org.forester.protein
Class BasicDomain

java.lang.Object
  org.forester.protein.BasicDomain

All Implemented Interfaces:

java.lang.Comparable<Domain>, Domain

public class BasicDomain
extends java.lang.Object
implements Domain

Constructor Summary

BasicDomain(java.lang.String id_str)

BasicDomain(java.lang.String id_str, int from, int to, short number, short total_count, double per_sequence_evalue, double per_sequence_score)

BasicDomain(java.lang.String id_str, int from, int to, short number, short total_count, double per_sequence_evalue, double per_sequence_score, double per_domain_evalue, double per_domain_score)

Method Summary

void	addGoId(GoId go_id)
int	compareTo(Domain domain) Basic domains are compared/sorted based upon their identifiers (case insensitive) and their numbers.
boolean	equals(java.lang.Object o) Basic domains are considered equal if they have the same identifier (case sensitive).
DomainId	getDomainId()
int	getFrom()
GoId	getGoId(int i)
int	getLength()
short	getNumber()
int	getNumberOfGoIds()
double	getPerDomainEvalue()
double	getPerDomainScore()
double	getPerSequenceEvalue()
double	getPerSequenceScore()
int	getTo()
short	getTotalCount()
int	hashCode()
java.lang.String	toString()
java.lang.StringBuffer	toStringBuffer()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

BasicDomain

public BasicDomain(java.lang.String id_str)

BasicDomain

public BasicDomain(java.lang.String id_str,
                   int from,
                   int to,
                   short number,
                   short total_count,
                   double per_sequence_evalue,
                   double per_sequence_score)

BasicDomain

public BasicDomain(java.lang.String id_str,
                   int from,
                   int to,
                   short number,
                   short total_count,
                   double per_sequence_evalue,
                   double per_sequence_score,
                   double per_domain_evalue,
                   double per_domain_score)

Method Detail

addGoId

public void addGoId(GoId go_id)

Specified by:

addGoId in interface Domain

compareTo

public int compareTo(Domain domain)

Basic domains are compared/sorted based upon their identifiers (case insensitive) and their numbers.

Specified by:

compareTo in interface java.lang.Comparable<Domain>

equals

public boolean equals(java.lang.Object o)

Basic domains are considered equal if they have the same identifier (case sensitive).

Overrides:

equals in class java.lang.Object

getDomainId

public DomainId getDomainId()

Specified by:

getDomainId in interface Domain

getFrom

public int getFrom()

Specified by:

getFrom in interface Domain

getGoId

public GoId getGoId(int i)

Specified by:

getGoId in interface Domain

getNumber

public short getNumber()

Specified by:

getNumber in interface Domain

getNumberOfGoIds

public int getNumberOfGoIds()

Specified by:

getNumberOfGoIds in interface Domain

getPerDomainEvalue

public double getPerDomainEvalue()

Specified by:

getPerDomainEvalue in interface Domain

getPerDomainScore

public double getPerDomainScore()

Specified by:

getPerDomainScore in interface Domain

getPerSequenceEvalue

public double getPerSequenceEvalue()

Specified by:

getPerSequenceEvalue in interface Domain

getPerSequenceScore

public double getPerSequenceScore()

Specified by:

getPerSequenceScore in interface Domain

getTo

public int getTo()

Specified by:

getTo in interface Domain

getTotalCount

public short getTotalCount()

Specified by:

getTotalCount in interface Domain

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

toStringBuffer

public java.lang.StringBuffer toStringBuffer()

getLength

public int getLength()

Specified by:

getLength in interface Domain