PIP.Domains
Class Domain

java.lang.Object
  PIP.Collections.Persistent.AbstractCollection<E>
      PIP.Collections.Persistent.AbstractList<T>
          PIP.Collections.Piecewise<Residue>
              PIP.Domains.Domain

All Implemented Interfaces:

java.io.Serializable, java.lang.Iterable<Residue>, java.util.Collection<Residue>, java.util.List<Residue>

public class Domain
extends Piecewise<Residue>
implements java.io.Serializable

See Also:

Serialized Form

Constructor Summary

Domain(java.lang.String id, Family f)

Method Summary

boolean	containsNucAcids()
boolean	equals(java.lang.Object o) Compares the specified object with this list for equality.
Assembly	getAssembly()
char	getChainType()
Family	getFamily()
Family	getFamily(FamilyType ft)
java.lang.String	getId()
int	getNumberInAssembly()
int	getNumberOfAtoms()
int	getPositionInAssembly()
java.util.Set<Residue>	getResiduesInteractingWithLigands(double maxResDist, double max_plus_VDW, java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Double>> VDWmap)
java.util.Set<Residue>	getResiduesInteractingWithOtherDomains()
java.util.List<Residue>	getResiduesThatHaveCoordinates()
java.lang.String	getSequenceString()
java.lang.String	getSequenceStringWithXSequencesRemoved()
java.lang.String	getUniqueID()
boolean	isInteractingWithOtherDomain()
boolean	isNonAssemblyValid()
void	setUniqueID(java.lang.String uniqueID)

Methods inherited from class PIP.Collections.Piecewise

addRange, get, getRanges, size

Methods inherited from class PIP.Collections.Persistent.AbstractList

add, add, addAll, clear, hashCode, indexOf, iterator, lastIndexOf, listIterator, listIterator, remove, set, subList

Methods inherited from class PIP.Collections.Persistent.AbstractCollection

addAll, contains, containsAll, isEmpty, remove, removeAll, retainAll, toArray, toArray, toString

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

addAll, contains, containsAll, isEmpty, remove, removeAll, retainAll, toArray, toArray

Constructor Detail

Domain

public Domain(java.lang.String id,
              Family f)

Method Detail

getChainType

public char getChainType()

getSequenceStringWithXSequencesRemoved

public java.lang.String getSequenceStringWithXSequencesRemoved()

getSequenceString

public java.lang.String getSequenceString()

getPositionInAssembly

public int getPositionInAssembly()

getAssembly

public Assembly getAssembly()

isNonAssemblyValid

public boolean isNonAssemblyValid()

getFamily

public Family getFamily()

getFamily

public Family getFamily(FamilyType ft)
                 throws java.lang.Exception

Throws:

java.lang.Exception

getId

public java.lang.String getId()

equals

public boolean equals(java.lang.Object o)

Description copied from class: AbstractList

Compares the specified object with this list for equality. Returns true if and only if the specified object is also a list, both lists have the same size, and all corresponding pairs of elements in the two lists are equal. (Two elements e1 and e2 are equal if (e1==null ? e2==null : e1.equals(e2)).) In other words, two lists are defined to be equal if they contain the same elements in the same order.

This implementation first checks if the specified object is this list. If so, it returns true; if not, it checks if the specified object is a list. If not, it returns false; if so, it iterates over both lists, comparing corresponding pairs of elements. If any comparison returns false, this method returns false. If either iterator runs out of elements before the other it returns false (as the lists are of unequal length); otherwise it returns true when the iterations complete.

Specified by:

equals in interface java.util.Collection<Residue>

Specified by:

equals in interface java.util.List<Residue>

Overrides:

equals in class AbstractList<Residue>

Parameters:

o - the object to be compared for equality with this list.

Returns:

true if the specified object is equal to this list.

containsNucAcids

public boolean containsNucAcids()

getResiduesThatHaveCoordinates

public java.util.List<Residue> getResiduesThatHaveCoordinates()

getNumberOfAtoms

public int getNumberOfAtoms()

isInteractingWithOtherDomain

public boolean isInteractingWithOtherDomain()
                                     throws java.lang.Exception

Throws:

java.lang.Exception

getResiduesInteractingWithOtherDomains

public java.util.Set<Residue> getResiduesInteractingWithOtherDomains()
                                                              throws java.lang.Exception

Throws:

java.lang.Exception

getResiduesInteractingWithLigands

public java.util.Set<Residue> getResiduesInteractingWithLigands(double maxResDist,
                                                                double max_plus_VDW,
                                                                java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Double>> VDWmap)

getUniqueID

public java.lang.String getUniqueID()

setUniqueID

public void setUniqueID(java.lang.String uniqueID)

getNumberInAssembly

public int getNumberInAssembly()