public final class SequenceUtil
extends java.lang.Object
Modifier and Type | Field | 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]
|
Modifier and Type | Method | 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
|
public static final java.util.regex.Pattern WHITE_SPACE
public static final java.util.regex.Pattern DIGIT
public static final java.util.regex.Pattern NONWORD
public static final java.util.regex.Pattern AA
public static final java.util.regex.Pattern NON_AA
public static final java.util.regex.Pattern AMBIGUOUS_AA
public static final java.util.regex.Pattern NUCLEOTIDE
public static final java.util.regex.Pattern AMBIGUOUS_NUCLEOTIDE
public static final java.util.regex.Pattern NON_NUCLEOTIDE
public static boolean isNucleotideSequence(FastaSequence s)
public static boolean isNonAmbNucleotideSequence(java.lang.String sequence)
public static java.lang.String cleanSequence(java.lang.String sequence)
sequence
- public static java.lang.String deepCleanSequence(java.lang.String sequence)
sequence
- public static boolean isProteinSequence(java.lang.String sequence)
sequence
- public static boolean isAmbiguosProtein(java.lang.String sequence)
sequence
- public static void writeFasta(java.io.OutputStream outstream, java.util.List<FastaSequence> sequences, int width) throws java.io.IOException
outstream
- sequences
- width
- - the maximum number of characters to write in one linejava.io.IOException
public static java.util.List<FastaSequence> readFasta(java.io.InputStream inStream) throws java.io.IOException
inStream
- fromjava.io.IOException
public static void writeFasta(java.io.OutputStream os, java.util.List<FastaSequence> sequences) throws java.io.IOException
os
- sequences
- java.io.IOException