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java.lang.Objectfr.umlv.gramofone.commons.Parameters
public class Parameters
Singleton to manage with parameters of the programms (nb insertions, ..)
| Method Summary | |
|---|---|
static Parameters |
deserialize()
Deserialization of the parameters (loading) |
int |
getDelPenalty()
get the cost of a deletion |
java.lang.String |
getFastaFileDirectory()
get the directory for fasta files |
java.lang.String |
getHomeGramoDirectory()
|
double |
getHomologieThreshold()
get the homology threshold value for blast |
int |
getInsPenalty()
get the cost of an insertion |
static Parameters |
getInstance()
get the singleton instance of parameters |
double |
getLogEValue()
get the value of log(eValue) when eValue is 0 |
int |
getNDel()
Get the number of allowed deletions |
java.lang.String |
getNetworkFastaFile()
return the potential path to the fasta file for the network |
int |
getNIns()
Get the number of allowed insertions |
java.lang.String |
getPathBlast()
get the path of the blast bin directory |
java.lang.String |
getPatternFastaFile()
return the potential path to the fasta file for the pattern |
java.lang.String |
getPluginName()
get the plugin name |
int |
getTimeOut()
get the timeout in seconds for the LPB solver |
java.lang.String |
getTmpDirectory()
|
java.lang.String |
getVersion()
return the version of the plugin |
void |
interrupt(boolean value)
put the interrupt signal |
boolean |
isChooseFastaAsPattern()
if the pattern is determined by the fasta file or not |
boolean |
isChooseNetworkFastaFile()
if there is a path for the fasta file for the network or not |
boolean |
isChoosePatternFastaFile()
if there is a path for the fasta file for the pattern or not |
boolean |
isInterrupted()
check if plugin has to be interrupted |
boolean |
isModeBatch()
check if the plugin is in mode batch or not |
boolean |
isMultiSetHomologsPattern()
check if the pattern is as a multiset (same color for homologous proteins) |
boolean |
isOnlyFirstSolution()
check if only the first solution as to be returned |
void |
serialize()
Serialization of the parameters |
void |
setChooseNetworkFastaFile(boolean b)
set if there is a path for the fasta file for the network or not |
void |
setChoosePatternFastaFile(boolean chooseFastaFile)
set if there is a path for the fasta file for the pattern or not |
void |
setDefault()
set default values for options |
void |
setDelPenalty(int delPenalty)
set the cost of a deletion |
void |
setFastaAsPattern(boolean b)
set if the pattern is determined by the fasta file or not |
void |
setHomologieThreshold(double homologieThreshold)
set the homology threshold value for blast |
void |
setInsPenalty(int insPenalty)
set the cost of an insertion |
void |
setLogEValue(double logEValue)
set the value of log(eValue) when eValue is 0 |
void |
setModeBatch(boolean b)
set the mode batch |
void |
setMultiSetHomologsPattern(boolean b)
set the pattern as multiset (same color for homologous proteins) |
void |
setNDel(int del)
set the number of allowed deletions |
void |
setNetworkFastaFile(java.lang.String fastaNetworkFile)
set the path of fasta file for the network |
void |
setNIns(int ins)
set the number of allowed insertions |
void |
setOnlyFirstSolution(boolean onlyFirstSolution)
set the only first solution or not |
void |
setPathBlast(java.lang.String pathBlast)
set the path of the blast bin directory |
void |
setPatternFastaFile(java.lang.String patternFastaFile)
set the path of fasta file for the pattern |
void |
setTimeOut(int timeOut)
set the timeout in seconds for the LPB solver |
| Methods inherited from class java.lang.Object |
|---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Method Detail |
|---|
public static Parameters getInstance()
public void setDefault()
public int getNDel()
public void setNDel(int del)
del - public int getNIns()
public void setNIns(int ins)
ins - public int getTimeOut()
public void setTimeOut(int timeOut)
timeOut - public boolean isChooseNetworkFastaFile()
public void setChooseNetworkFastaFile(boolean b)
b - public boolean isChoosePatternFastaFile()
public void setChoosePatternFastaFile(boolean chooseFastaFile)
chooseFastaFile - public boolean isChooseFastaAsPattern()
public void setFastaAsPattern(boolean b)
b - public void setDelPenalty(int delPenalty)
delPenalty - public int getDelPenalty()
public void setInsPenalty(int insPenalty)
insPenalty - public int getInsPenalty()
public java.lang.String getPathBlast()
public void setPathBlast(java.lang.String pathBlast)
pathBlast - public java.lang.String getPatternFastaFile()
public void setPatternFastaFile(java.lang.String patternFastaFile)
patternFastaFile - public java.lang.String getNetworkFastaFile()
public void setNetworkFastaFile(java.lang.String fastaNetworkFile)
patternFastaFile - public double getHomologieThreshold()
public void setHomologieThreshold(double homologieThreshold)
homologieThreshold - public double getLogEValue()
public void setLogEValue(double logEValue)
logEValue - public boolean isInterrupted()
public void interrupt(boolean value)
public boolean isModeBatch()
public void setModeBatch(boolean b)
b - public void setMultiSetHomologsPattern(boolean b)
b - public boolean isMultiSetHomologsPattern()
public java.lang.String getPluginName()
public java.lang.String getVersion()
public java.lang.String getFastaFileDirectory()
public java.lang.String getTmpDirectory()
public java.lang.String getHomeGramoDirectory()
public boolean isOnlyFirstSolution()
public void setOnlyFirstSolution(boolean onlyFirstSolution)
onlyFirstSolution - public void serialize()
public static Parameters deserialize()
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