edu.mssm.crover.mutations.drivers
Class Mutant

java.lang.Object
  |
  +--edu.mssm.crover.mutations.drivers.Mutant

public class Mutant
extends java.lang.Object

A mutant contains several mutations done simultaneously. Mutants are real proteins.


Field Summary
protected  short cumulative_type_signature
          Exposes the type of mutations that were used to build this mutant.
 java.lang.String description
          Description string for this mutant.
 java.lang.String descriptionURL
           
protected  Mutation[] mutations
           
protected  short pure_type_signature
          Exposes the type of mutations that were used to build this mutant.
 
Constructor Summary
Mutant()
           
 
Method Summary
 void addDescriptionURL(java.lang.String url)
           
 void addPhenotype(java.lang.String phenotype)
           
 void appendMutation(Mutation m)
           
 java.lang.String getDescription()
           
 java.util.Collection getDescriptionURLs()
           
 java.lang.String getID()
           
 Mutation[] getMutations()
           
 java.util.Collection getPhenotypes()
           
 boolean hasSignature(short pure_type_signature, boolean filter_by_pure_signature, short cumulative_type_signature, boolean filter_by_cumulative_signature, boolean filter_by_exact_cumulative_signature)
          checks if this mutant matches pure and cumulative signatures.
 boolean removeMutation(Mutation mutation)
          Removes a mutation from this mutant.
 void setDescription(java.lang.String desc)
           
 void setID(java.lang.String mutant_id)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

mutations

protected Mutation[] mutations

descriptionURL

public java.lang.String descriptionURL

description

public java.lang.String description
Description string for this mutant.


pure_type_signature

protected short pure_type_signature
Exposes the type of mutations that were used to build this mutant. pure_type_signature is a combination of bits. The bit that correspond to a given mutation type is set when the mutant is made of a pure combination of this type of mutations. For instance, mutants that contain only point mutations will have
pure_type_signature=POINT_MUTATION.value
. A mutant that contains a point mutation and a deletion will have a pure type signature of 0 (a mix of types).


cumulative_type_signature

protected short cumulative_type_signature
Exposes the type of mutations that were used to build this mutant. cumlative_type_signature is a combination of bits. The bit that correspond to a given mutation type is set when the mutant is made of at least one occurence of this type of mutations. For instance, mutants that contain at least a point mutation will have
cumulative_type_signature&&POINT_MUTATION.value == true.
A mutant that contains a point mutation and a deletion will have a cumulative type signature of POINT_MUTATION.value |DELETION_MUTATION.value.

Constructor Detail

Mutant

public Mutant()
Method Detail

addDescriptionURL

public void addDescriptionURL(java.lang.String url)

getDescriptionURLs

public java.util.Collection getDescriptionURLs()

setDescription

public void setDescription(java.lang.String desc)

getDescription

public java.lang.String getDescription()

addPhenotype

public void addPhenotype(java.lang.String phenotype)

getPhenotypes

public java.util.Collection getPhenotypes()

appendMutation

public void appendMutation(Mutation m)

getMutations

public Mutation[] getMutations()

removeMutation

public boolean removeMutation(Mutation mutation)
Removes a mutation from this mutant.

Returns:
True if the mutation has been found and removed, false otherwise.

getID

public java.lang.String getID()

setID

public void setID(java.lang.String mutant_id)

hasSignature

public boolean hasSignature(short pure_type_signature,
                            boolean filter_by_pure_signature,
                            short cumulative_type_signature,
                            boolean filter_by_cumulative_signature,
                            boolean filter_by_exact_cumulative_signature)
checks if this mutant matches pure and cumulative signatures.

Parameters:
pure_type_signature - pure_type_signature
cumulative_type_signature - cumulative_type_signature


Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.