EntityChecker

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

val AllKeysStopSuffixes: Set[String]

The set of words to remove from all keys to create a lookup key.

val AuxBioProcessFilename: String

Filename of the auxiliary biological processes file.

val AuxCellLocationFilename: String

Filename of the auxiliary cellular location file.

val AuxChemicalFilename: String

Filename of the auxiliary small molecule (chemical) file.

val AuxMetaboliteFilename: String

Filename of the auxiliary small molecule (metabolite) file.

val AuxProteinFamilyFilename: String

Filename of the auxiliary protein family file.

val AuxProteinFilename: String

Filename of the auxiliary protein file.

val AuxTissueTypeFilename: String

Filename of the auxiliary protein file.

val FamilyStopSuffixes: Set[String]

The set of words to remove from a key to create a protein family lookup key.

val GendCellLocationFilename: String

Filename of the cellular location file generated by the entity checker.

val GendCellLocationPrefix: String

Prefix string for cellular location IDs generated by the entity checker.

val GendChemicalFilename: String

Filename of the small molecule file generated by the entity checker.

val GendChemicalPrefix: String

Prefix string for small molecule IDs generated by the entity checker.

val GendProteinFilename: String

Filename of the protein/family file generated by the entity checker.

val GendProteinPrefix: String

Prefix string for protein/family IDs generated by the entity checker.

val HumanLabels: Set[String]

The set of words to remove from the text to create a lookup key.

val KBDirFilePath: String

File Path to the directory which holds the entity knowledge bases.

val KBDirResourcePath: String

Resource Path to the directory which holds the entity knowledge bases.

val KeyCharactersToRemove: Set[Char]

The set of characters to remove from the text to create a lookup key.

val ManualCellLocationFilename: String

Filename of the manually maintained cellular location file.

val ManualChemicalFilename: String

Filename of the manually maintained small molecule file.

val ManualProteinFamilyFilename: String

Filename of the manually maintained protein family file.

val ManualProteinFilename: String

Filename of the manually maintained protein file.

val ProteinStopSuffixes: Set[String]

The set of words to remove from a key to create a protein lookup key.

val StaticCellLocationFilename: String

Filename of the static cellular location file.

val StaticCellLocationKBLookup: StaticCellLocationKBLookup

val StaticChemicalFilename: String

Filename of the static small molecule (chemical) file.

val StaticChemicalKBLookup: StaticChemicalKBLookup

val StaticMetaboliteFilename: String

Filename of the static small molecule (chemical) file.

val StaticMetaboliteKBLookup: StaticMetaboliteKBLookup

val StaticProteinFamilyFilename: String

Filename of the static protein family file.

val StaticProteinFamilyKBLookup: StaticProteinFamilyKBLookup

val StaticProteinFilename: String

Filename of the static protein file.

val StaticProteinKBLookup: StaticProteinKBLookup

val StaticTissueTypeFilename: String

Filename of the static tissue type file.

def args: Array[String]

final def asInstanceOf[T0]: T0

val cellLocationSearcher: Seq[StaticCellLocationKBLookup]

Search sequence for sub cellular locations terms.

val chemSearcher: Seq[LocalKBLookup]

Search sequence for small molecules.

def clone(): AnyRef

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

val executionStart: Long

val filepath: String

def finalize(): Unit

val fis: FileInputStream

final def getClass(): Class[_]

def hashCode(): Int

final def isInstanceOf[T0]: Boolean

def main(args: Array[String]): Unit

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

val proteinSearcher: Seq[LocalKBLookup]

Search sequence for resolving proteins.

def readAndCheckBioPax(fis: InputStream): Unit

Read the BioPAX model from the given input stream and check the entities.

final def synchronized[T0](arg0: ⇒ T0): T0

def toString(): String

final def wait(): Unit

final def wait(arg0: Long, arg1: Int): Unit

final def wait(arg0: Long): Unit

def delayedInit(body: ⇒ Unit): Unit