Package | Description |
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com.compomics.util.experiment.identification.protein_sequences |
Protein sequence handling related classes.
|
com.compomics.util.nucleotide |
Useful objects for modeling and handling nucleotides.
|
com.compomics.util.protein |
Classes concerning useful Objects and their operations for modeling and handling proteins.
|
Modifier and Type | Method and Description |
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Header |
SequenceFactory.getHeader(String accession)
Returns the desired header for the protein in the FASTA file.
|
Header |
SequenceFactory.HeaderIterator.getNext()
Returns the next header in the FASTA file.
|
Modifier and Type | Method and Description |
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Header |
NucleotideSequence.getHeader()
This method reports on the nucleotide header.
|
Modifier and Type | Method and Description |
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void |
NucleotideSequence.setHeader(Header aHeader)
This method sets the header.
|
Constructor and Description |
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NucleotideSequence(Header aHeader,
NucleotideSequenceImpl aSequence)
This constructor allows the passing of a Header, as well as an
AASequenceImpl for this Protein.
|
Modifier and Type | Method and Description |
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Header |
Protein.getHeader()
This method reports on the header for the current
protein.
|
static Header |
Header.parseFromFASTA(String aFASTAHeader)
Factory method that constructs a Header instance based on a FASTA header
line.
|
Modifier and Type | Method and Description |
---|---|
void |
Protein.setHeader(Header aHeader)
Simple setter for the header.
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Constructor and Description |
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Protein(Header aHeader,
AASequenceImpl aSequence)
This constructor allows the passing of a Header, as well as an
AASequenceImpl for this Protein.
|
Protein(Header aHeader,
AASequenceImpl aSequence,
boolean aTruncated,
int aTruncationPosition)
This constructor allows the passing of a Header, as well as an
AASequenceImpl for this Protein.
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