Package org.forester.protein
Class BasicProtein
- java.lang.Object
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- org.forester.protein.BasicProtein
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Field Summary
Fields Modifier and Type Field Description static java.util.Comparator<Domain>
DomainMidPositionComparator
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Constructor Summary
Constructors Constructor Description BasicProtein(java.lang.String id_str, java.lang.String species_str, int length)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addProteinDomain(Domain protein_domain)
boolean
contains(java.util.List<java.lang.String> query_domain_ids, boolean in_nc_order)
If in_nc_order is set to true, this should return true only and only if the order in List 'domains' and this protein (as determined by the start positions of the domains of this proteins, _not_ by their index) are the same (interspersing, 'other', domains in this are ignored).java.lang.String
getAccession()
java.lang.String
getDescription()
java.util.List<Domain>
getDomainsSortedByPosition()
int
getLength()
java.lang.String
getName()
int
getNumberOfProteinDomains()
Domain
getProteinDomain(int index)
int
getProteinDomainCount(java.lang.String domain_id)
java.util.List<Domain>
getProteinDomains()
java.util.List<Domain>
getProteinDomains(java.lang.String domain_id)
ProteinId
getProteinId()
Species
getSpecies()
void
setAccession(java.lang.String accession)
void
setDescription(java.lang.String description)
void
setName(java.lang.String name)
java.lang.String
toDomainArchitectureString(java.lang.String separator)
java.lang.String
toDomainArchitectureString(java.lang.String separator, int repeats_limit, java.lang.String repeat_separator)
java.lang.String
toString()
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Field Detail
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DomainMidPositionComparator
public static java.util.Comparator<Domain> DomainMidPositionComparator
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Method Detail
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addProteinDomain
public void addProteinDomain(Domain protein_domain)
- Specified by:
addProteinDomain
in interfaceProtein
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contains
public boolean contains(java.util.List<java.lang.String> query_domain_ids, boolean in_nc_order)
Description copied from interface:Protein
If in_nc_order is set to true, this should return true only and only if the order in List 'domains' and this protein (as determined by the start positions of the domains of this proteins, _not_ by their index) are the same (interspersing, 'other', domains in this are ignored). If in_nc_order is set to false, this should return true only and only if this contains all domains listed in 'domains' (order and count do not matter).
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getAccession
public java.lang.String getAccession()
- Specified by:
getAccession
in interfaceProtein
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getDescription
public java.lang.String getDescription()
- Specified by:
getDescription
in interfaceProtein
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getDomainsSortedByPosition
public java.util.List<Domain> getDomainsSortedByPosition()
- Specified by:
getDomainsSortedByPosition
in interfaceProtein
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getNumberOfProteinDomains
public int getNumberOfProteinDomains()
- Specified by:
getNumberOfProteinDomains
in interfaceProtein
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getProteinDomain
public Domain getProteinDomain(int index)
- Specified by:
getProteinDomain
in interfaceProtein
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getProteinDomainCount
public int getProteinDomainCount(java.lang.String domain_id)
- Specified by:
getProteinDomainCount
in interfaceProtein
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getProteinDomains
public java.util.List<Domain> getProteinDomains()
- Specified by:
getProteinDomains
in interfaceProtein
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getProteinDomains
public java.util.List<Domain> getProteinDomains(java.lang.String domain_id)
- Specified by:
getProteinDomains
in interfaceProtein
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getProteinId
public ProteinId getProteinId()
- Specified by:
getProteinId
in interfaceProtein
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getSpecies
public Species getSpecies()
- Specified by:
getSpecies
in interfaceProtein
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setAccession
public void setAccession(java.lang.String accession)
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setDescription
public void setDescription(java.lang.String description)
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setName
public void setName(java.lang.String name)
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toDomainArchitectureString
public java.lang.String toDomainArchitectureString(java.lang.String separator)
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toDomainArchitectureString
public java.lang.String toDomainArchitectureString(java.lang.String separator, int repeats_limit, java.lang.String repeat_separator)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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