Package jebl.evolution.io
Class FastaImporter
- java.lang.Object
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- jebl.evolution.io.FastaImporter
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from interface jebl.evolution.io.ImmediateSequenceImporter
ImmediateSequenceImporter.Callback
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
descriptionPropertyName
Name of Jebl sequence property which stores sequence description (i.e.
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Constructor Summary
Constructors Constructor 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.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.List<Sequence>
importSequences()
importSequences.void
importSequences(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener)
void
setIllegalCharacterPolicy(IllegalCharacterPolicy newPolicy)
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Field Detail
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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
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Constructor Detail
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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
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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.
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Method Detail
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setIllegalCharacterPolicy
public void setIllegalCharacterPolicy(IllegalCharacterPolicy newPolicy)
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importSequences
public final java.util.List<Sequence> importSequences() throws java.io.IOException, ImportException
Description copied from interface:SequenceImporter
importSequences.- Specified by:
importSequences
in interfaceSequenceImporter
- Returns:
- sequences from file.
- Throws:
java.io.IOException
ImportException
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importSequences
public void importSequences(ImmediateSequenceImporter.Callback callback, ProgressListener progressListener) throws java.io.IOException, ImportException
- Specified by:
importSequences
in interfaceImmediateSequenceImporter
- Throws:
java.io.IOException
ImportException
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