Serialized Form


Package fr.umlv.gramofone.batch

Class fr.umlv.gramofone.batch.DoublonFasta extends java.lang.Object implements Serializable

Class fr.umlv.gramofone.batch.ParseFasta extends java.lang.Object implements Serializable

Class fr.umlv.gramofone.batch.ParseFlat extends java.lang.Object implements Serializable


Package fr.umlv.gramofone.commons

Class fr.umlv.gramofone.commons.Parameters extends java.lang.Object implements Serializable

serialVersionUID: -787795165674390565L

Serialized Fields

NDel

int NDel

NIns

int NIns

delPenalty

int delPenalty

insPenalty

int insPenalty

timeOut

int timeOut

pathBlast

java.lang.String pathBlast

patternFastaFile

java.lang.String patternFastaFile

networkFastaFile

java.lang.String networkFastaFile

choosePatternFastaFile

boolean choosePatternFastaFile

chooseNetworkFastaFile

boolean chooseNetworkFastaFile

chooseFastaAsPattern

boolean chooseFastaAsPattern

homologieThreshold

double homologieThreshold

logEValue

double logEValue

modeBatch

boolean modeBatch

multiSetHomologsPattern

boolean multiSetHomologsPattern

onlyFirstSolution

boolean onlyFirstSolution

interupted

boolean interupted

fastaFileDirectory

java.lang.String fastaFileDirectory

Package fr.umlv.gramofone.graphs

Class fr.umlv.gramofone.graphs.Edge extends java.lang.Object implements Serializable

serialVersionUID: 4221348762459716321L

Serialized Fields

u

int u

v

int v

weight

float weight

id

int id

Class fr.umlv.gramofone.graphs.Edges extends java.lang.Object implements Serializable

serialVersionUID: -6736303714629048676L

Serialized Fields

edges

java.util.HashMap<K,V> edges

edgesUnique

java.util.HashSet<E> edgesUnique

Class fr.umlv.gramofone.graphs.MyGraph extends java.lang.Object implements Serializable

serialVersionUID: -5441829722634284668L

Serialized Fields

nodes

java.util.List<E> nodes

color2Nodes

java.util.HashMap<K,V> color2Nodes

node2Colors

java.util.HashMap<K,V> node2Colors

nodesWithoutColors

java.util.HashSet<E> nodesWithoutColors

edges

Edges edges

pattern

MyPattern pattern

Ndel

int Ndel

Nins

int Nins

network

CyNetwork network

originalCyNetwork

CyNetwork originalCyNetwork

connectedComponent

java.util.LinkedList<E> connectedComponent

previouslyDeletedProteins

java.util.Set<E> previouslyDeletedProteins

Class fr.umlv.gramofone.graphs.MyPattern extends java.lang.Object implements Serializable

serialVersionUID: -8173667139838185591L

Serialized Fields

id2Occurence

java.util.HashMap<K,V> id2Occurence

colors2Occurence

java.util.HashMap<K,V> colors2Occurence

id2Color

java.util.HashMap<K,V> id2Color

color2Id

java.util.HashMap<K,V> color2Id

patternName

java.lang.String patternName

totalMotifSize

int totalMotifSize