A B C D E F G H I K L M N O P Q R S T U V 

A

addColumn(Object) - Method in class slib.utils.impl.MatrixDynamic
 
addParam(String, Object) - Method in class slib.utils.i.Conf
Add the parameter to the configuration Override existing parameter if one exists.
addParameter(String, Object) - Method in interface slib.utils.i.Parametrable
 
addParameter(String, Object) - Method in class slib.utils.impl.ParametrableImpl
 
addRow(Object) - Method in class slib.utils.impl.MatrixDynamic
 
addTask() - Method in class slib.utils.threads.PoolLocker
 
awaitFreeResource() - Method in class slib.utils.threads.PoolLocker
 

B

BigFileReader - Class in slib.utils.impl
 
BigFileReader(String) - Constructor for class slib.utils.impl.BigFileReader
 
buildSet(X) - Static method in class slib.utils.impl.SetUtils
Build a Set containing the given object of type X.

C

capacity - Variable in class slib.utils.threads.PoolLocker
 
CheckableValidity - Interface in slib.utils.i
 
clear() - Method in interface slib.utils.i.Parametrable
 
clear() - Method in class slib.utils.impl.ParametrableImpl
 
close() - Method in class slib.utils.impl.BigFileReader
 
close() - Method in class slib.utils.impl.QueryFileIterator
 
close() - Method in interface slib.utils.impl.QueryIterator
Close the opened repository
compareTo(Pair<TYPEA, TYPEB>) - Method in class slib.utils.Pair
 
Conf - Class in slib.utils.i
Generic Configuration class used to build object storing a configuration as key value pairs.
Conf() - Constructor for class slib.utils.i.Conf
 
containsParam(String) - Method in class slib.utils.i.Conf
Return true if the given parameter is stored in the current configuration.
containsParams() - Method in class slib.utils.i.Conf
Check if the configuration contains at least one parameter.

D

DEF_NAMESPACE_FLAG - Static variable in class slib.utils.impl.OBOconstants
 

E

elapsedTime() - Method in class slib.utils.impl.Timer
 
equals(Object) - Method in class slib.utils.impl.QueryEntry
 
equals(Object) - Method in class slib.utils.Pair
 
error(String) - Static method in class slib.utils.impl.Util
Only throw a critical exception passing the given message
existsParam(String) - Method in interface slib.utils.i.Parametrable
 
existsParam(String) - Method in class slib.utils.impl.ParametrableImpl
 
exit(Object) - Static method in class slib.utils.impl.UtilDebug
 
exit() - Static method in class slib.utils.impl.UtilDebug
 
exitAndPrint(String) - Static method in class slib.utils.impl.UtilDebug
 

F

forceShutdown() - Method in class slib.utils.threads.PoolWorker
 
FORMAT_VERSION_FLAG - Static variable in class slib.utils.impl.OBOconstants
 
freeResource(int) - Method in class slib.utils.threads.ThreadManager
 

G

getAverage() - Method in class slib.utils.impl.MatrixDouble
Return the average of contained valued.
getCapacity() - Method in class slib.utils.threads.PoolLocker
 
getColumn(C) - Method in class slib.utils.impl.MatrixDouble
Return the column associated to the given element
getColumn(Object) - Method in class slib.utils.impl.MatrixDynamic
 
getColumnElements() - Method in class slib.utils.impl.MatrixDouble
 
getKey() - Method in class slib.utils.impl.QueryEntry
 
getKey() - Method in class slib.utils.Pair
 
getLoad() - Method in class slib.utils.threads.PoolLocker
 
getMatrix() - Method in class slib.utils.impl.MatrixDouble
 
getMax() - Method in class slib.utils.impl.MatrixDouble
 
getMax(HashMap<X, Integer>) - Static method in class slib.utils.impl.SetUtils
 
getMaxColumn(C) - Method in class slib.utils.impl.MatrixDouble
 
getMaxLoadPoolWorker() - Method in class slib.utils.threads.ThreadManager
 
getMaxRow(R) - Method in class slib.utils.impl.MatrixDouble
 
getMaxThread() - Method in class slib.utils.threads.ThreadManager
 
getMin() - Method in class slib.utils.impl.MatrixDouble
Return the minimal value stored in the matrix
getNbColumns() - Method in class slib.utils.impl.MatrixDouble
 
getNbColumns() - Method in class slib.utils.impl.MatrixDynamic
 
getNbRows() - Method in class slib.utils.impl.MatrixDouble
 
getNbRows() - Method in class slib.utils.impl.MatrixDynamic
 
getNumberQueries() - Method in class slib.utils.impl.QueryFileIterator
 
getNumberQueries() - Method in interface slib.utils.impl.QueryIterator
 
getParam(String) - Method in class slib.utils.i.Conf
Return the value associated to the given parameter as an Object.
getParamAsDouble(String) - Method in class slib.utils.i.Conf
Return the value associated to the given parameter as a double value.
getParamAsString(String) - Method in class slib.utils.i.Conf
Return the value associated to the given parameter as aString.
getParameter(String) - Method in interface slib.utils.i.Parametrable
 
getParameter(String) - Method in class slib.utils.impl.ParametrableImpl
 
getParams() - Method in class slib.utils.i.Conf
Getter of the Map storing the entry loaded in the configuration.
getParams() - Method in interface slib.utils.i.Parametrable
 
getParams() - Method in class slib.utils.impl.ParametrableImpl
Can be null
getPool() - Method in class slib.utils.threads.PoolWorker
 
getPoolWorker(int) - Method in class slib.utils.threads.ThreadManager
 
getProperty(String) - Method in class slib.utils.impl.OProperty
 
getPropertyKeys() - Method in class slib.utils.impl.OProperty
 
getRow(R) - Method in class slib.utils.impl.MatrixDouble
Return the row associated to the given element
getRow(Object) - Method in class slib.utils.impl.MatrixDynamic
 
getRowElements() - Method in class slib.utils.impl.MatrixDouble
 
getSingleton() - Static method in class slib.utils.threads.ThreadManager
 
getSum() - Method in class slib.utils.impl.MatrixDouble
Compute the sum of the values contained in the matrix.
getValue(C, R) - Method in class slib.utils.impl.MatrixDouble
 
getValue(Object, Object) - Method in class slib.utils.impl.MatrixDynamic
 
getValue() - Method in class slib.utils.impl.QueryEntry
 
getValue() - Method in class slib.utils.Pair
 
getValueCheckIndex(C, R) - Method in class slib.utils.impl.MatrixDouble
 

H

hashCode() - Method in class slib.utils.impl.QueryEntry
 
hashCode() - Method in class slib.utils.Pair
 
hasNext() - Method in class slib.utils.impl.BigFileReader
 
hasNext() - Method in class slib.utils.impl.QueryFileIterator
 
hasNext() - Method in interface slib.utils.impl.QueryIterator
 

I

intersection(Collection<X>, Collection<X>) - Static method in class slib.utils.impl.SetUtils
Compute the intersection of two collections
IO_RuntimeException - Exception in slib.utils.impl
TODO modify or remove
IO_RuntimeException(String) - Constructor for exception slib.utils.impl.IO_RuntimeException
 
ISA_FLAG - Static variable in class slib.utils.impl.OBOconstants
 
isInColumnIndex(C) - Method in class slib.utils.impl.MatrixDouble
 
isInColumnIndex(Object) - Method in class slib.utils.impl.MatrixDynamic
 
isInIndexed(Object) - Method in class slib.utils.impl.MatrixDynamic
 
isInRowIndex(R) - Method in class slib.utils.impl.MatrixDouble
 
isInRowIndex(Object) - Method in class slib.utils.impl.MatrixDynamic
 
isSquare() - Method in class slib.utils.impl.MatrixDouble
 
isSquare() - Method in class slib.utils.impl.MatrixDynamic
 
isValid() - Method in interface slib.utils.i.CheckableValidity
 
isValid() - Method in class slib.utils.impl.QueryEntry
Only check if K and V are defined anf if their are not equals to empty string

K

Key_ - Variable in class slib.utils.Pair
 

L

lock - Variable in class slib.utils.threads.PoolLocker
 

M

MatrixDouble<C,R> - Class in slib.utils.impl
Class used to represent a Matrix which can be used to store values associated to pairs of elements.
MatrixDouble(Set<C>, Set<R>) - Constructor for class slib.utils.impl.MatrixDouble
Create a matrix filled with null values considering the given indexes.
MatrixDouble(Set<C>, Set<R>, Double) - Constructor for class slib.utils.impl.MatrixDouble
Create a matrix filled with null values considering the given indexes
MatrixDynamic<N extends Number> - Class in slib.utils.impl
 
MatrixDynamic(Set<Object>, Set<Object>) - Constructor for class slib.utils.impl.MatrixDynamic
 

N

NAME_FLAG - Static variable in class slib.utils.impl.OBOconstants
 
next() - Method in class slib.utils.impl.BigFileReader
 
next() - Method in class slib.utils.impl.QueryFileIterator
Note the Query Entry returned can be equal to null if the line is not in agreement with the expectations i.e.
next() - Method in interface slib.utils.impl.QueryIterator
 
nextTrimmed() - Method in class slib.utils.impl.BigFileReader
 
nextValids(int) - Method in class slib.utils.impl.QueryFileIterator
 
nextValids(int) - Method in interface slib.utils.impl.QueryIterator
Return a List containing the next valid queries.

O

OBOconstants - Class in slib.utils.impl
 
OBOconstants() - Constructor for class slib.utils.impl.OBOconstants
 
OBSOLETE_FLAG - Static variable in class slib.utils.impl.OBOconstants
 
OProperty - Class in slib.utils.impl
 
OProperty() - Constructor for class slib.utils.impl.OProperty
 

P

Pair<TYPEA,TYPEB> - Class in slib.utils
 
Pair(TYPEA, TYPEB) - Constructor for class slib.utils.Pair
 
Parametrable - Interface in slib.utils.i
 
ParametrableImpl - Class in slib.utils.impl
 
ParametrableImpl() - Constructor for class slib.utils.impl.ParametrableImpl
 
PoolLocker - Class in slib.utils.threads
 
PoolLocker(int) - Constructor for class slib.utils.threads.PoolLocker
 
PoolWorker - Class in slib.utils.threads
 
PoolWorker(int) - Constructor for class slib.utils.threads.PoolWorker
 
properties - Variable in class slib.utils.impl.OProperty
 

Q

QueryEntry - Class in slib.utils.impl
 
QueryEntry() - Constructor for class slib.utils.impl.QueryEntry
 
QueryEntry(String, String) - Constructor for class slib.utils.impl.QueryEntry
 
QueryFileIterator - Class in slib.utils.impl
Query Iterator implementing the QueryIterator interface used to iterate through the queries defined in a tabular delimited file i.e.
QueryFileIterator(String) - Constructor for class slib.utils.impl.QueryFileIterator
Constructor of a QueryFileIterator
QueryFileIterator(String, String) - Constructor for class slib.utils.impl.QueryFileIterator
Constructor of a QueryFileIterator
QueryIterator - Interface in slib.utils.impl
Interface defining the generic behavior a Query iterator must follows.

R

RELATIONSHIP_FLAG - Static variable in class slib.utils.impl.OBOconstants
 
removeParam(String) - Method in class slib.utils.i.Conf
Remove the entry corresponding to the given key if one is stored.
removeParameter(String) - Method in interface slib.utils.i.Parametrable
 
removeParameter(String) - Method in class slib.utils.impl.ParametrableImpl
 
removeProperty(String) - Method in class slib.utils.impl.OProperty
 
running - Variable in class slib.utils.threads.PoolLocker
 

S

setMaxThread(int) - Method in class slib.utils.threads.ThreadManager
 
setParams(HashMap<String, Object>) - Method in class slib.utils.i.Conf
Set the current map to the given.
setProperty(String, Object) - Method in class slib.utils.impl.OProperty
 
SetUtils - Class in slib.utils.impl
 
SetUtils() - Constructor for class slib.utils.impl.SetUtils
 
setValue(C, R, Double) - Method in class slib.utils.impl.MatrixDouble
 
setValue(Object, Object, N) - Method in class slib.utils.impl.MatrixDynamic
 
setValue(String) - Method in class slib.utils.impl.QueryEntry
 
shutdown() - Method in class slib.utils.threads.PoolWorker
 
shutdown(long, TimeUnit) - Method in class slib.utils.threads.PoolWorker
 
slib.utils - package slib.utils
 
slib.utils.ex - package slib.utils.ex
 
slib.utils.i - package slib.utils.i
 
slib.utils.impl - package slib.utils.impl
 
slib.utils.threads - package slib.utils.threads
 
SLIB_Ex_Critic - Exception in slib.utils.ex
 
SLIB_Ex_Critic(String) - Constructor for exception slib.utils.ex.SLIB_Ex_Critic
 
SLIB_Ex_Critic(Throwable) - Constructor for exception slib.utils.ex.SLIB_Ex_Critic
 
SLIB_Ex_Critic(String, Throwable) - Constructor for exception slib.utils.ex.SLIB_Ex_Critic
 
SLIB_Ex_Warning - Exception in slib.utils.ex
 
SLIB_Ex_Warning(String) - Constructor for exception slib.utils.ex.SLIB_Ex_Warning
 
SLIB_Exception - Exception in slib.utils.ex
 
SLIB_Exception(String) - Constructor for exception slib.utils.ex.SLIB_Exception
 
SLIB_Exception(Throwable) - Constructor for exception slib.utils.ex.SLIB_Exception
 
SLIB_Exception(String, Throwable) - Constructor for exception slib.utils.ex.SLIB_Exception
 
start() - Method in class slib.utils.impl.Timer
 
stop() - Method in class slib.utils.impl.Timer
 
stringToBoolean(String) - Static method in class slib.utils.impl.Util
Convert the given String to a boolean value.
stringToDouble(String) - Static method in class slib.utils.impl.Util
 
stringToInteger(String) - Static method in class slib.utils.impl.Util
 
stringToLong(String) - Static method in class slib.utils.impl.Util
 

T

taskComplete() - Method in class slib.utils.threads.PoolLocker
 
TERM_FLAG - Static variable in class slib.utils.impl.OBOconstants
 
TERM_ID_FLAG - Static variable in class slib.utils.impl.OBOconstants
 
ThreadManager - Class in slib.utils.threads
 
Timer - Class in slib.utils.impl
 
Timer() - Constructor for class slib.utils.impl.Timer
 
toString() - Method in class slib.utils.i.Conf
 
toString() - Method in class slib.utils.impl.MatrixDouble
 
toString() - Method in class slib.utils.impl.QueryEntry
 
toString() - Method in class slib.utils.Pair
 
TYPEDEF_FLAG - Static variable in class slib.utils.impl.OBOconstants
 
TYPEDEF_ID_FLAG - Static variable in class slib.utils.impl.OBOconstants
 
TYPEDEF_INVERSE_OF_FLAG - Static variable in class slib.utils.impl.OBOconstants
 
TYPEDEF_ISTRANSIVE_FLAG - Static variable in class slib.utils.impl.OBOconstants
 
TYPEDEF_SYMMETRIC_FLAG - Static variable in class slib.utils.impl.OBOconstants
 
TYPEDEF_XREF - Static variable in class slib.utils.impl.OBOconstants
 

U

union(Collection<X>, Collection<X>) - Static method in class slib.utils.impl.SetUtils
Compute the union of two collections
Util - Class in slib.utils.impl
 
Util() - Constructor for class slib.utils.impl.Util
 
UtilDebug - Class in slib.utils.impl
 
UtilDebug() - Constructor for class slib.utils.impl.UtilDebug
 

V

Value_ - Variable in class slib.utils.Pair
 
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