Constructor and Description |
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AminoAcidSequence()
Default constructor, this will make a empty Peptide object
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AminoAcidSequence(AminoAcid... residues)
Constructor to ake a Peptide object with specified amino acids.
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Modifier and Type | Method and Description |
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void |
addAminoAcid(AminoAcid residue)
Add a new amino acid to the end of the Peptide.
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void |
addAminoAcids(Collection<AminoAcid> residues)
Add a collection of amino acids to the end of the Peptide.
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boolean |
equals(Object o) |
AminoAcid |
getAminoAcid(int index)
Returns the amino acid with specified index
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List<AminoAcid> |
getAminoAcids()
Returns a new list of amino acids
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double |
getAvgMass()
Get the sum of average mass.
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int |
getLength()
Return the length of the peptide.
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double |
getMonoMass()
Get the sum of monoisotopic mass.
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int |
getNumberOfAminoAcids()
Return the number of amino acids
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String |
getOneLetterCodeString()
Get the string of peptide in one letter format.
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String |
getThreeLetterCodeString()
Get the string of peptide in three letter format.
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int |
hashCode() |
void |
remove(int index)
Remove amino acid at the index.
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void |
removeAll()
Remove all amino acid
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String |
toString()
This method calls getOneLetterCodeString()
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public AminoAcidSequence()
public AminoAcidSequence(AminoAcid... residues)
residues
- a list of amino acidspublic List<AminoAcid> getAminoAcids()
public AminoAcid getAminoAcid(int index)
index
- index is zero based.public int getNumberOfAminoAcids()
public void addAminoAcid(AminoAcid residue)
residue
- amino acidpublic void addAminoAcids(Collection<AminoAcid> residues)
residues
- a collection of amino acidspublic void removeAll()
public void remove(int index)
index
- index of the amino acidpublic double getAvgMass()
getAvgMass
in interface Mass
public double getMonoMass()
getMonoMass
in interface Mass
public int getLength()
public String getThreeLetterCodeString()
public String getOneLetterCodeString()
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