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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 a
String
.
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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B
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