SequenceUtil

java.lang.Object
- org.biojava.nbio.data.sequence.SequenceUtil

```
public final class SequenceUtil
extends java.lang.Object
```
Utility class for operations on sequences

Since:

3.0.2

Version:

1.0

Author:

Peter Troshin

Field Summary

Fields
Modifier and Type	Field and Description
`static java.util.regex.Pattern`	`AA` Valid Amino acids
`static java.util.regex.Pattern`	`AMBIGUOUS_AA` Same as AA pattern but with two additional letters - XU
`static java.util.regex.Pattern`	`AMBIGUOUS_NUCLEOTIDE` Ambiguous nucleotide
`static java.util.regex.Pattern`	`DIGIT` A digit
`static java.util.regex.Pattern`	`NON_AA` inversion of AA pattern
`static java.util.regex.Pattern`	`NON_NUCLEOTIDE` Non nucleotide
`static java.util.regex.Pattern`	`NONWORD` Non word
`static java.util.regex.Pattern`	`NUCLEOTIDE` Nucleotides a, t, g, c, u
`static java.util.regex.Pattern`	`WHITE_SPACE` A whitespace character: [\t\n\x0B\f\r]

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static java.lang.String`	`cleanSequence(java.lang.String sequence)` Removes all whitespace chars in the sequence string
`static java.lang.String`	`deepCleanSequence(java.lang.String sequence)` Removes all special characters and digits as well as whitespace chars from the sequence
`static boolean`	`isAmbiguosProtein(java.lang.String sequence)` Check whether the sequence confirms to amboguous protein sequence
`static boolean`	`isNonAmbNucleotideSequence(java.lang.String sequence)` Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one (!) - B char
`static boolean`	`isNucleotideSequence(FastaSequence s)`
`static boolean`	`isProteinSequence(java.lang.String sequence)`
`static java.util.List<FastaSequence>`	`readFasta(java.io.InputStream inStream)` Reads fasta sequences from inStream into the list of FastaSequence objects
`static void`	`writeFasta(java.io.OutputStream os, java.util.List<FastaSequence> sequences)` Writes FastaSequence in the file, each sequence will take one line only
`static void`	`writeFasta(java.io.OutputStream outstream, java.util.List<FastaSequence> sequences, int width)` Writes list of FastaSequeces into the outstream formatting the sequence so that it contains width chars on each line

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - WHITE_SPACE
```
public static final java.util.regex.Pattern WHITE_SPACE
```
    A whitespace character: [\t\n\x0B\f\r]
  - DIGIT
```
public static final java.util.regex.Pattern DIGIT
```
    A digit
  - NONWORD
```
public static final java.util.regex.Pattern NONWORD
```
    Non word
  - AA
```
public static final java.util.regex.Pattern AA
```
    Valid Amino acids
  - NON_AA
```
public static final java.util.regex.Pattern NON_AA
```
    inversion of AA pattern
  - AMBIGUOUS_AA
```
public static final java.util.regex.Pattern AMBIGUOUS_AA
```
    Same as AA pattern but with two additional letters - XU
  - NUCLEOTIDE
```
public static final java.util.regex.Pattern NUCLEOTIDE
```
    Nucleotides a, t, g, c, u
  - AMBIGUOUS_NUCLEOTIDE
```
public static final java.util.regex.Pattern AMBIGUOUS_NUCLEOTIDE
```
    Ambiguous nucleotide
  - NON_NUCLEOTIDE
```
public static final java.util.regex.Pattern NON_NUCLEOTIDE
```
    Non nucleotide
- Method Detail
  - isNucleotideSequence
```
public static boolean isNucleotideSequence(FastaSequence s)
```
    Returns:
    
    true is the sequence contains only letters a,c, t, g, u
  - isNonAmbNucleotideSequence
```
public static boolean isNonAmbNucleotideSequence(java.lang.String sequence)
```
    Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one (!) - B char
  - cleanSequence
```
public static java.lang.String cleanSequence(java.lang.String sequence)
```
    Removes all whitespace chars in the sequence string
    
    Parameters:
    
    sequence -
    
    Returns:
    
    cleaned up sequence
  - deepCleanSequence
```
public static java.lang.String deepCleanSequence(java.lang.String sequence)
```
    Removes all special characters and digits as well as whitespace chars from the sequence
    
    Parameters:
    
    sequence -
    
    Returns:
    
    cleaned up sequence
  - isProteinSequence
```
public static boolean isProteinSequence(java.lang.String sequence)
```
    Parameters:
    
    sequence -
    
    Returns:
    
    true is the sequence is a protein sequence, false overwise
  - isAmbiguosProtein
```
public static boolean isAmbiguosProtein(java.lang.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
  - writeFasta
```
public static void writeFasta(java.io.OutputStream outstream,
                              java.util.List<FastaSequence> sequences,
                              int width)
                       throws java.io.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:
    
    java.io.IOException
  - readFasta
```
public static java.util.List<FastaSequence> readFasta(java.io.InputStream inStream)
                                               throws java.io.IOException
```
    Reads fasta sequences from inStream into the list of FastaSequence objects
    
    Parameters:
    
    inStream - from
    
    Returns:
    
    list of FastaSequence objects
    
    Throws:
    
    java.io.IOException
  - writeFasta
```
public static void writeFasta(java.io.OutputStream os,
                              java.util.List<FastaSequence> sequences)
                       throws java.io.IOException
```
    Writes FastaSequence in the file, each sequence will take one line only
    
    Parameters:
    
    os -
    
    sequences -
    
    Throws:
    
    java.io.IOException

Class SequenceUtil

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

WHITE_SPACE

DIGIT

NONWORD

AA

NON_AA

AMBIGUOUS_AA

NUCLEOTIDE

AMBIGUOUS_NUCLEOTIDE

NON_NUCLEOTIDE

Method Detail

isNucleotideSequence

isNonAmbNucleotideSequence

cleanSequence

deepCleanSequence

isProteinSequence

isAmbiguosProtein

writeFasta

readFasta

writeFasta