Package org.biojava.nbio.data.sequence
Class FastaSequence
- java.lang.Object
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- org.biojava.nbio.data.sequence.FastaSequence
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- All Implemented Interfaces:
Comparable<FastaSequence>
public final class FastaSequence extends Object implements Comparable<FastaSequence>
A FASTA formatted sequence. Please note that this class does not make any assumptions as to what sequence it store e.g. it could be nucleotide, protein or even gapped alignment sequence! The only guarantee it makes is that the sequence does not contain white space characters e.g. spaces, new lines etc- Since:
- 3.0.2
- Version:
- 1.0
- Author:
- pvtroshin
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Constructor Summary
Constructors Constructor Description FastaSequence(String id, String sequence)
Upon construction the any whitespace characters are removed from the sequence
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description int
compareTo(FastaSequence o)
static int
countMatchesInSequence(String theString, String theRegExp)
boolean
equals(Object obj)
String
getFormatedSequence(int width)
Format sequence per width letter in one string.String
getFormattedFasta()
String
getId()
Gets the value of idint
getLength()
String
getOnelineFasta()
String
getSequence()
Gets the value of sequenceint
hashCode()
String
toString()
Same as oneLineFasta
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Constructor Detail
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FastaSequence
public FastaSequence(String id, String sequence)
Upon construction the any whitespace characters are removed from the sequence- Parameters:
id
-sequence
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Method Detail
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getSequence
public String getSequence()
Gets the value of sequence- Returns:
- the value of sequence
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countMatchesInSequence
public static int countMatchesInSequence(String theString, String theRegExp)
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getFormattedFasta
public String getFormattedFasta()
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getOnelineFasta
public String getOnelineFasta()
- Returns:
- one line name, next line sequence, no matter what the sequence length is
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getFormatedSequence
public String getFormatedSequence(int width)
Format sequence per width letter in one string. Without spaces.- Returns:
- multiple line formated sequence, one line width letters length
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getLength
public int getLength()
- Returns:
- sequence length
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compareTo
public int compareTo(FastaSequence o)
- Specified by:
compareTo
in interfaceComparable<FastaSequence>
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