested classes/interfaces inherited from interface jebl.evolution.io.ImmediateSequenceImporter
ImmediateSequenceImporter.Callback
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String
Name of Jebl sequence property which stores sequence description (i.e. -
Constructor Summary
ConstructorsConstructorDescriptionFastaImporter
(File file, SequenceType sequenceType) Use this constructor if you are reading from a file.FastaImporter
(Reader reader, SequenceType sequenceType) This constuctor takes a reader. -
Method Summary
Modifier and TypeMethodDescriptionimportSequences.void
importSequences
(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener) void
setIllegalCharacterPolicy
(IllegalCharacterPolicy newPolicy)
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Field Details
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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:
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Constructor Details
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FastaImporter
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:
FileNotFoundException
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FastaImporter
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.
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Method Details
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setIllegalCharacterPolicy
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importSequences
Description copied from interface:SequenceImporter
importSequences.- Specified by:
importSequences
in interfaceSequenceImporter
- Returns:
- sequences from file.
- Throws:
IOException
ImportException
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importSequences
public void importSequences(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener) throws IOException, ImportException - Specified by:
importSequences
in interfaceImmediateSequenceImporter
- Throws:
IOException
ImportException
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