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java.lang.Objectcompbio.data.sequence.FastaSequence
@Immutable public class FastaSequence
A FASTA formatted sequence. Please note that this class does not make any assumptions as to what sequence it stores 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
Constructor Summary | |
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FastaSequence(java.lang.String id,
java.lang.String sequence)
Upon construction the any whitespace characters are removed from the sequence |
Method Summary | |
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static int |
countMatchesInSequence(java.lang.String theString,
java.lang.String theRegExp)
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boolean |
equals(java.lang.Object obj)
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java.lang.String |
getFormatedSequence(int width)
Format sequence per width letter in one string. |
java.lang.String |
getFormattedFasta()
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java.lang.String |
getId()
Gets the value of id |
int |
getLength()
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java.lang.String |
getOnelineFasta()
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java.lang.String |
getSequence()
Gets the value of sequence |
int |
hashCode()
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java.lang.String |
toString()
Same as oneLineFasta |
Methods inherited from class java.lang.Object |
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getClass, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public FastaSequence(java.lang.String id, java.lang.String sequence)
id
- sequence
- Method Detail |
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public java.lang.String getId()
public java.lang.String getSequence()
public static int countMatchesInSequence(java.lang.String theString, java.lang.String theRegExp)
public java.lang.String getFormattedFasta()
public java.lang.String getOnelineFasta()
public java.lang.String getFormatedSequence(int width)
public int getLength()
public java.lang.String toString()
toString
in class java.lang.Object
public int hashCode()
hashCode
in class java.lang.Object
public boolean equals(java.lang.Object obj)
equals
in class java.lang.Object
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