public class IntermediateGroup extends Object
Constructor and Description |
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IntermediateGroup(int id)
Basic Constructor, sets all the maps to null and score to NaN.
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Modifier and Type | Method and Description |
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void |
addChild(IntermediateGroup child)
Adds a child to the set of children.
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void |
addParent(IntermediateGroup parent)
Adds a new group to the set of parents.
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void |
addPeptide(IntermediatePeptide peptide)
Adds a single peptide to the group.
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void |
addProtein(IntermediateProtein protein)
Adds a new protein to the map of proteins.
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boolean |
directlyConnectedToProtein(IntermediateProtein protein)
Returns true, if the group is directly connected to the dbSequence.
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boolean |
equals(Object obj) |
Set<IntermediateGroup> |
getAllChildren()
Getter for all children groups of this group, including children's
children and so on.
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Set<IntermediateGroup> |
getAllPeptideChildren()
Getter for all children groups of this group that have at least one
peptide, recursive, i.e.
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Set<IntermediatePeptide> |
getAllPeptides()
getter for all peptides, including all children's peptides.
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Set<IntermediateProtein> |
getAllProteins()
Getter for the intermediateProtein of this group and all the parents.
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Set<IntermediateGroup> |
getChildren()
Getter for the children set
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Integer |
getID()
Getter for the ID.
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Set<IntermediateGroup> |
getParents()
Getter for the parents.
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Set<IntermediatePeptide> |
getPeptides()
Getter for the peptides.
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Set<IntermediateProtein> |
getProteins()
Getter for the proteins.
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Integer |
getTreeID()
Getter for the group's treeID.
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int |
hashCode() |
void |
removeProtein(IntermediateProtein protein)
Removes the given dbSequence from the directly connected dbSequences
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void |
setID(Integer id)
Setter for the ID.
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void |
setPeptides(Collection<IntermediatePeptide> peptides)
Setter for the peptides.
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void |
setTreeID(Integer id)
Setter for the treeID.
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public IntermediateGroup(int id)
id
- public void setID(Integer id)
public Integer getID()
public void setTreeID(Integer id)
id
- public Integer getTreeID()
public void setPeptides(Collection<IntermediatePeptide> peptides)
peptides
- public void addPeptide(IntermediatePeptide peptide)
peptides
- public Set<IntermediatePeptide> getPeptides()
public Set<IntermediatePeptide> getAllPeptides()
public void addChild(IntermediateGroup child)
peptides
- public Set<IntermediateGroup> getChildren()
public Set<IntermediateGroup> getAllChildren()
public Set<IntermediateGroup> getAllPeptideChildren()
public void addParent(IntermediateGroup parent)
parent
- public Set<IntermediateGroup> getParents()
public void addProtein(IntermediateProtein protein)
If the map is not yet initialized, initialize it.
dbSeq
- public void removeProtein(IntermediateProtein protein)
dbSeq
- public Set<IntermediateProtein> getProteins()
public Set<IntermediateProtein> getAllProteins()
public boolean directlyConnectedToProtein(IntermediateProtein protein)
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