BasicProtein

java.lang.Object
- org.forester.protein.BasicProtein

All Implemented Interfaces:: Protein

public class BasicProtein
extends java.lang.Object
implements Protein

Field Summary

Fields
Modifier and Type Field and Description

static java.util.Comparator<Domain> DomainMidPositionComparator

Fields
Modifier and Type	Field and Description
`static java.util.Comparator<Domain>`	`DomainMidPositionComparator`

Constructor Summary

Constructors
Constructor and Description

BasicProtein(java.lang.String id_str, java.lang.String species_str, int length)

Constructors
Constructor and Description
`BasicProtein(java.lang.String id_str, java.lang.String species_str, int length)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - DomainMidPositionComparator
```
public static java.util.Comparator<Domain> DomainMidPositionComparator
```
- Constructor Detail
  - BasicProtein
```
public BasicProtein(java.lang.String id_str,
                    java.lang.String species_str,
                    int length)
```
- Method Detail
  - addProteinDomain
```
public void addProteinDomain(Domain protein_domain)
```
    Specified by:
    
    addProteinDomain in interface Protein
  - 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).
    
    Specified by:
    
    contains in interface Protein
    
    Parameters:
    
    query_domain_ids - a list of domain ids in a certain order.
    
    in_nc_order - to consider order
    
    Returns:
  - getAccession
```
public java.lang.String getAccession()
```
    Specified by:
    
    getAccession in interface Protein
  - getDescription
```
public java.lang.String getDescription()
```
    Specified by:
    
    getDescription in interface Protein
  - getDomainsSortedByPosition
```
public java.util.List<Domain> getDomainsSortedByPosition()
```
    Specified by:
    
    getDomainsSortedByPosition in interface Protein
  - getLength
```
public int getLength()
```
    Specified by:
    
    getLength in interface Protein
  - getName
```
public java.lang.String getName()
```
    Specified by:
    
    getName in interface Protein
  - getNumberOfProteinDomains
```
public int getNumberOfProteinDomains()
```
    Specified by:
    
    getNumberOfProteinDomains in interface Protein
  - getProteinDomain
```
public Domain getProteinDomain(int index)
```
    Specified by:
    
    getProteinDomain in interface Protein
  - getProteinDomainCount
```
public int getProteinDomainCount(java.lang.String domain_id)
```
    Specified by:
    
    getProteinDomainCount in interface Protein
  - getProteinDomains
```
public java.util.List<Domain> getProteinDomains()
```
    Specified by:
    
    getProteinDomains in interface Protein
  - getProteinDomains
```
public java.util.List<Domain> getProteinDomains(java.lang.String domain_id)
```
    Specified by:
    
    getProteinDomains in interface Protein
  - getProteinId
```
public ProteinId getProteinId()
```
    Specified by:
    
    getProteinId in interface Protein
  - getSpecies
```
public Species getSpecies()
```
    Specified by:
    
    getSpecies in interface Protein
  - setAccession
```
public void setAccession(java.lang.String accession)
```
  - setDescription
```
public void setDescription(java.lang.String description)
```
  - setName
```
public void setName(java.lang.String name)
```
  - toDomainArchitectureString
```
public java.lang.String toDomainArchitectureString(java.lang.String separator)
```
  - toDomainArchitectureString
```
public java.lang.String toDomainArchitectureString(java.lang.String separator,
                                                   int repeats_limit,
                                                   java.lang.String repeat_separator)
```
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object

Class BasicProtein

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DomainMidPositionComparator

Constructor Detail

BasicProtein

Method Detail

addProteinDomain

contains

getAccession

getDescription

getDomainsSortedByPosition

getLength

getName

getNumberOfProteinDomains

getProteinDomain

getProteinDomainCount

getProteinDomains

getProteinDomains

getProteinId

getSpecies

setAccession

setDescription

setName

toDomainArchitectureString

toDomainArchitectureString

toString