public class Peptide extends Object
Constructor and Description |
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Peptide(List<AminoAcid> acidList)
Create a peptide without PTM.
|
Peptide(List<AminoAcid> acidList,
Group n_terminal,
Group c_terminal)
Create a peptide without PTM.
|
Peptide(List<AminoAcid> acidList,
Group n_terminal,
Group c_terminal,
Map<Integer,PTModification> ptm)
Create a peptide with PTM.
|
Peptide(List<AminoAcid> acidList,
Map<Integer,PTModification> ptm)
Create a peptide with PTM.
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Peptide(String sequence)
Create a peptide without PTM.
|
Peptide(String sequence,
Group n_terminal,
Group c_terminal)
Create a peptide without PTM.
|
Peptide(String sequence,
Group n_terminal,
Group c_terminal,
Map<Integer,PTModification> ptm)
Create a peptide with PTM.
|
Peptide(String sequence,
Map<Integer,PTModification> ptm)
Create a peptide with PTM.
|
Modifier and Type | Method and Description |
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boolean |
addALLModification(Map<Integer,PTModification> modifications)
If patch add modifications, we will rollback to the point of before patch add.
|
boolean |
addModification(Integer position,
PTModification modification)
Add a modification into peptide.
|
void |
clearModifications() |
boolean |
equals(Object o) |
List<AminoAcid> |
getAminoAcids() |
Group |
getCTerminalGroup() |
int |
getLength() |
Group |
getNTerminalGroup() |
Map<Integer,PTModification> |
getPTM() |
String |
getSequence() |
int |
hashCode() |
void |
removeModification(int location) |
void |
removeModification(PTModification modification) |
String |
toString() |
public Peptide(String sequence)
sequence
- can not set null or space string. System will translate sequence into a list of
AminoAcid
. If can not recognize the amino acid character, system will throw
IllegalArgumentException.public Peptide(String sequence, Group n_terminal, Group c_terminal)
sequence
- can not set null or space string. System will translate sequence into a list of
AminoAcid
. If can not recognize the amino acid character, system will throw
IllegalArgumentException.n_terminal
- can set null, if peptide have no N terminal.c_terminal
- can set null, if peptide have no C terminal.public Peptide(String sequence, Map<Integer,PTModification> ptm)
sequence
- can not set null or space string. System will translate sequence into a list of
AminoAcid
. If can not recognize the amino acid character, system will throw
IllegalArgumentException.ptm
- can set null, if no PTM on the peptide. Otherwise,
system call addALLModification(java.util.Map)
method to put ptm.public Peptide(String sequence, Group n_terminal, Group c_terminal, Map<Integer,PTModification> ptm)
sequence
- can not set null or space string. System will translate sequence into a list of
AminoAcid
. If can not recognize the amino acid character, system will throw
IllegalArgumentException.n_terminal
- can set null, if peptide have no N terminal.c_terminal
- can set null, if peptide have no C terminal.ptm
- can set null, if no PTM on the peptide. Otherwise,
system call addALLModification(java.util.Map)
method to put ptm.public Peptide(List<AminoAcid> acidList)
acidList
- amino acid list. Can not set null or empty list.public Peptide(List<AminoAcid> acidList, Group n_terminal, Group c_terminal)
acidList
- amino acid list. Can not set null or empty list.n_terminal
- can set null, if peptide have no N terminal.c_terminal
- can set null, if peptide have no C terminal.public Peptide(List<AminoAcid> acidList, Map<Integer,PTModification> ptm)
acidList
- amino acid list. Can not set null or empty list.ptm
- can set null, if no PTM on the peptide. Otherwise,
system call addALLModification(java.util.Map)
method to put ptm.public Peptide(List<AminoAcid> acidList, Group n_terminal, Group c_terminal, Map<Integer,PTModification> ptm)
acidList
- amino acid list. Can not set null or empty list.n_terminal
- can set null, if peptide have no N terminal.c_terminal
- can set null, if peptide have no C terminal.ptm
- can set null, if no PTM on the peptide. Otherwise,
system call addALLModification(java.util.Map)
method to put ptm.public boolean addModification(Integer position, PTModification modification)
position
- value [0..peptide.length-1]. If overflow, return false.modification
- if null, return false.public boolean addALLModification(Map<Integer,PTModification> modifications)
public void removeModification(int location)
public void removeModification(PTModification modification)
public void clearModifications()
public String getSequence()
public Group getNTerminalGroup()
public Group getCTerminalGroup()
public int getLength()
public Map<Integer,PTModification> getPTM()
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.