class PickLongIndices extends FgBioTool with LazyLogging
- Annotations
- @ClpAnnotation()
Linear Supertypes
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Inherited
- PickLongIndices
- LazyLogging
- FgBioTool
- AnyRef
- Any
Implicitly
- by any2stringadd
- by StringFormat
- by Ensuring
- by ArrowAssoc
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Visibility
- Public
- All
Instance Constructors
- new PickLongIndices(length: Int = 8, numberOfIndices: Int, editDistance: Int = 3, output: FgBioDef.FilePath, allowReverses: Boolean = false, allowReverseComplements: Boolean = false, allowPalindromes: Boolean = false, maxHomopolymer: Int = 2, minGc: Double = 0.2, maxGc: Double = 0.8, existing: Option[FgBioDef.FilePath] = None, seed: Int = 1, attempts: Int = 1e5.toInt, viennaRnaDir: Option[FgBioDef.DirPath] = None, temperature: Double = 25d, minDeltaG: Double = 10, adapters: Seq[String] = Seq(), avoidSequence: Seq[String] = ...)
Value Members
-
final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
##(): Int
- Definition Classes
- AnyRef → Any
-
def
+(other: String): String
- Implicit
- This member is added by an implicit conversion from PickLongIndices to any2stringadd[PickLongIndices] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
-
def
->[B](y: B): (PickLongIndices, B)
- Implicit
- This member is added by an implicit conversion from PickLongIndices to ArrowAssoc[PickLongIndices] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc
- Annotations
- @inline()
-
final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
- val adapters: Seq[String]
- val allowPalindromes: Boolean
- val allowReverseComplements: Boolean
- val allowReverses: Boolean
-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
- val attempts: Int
- val avoidSequence: Seq[String]
-
def
clone(): AnyRef
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
- val editDistance: Int
-
def
ensuring(cond: (PickLongIndices) ⇒ Boolean, msg: ⇒ Any): PickLongIndices
- Implicit
- This member is added by an implicit conversion from PickLongIndices to Ensuring[PickLongIndices] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: (PickLongIndices) ⇒ Boolean): PickLongIndices
- Implicit
- This member is added by an implicit conversion from PickLongIndices to Ensuring[PickLongIndices] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean, msg: ⇒ Any): PickLongIndices
- Implicit
- This member is added by an implicit conversion from PickLongIndices to Ensuring[PickLongIndices] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean): PickLongIndices
- Implicit
- This member is added by an implicit conversion from PickLongIndices to Ensuring[PickLongIndices] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
def
execute(): Unit
The main method!
The main method!
- Definition Classes
- PickLongIndices → FgBioTool
- val existing: Option[FgBioDef.FilePath]
-
def
fail(exit: Int, message: String): Nothing
Fail with a specific error code and message.
Fail with a specific error code and message.
- Definition Classes
- FgBioTool
-
def
fail(message: String): Nothing
Fail with the default exit code and a message.
Fail with the default exit code and a message.
- Definition Classes
- FgBioTool
-
def
fail(exit: Int): Nothing
Fail with just an exit code.
Fail with just an exit code.
- Definition Classes
- FgBioTool
-
def
finalize(): Unit
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] )
-
def
formatted(fmtstr: String): String
- Implicit
- This member is added by an implicit conversion from PickLongIndices to StringFormat[PickLongIndices] performed by method StringFormat in scala.Predef.
- Definition Classes
- StringFormat
- Annotations
- @inline()
-
final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
-
def
hashCode(): Int
- Definition Classes
- AnyRef → Any
-
def
invalid(message: String): Nothing
Generates a new validation exception with the given message.
Generates a new validation exception with the given message.
- Definition Classes
- FgBioTool
-
final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
- val length: Int
-
lazy val
logger: Logger
- Attributes
- protected
- Definition Classes
- LazyLogging
- val maxGc: Double
- val maxHomopolymer: Int
- val minDeltaG: Double
- val minGc: Double
-
final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- val numberOfIndices: Int
- val output: FgBioDef.FilePath
- val seed: Int
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
- val temperature: Double
-
def
toString(): String
- Definition Classes
- AnyRef → Any
-
def
validate(test: Boolean, message: ⇒ String): Unit
Generates a validation exception if the test value is false.
Generates a validation exception if the test value is false.
- Definition Classes
- FgBioTool
- val viennaRnaDir: Option[FgBioDef.DirPath]
-
final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
def
→[B](y: B): (PickLongIndices, B)
- Implicit
- This member is added by an implicit conversion from PickLongIndices to ArrowAssoc[PickLongIndices] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc