Package org.biojava.nbio.data.sequence
Class SequenceUtil
- java.lang.Object
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- org.biojava.nbio.data.sequence.SequenceUtil
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public final class SequenceUtil extends Object
Utility class for operations on sequences- Since:
- 3.0.2
- Version:
- 1.0
- Author:
- Peter Troshin
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Field Summary
Fields Modifier and Type Field Description static Pattern
AA
Valid Amino acidsstatic Pattern
AMBIGUOUS_AA
Same as AA pattern but with one additional letters - Xstatic Pattern
AMBIGUOUS_NUCLEOTIDE
Ambiguous nucleotidestatic Pattern
DIGIT
A digitstatic Pattern
NON_AA
inversion of AA patternstatic Pattern
NON_NUCLEOTIDE
Non nucleotidestatic Pattern
NONWORD
Non wordstatic Pattern
NUCLEOTIDE
Nucleotides a, t, g, c, ustatic Pattern
WHITE_SPACE
A whitespace character: [\t\n\x0B\f\r]
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static String
cleanSequence(String sequence)
Removes all whitespace chars in the sequence stringstatic String
deepCleanSequence(String sequence)
Removes all special characters and digits as well as whitespace chars from the sequencestatic boolean
isAmbiguosProtein(String sequence)
Check whether the sequence confirms to amboguous protein sequencestatic boolean
isNonAmbNucleotideSequence(String sequence)
Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one (!)static boolean
isNucleotideSequence(FastaSequence s)
static boolean
isProteinSequence(String sequence)
static List<FastaSequence>
readFasta(InputStream inStream)
Reads fasta sequences from inStream into the list of FastaSequence objectsstatic void
writeFasta(OutputStream os, List<FastaSequence> sequences)
Writes FastaSequence in the file, each sequence will take one line onlystatic void
writeFasta(OutputStream outstream, List<FastaSequence> sequences, int width)
Writes list of FastaSequeces into the outstream formatting the sequence so that it contains width chars on each line
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Field Detail
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WHITE_SPACE
public static final Pattern WHITE_SPACE
A whitespace character: [\t\n\x0B\f\r]
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AMBIGUOUS_AA
public static final Pattern AMBIGUOUS_AA
Same as AA pattern but with one additional letters - X
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NUCLEOTIDE
public static final Pattern NUCLEOTIDE
Nucleotides a, t, g, c, u
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AMBIGUOUS_NUCLEOTIDE
public static final Pattern AMBIGUOUS_NUCLEOTIDE
Ambiguous nucleotide
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NON_NUCLEOTIDE
public static final Pattern NON_NUCLEOTIDE
Non nucleotide
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Method Detail
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isNucleotideSequence
public static boolean isNucleotideSequence(FastaSequence s)
- Returns:
- true is the sequence contains only letters a,c, t, g, u
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isNonAmbNucleotideSequence
public static boolean isNonAmbNucleotideSequence(String sequence)
Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one (!) - B char
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cleanSequence
public static String cleanSequence(String sequence)
Removes all whitespace chars in the sequence string- Parameters:
sequence
-- Returns:
- cleaned up sequence
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deepCleanSequence
public static String deepCleanSequence(String sequence)
Removes all special characters and digits as well as whitespace chars from the sequence- Parameters:
sequence
-- Returns:
- cleaned up sequence
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isProteinSequence
public static boolean isProteinSequence(String sequence)
- Parameters:
sequence
-- Returns:
- true is the sequence is a protein sequence, false overwise
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isAmbiguosProtein
public static boolean isAmbiguosProtein(String sequence)
Check whether the sequence confirms to amboguous protein sequence- Parameters:
sequence
-- Returns:
- return true only if the sequence if ambiguous protein sequence Return false otherwise. e.g. if the sequence is non-ambiguous protein or DNA
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writeFasta
public static void writeFasta(OutputStream outstream, List<FastaSequence> sequences, int width) throws IOException
Writes list of FastaSequeces into the outstream formatting the sequence so that it contains width chars on each line- Parameters:
outstream
-sequences
-width
- - the maximum number of characters to write in one line- Throws:
IOException
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readFasta
public static List<FastaSequence> readFasta(InputStream inStream) throws IOException
Reads fasta sequences from inStream into the list of FastaSequence objects- Parameters:
inStream
- from- Returns:
- list of FastaSequence objects
- Throws:
IOException
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writeFasta
public static void writeFasta(OutputStream os, List<FastaSequence> sequences) throws IOException
Writes FastaSequence in the file, each sequence will take one line only- Parameters:
os
-sequences
-- Throws:
IOException
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