Package org.forester.io.parsers
Class FastaParser
- java.lang.Object
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- org.forester.io.parsers.FastaParser
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public class FastaParser extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description static java.util.regex.Pattern
FASTA_DESC_LINE
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Constructor Summary
Constructors Constructor Description FastaParser()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static boolean
isLikelyFasta(java.io.File f)
static boolean
isLikelyFasta(java.io.InputStream is)
static void
main(java.lang.String[] args)
static java.util.List<MolecularSequence>
parse(java.io.File f)
static java.util.List<MolecularSequence>
parse(java.io.InputStream is)
static Msa
parseMsa(byte[] bytes)
static Msa
parseMsa(java.io.File f)
static Msa
parseMsa(java.io.InputStream is)
static Msa
parseMsa(java.lang.String s)
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Method Detail
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main
public static void main(java.lang.String[] args)
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isLikelyFasta
public static boolean isLikelyFasta(java.io.File f) throws java.io.IOException
- Throws:
java.io.IOException
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isLikelyFasta
public static boolean isLikelyFasta(java.io.InputStream is) throws java.io.IOException
- Throws:
java.io.IOException
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parseMsa
public static Msa parseMsa(java.io.File f) throws java.io.IOException
- Throws:
java.io.IOException
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parseMsa
public static Msa parseMsa(java.io.InputStream is) throws java.io.IOException
- Throws:
java.io.IOException
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parseMsa
public static Msa parseMsa(java.lang.String s) throws java.io.IOException
- Throws:
java.io.IOException
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parseMsa
public static Msa parseMsa(byte[] bytes) throws java.io.IOException
- Throws:
java.io.IOException
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parse
public static java.util.List<MolecularSequence> parse(java.io.File f) throws java.io.IOException
- Throws:
java.io.IOException
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parse
public static java.util.List<MolecularSequence> parse(java.io.InputStream is) throws java.io.IOException
- Throws:
java.io.IOException
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