InMemoryKB

Instance Constructors

new InMemoryKB(namespace: String, hasSpeciesInfo: Boolean, metaInfo: IMKBMetaInfo)

Additional constructor to add namespace to meta information for reference.
new InMemoryKB(hasSpeciesInfo: Boolean = false, metaInfo: IMKBMetaInfo = new IMKBMetaInfo())

Type Members

type KeyTransforms = Seq[(String) ⇒ String]

Type alias for functions which take a text string and return a potential key string.
Type alias for functions which take a text string and return a potential key string.

Definition Classes
KBKeyTransforms
type SpeciesNameSet = Set[String]

Species name sets.
Species name sets.

Definition Classes
Speciated

Value Members

final def !=(arg0: Any): Boolean

Definition Classes
AnyRef → Any
final def ##(): Int

Definition Classes
AnyRef → Any
final def ==(arg0: Any): Boolean

Definition Classes
AnyRef → Any
def SpeciesNameSet(xs: String*): Set[String]

Definition Classes
Speciated
def addEntry(entry: KBEntry): HashMap[String, Set[KBEntry]] with MultiMap[String, KBEntry]

Add the given entry to this KB, if it is unique.
def applyTransforms(text: String, transformFns: KeyTransforms): Seq[String]

Return a sequence of alternate keys, one for each of the given key transforms.
Return a sequence of alternate keys, one for each of the given key transforms.

Definition Classes
KBKeyTransforms
final def asInstanceOf[T0]: T0

Definition Classes
Any
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
def containsHumanNsId(nsIdSeq: Seq[String]): Boolean

Tell whether the given sequence of namespace/ID strings contains a human nsId.
Tell whether the given sequence of namespace/ID strings contains a human nsId.

Definition Classes
Speciated
def containsHumanSpecies(speciesSeq: Seq[String]): Boolean

Tell whether the given sequence of species strings contain a human species label.
Tell whether the given sequence of species strings contain a human species label.

Definition Classes
Speciated
def entries: Seq[KBEntry]

Return an sequence over the entries in this KB.
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def equals(arg0: Any): Boolean

Definition Classes
AnyRef → Any
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
final def getClass(): Class[_]

Definition Classes
AnyRef → Any
def hasHumanNsId(nsId: String): Boolean

Tell whether the given namespace/ID string is an ID for humans or not.
Tell whether the given namespace/ID string is an ID for humans or not.

Definition Classes
Speciated
val hasSpeciesInfo: Boolean
def hashCode(): Int

Definition Classes
AnyRef → Any
def hyphenatedProteinKey(text: String): String

Check for one of several types of hyphen-separated strings and, if found, extract and return the candidate text portion, else return the text unchanged.
Check for one of several types of hyphen-separated strings and, if found, extract and return the candidate text portion, else return the text unchanged.

Definition Classes
ReachKBKeyTransforms
def isHumanSpecies(species: String): Boolean

Tell whether the given species string is label for humans or not.
Tell whether the given species string is label for humans or not.

Definition Classes
Speciated
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
def isMemberOf(species: String, speciesSet: SpeciesNameSet): Boolean

Tell whether the given species string is a member of the given set of species.
Tell whether the given species string is a member of the given set of species.

Definition Classes
Speciated
def lookupAll(key: String): Resolutions

Return resolutions for the set of all KB entries for the given key.
def lookupByASpecies(key: String, species: String): Resolutions

Find the set of KB entries, for the given key, which match the given single species.
Find the set of KB entries, for the given key, which match the given single species. Returns resolutions for matching entries or None.
def lookupBySpecies(key: String, speciesSet: SpeciesNameSet): Resolutions

Finds the set of KB entries, for the given key, which contains a species in the given set of species.
Finds the set of KB entries, for the given key, which contains a species in the given set of species. Returns resolutions for matching entries or None.
def lookupHuman(key: String): Resolutions

Finds the set of KB entries, for the given key, which have humans as the species.
Finds the set of KB entries, for the given key, which have humans as the species. Returns resolutions for matching entries or None.
def lookupNoSpecies(key: String): Resolutions

Find the set of KB entries, for the given key, which do not contain a species.
Find the set of KB entries, for the given key, which do not contain a species. Returns resolutions for matching entries or None.
def lookupsAll(allKeys: Seq[String]): Resolutions

Try lookups for all given keys until one succeeds or all fail.
def lookupsByASpecies(allKeys: Seq[String], species: String): Resolutions

Try lookups for all given keys until one succeeds or all fail.
def lookupsBySpecies(allKeys: Seq[String], speciesSet: SpeciesNameSet): Resolutions

Try lookups for all given keys until one succeeds or all fail.
def lookupsHuman(allKeys: Seq[String]): Resolutions

Try lookups for all given keys until one succeeds or all fail.
def lookupsNoSpecies(allKeys: Seq[String]): Resolutions

Try lookups for all given keys until one succeeds or all fail.
def makeCanonicalKey(text: String): String

Canonicalize the given text string into a key for both storage and lookup.
Canonicalize the given text string into a key for both storage and lookup.

Definition Classes
ReachKBKeyTransforms
def makeResolution(entry: Option[KBEntry]): Option[KBResolution]

Wrap the given optional KB entry in a new singleton-sequence of resolutions formed from this KB and the given KB entry.
val metaInfo: IMKBMetaInfo
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def newResolution(entry: KBEntry): KBResolution

Wrap the given KB entry in a new KB resolution formed from this KB and the given KB entry.
def newResolutions(entries: Option[Seq[KBEntry]]): Resolutions

Wrap the given sequence of KB entries in a sequence of resolutions formed from this KB and the given KB entries.
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
def reachAlternateKeys(text: String, transformFns: KeyTransforms): Seq[String]

Return alternate lookup keys created from the given text string and transform functions.
Return alternate lookup keys created from the given text string and transform functions.

Definition Classes
ReachKBKeyTransforms
def stripFamilySuffixes(text: String): String

Return the portion of the text string minus one of the protein family suffixes, if found in the given text string, else return the text lowercased.
Return the portion of the text string minus one of the protein family suffixes, if found in the given text string, else return the text lowercased.

Definition Classes
ReachKBKeyTransforms
def stripMutantProtein(text: String): String

Return the portion of the text string before a trailing mutation phrase, if found in the given text string, else return the text unchanged.
Return the portion of the text string before a trailing mutation phrase, if found in the given text string, else return the text unchanged.

Definition Classes
ReachKBKeyTransforms
def stripOrganCellTypeSuffixes(text: String): String

Return the portion of the text string minus one of the organ-cell-type suffixes, if found in the given text string, else return the text unchanged.
Return the portion of the text string minus one of the organ-cell-type suffixes, if found in the given text string, else return the text unchanged.

Definition Classes
ReachKBKeyTransforms
def stripPTMPrefixes(text: String): String

Return the portion of the text string minus any of the PTM-related prefixes, if found in the given text string, else return the text unchanged.
Return the portion of the text string minus any of the PTM-related prefixes, if found in the given text string, else return the text unchanged.

Definition Classes
ReachKBKeyTransforms
def stripProteinSuffixes(text: String): String

Return the portion of the text string minus one of the protein suffixes, if found in the given text string, else return the text lowercased.
Return the portion of the text string minus one of the protein suffixes, if found in the given text string, else return the text lowercased.

Definition Classes
ReachKBKeyTransforms
def stripSuffixes(suffixes: Seq[String], text: String): String

Try to remove all of the suffixes in the given set from the given text.
Try to remove all of the suffixes in the given set from the given text.

Definition Classes
KBKeyTransforms
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
val theKB: HashMap[String, Set[KBEntry]] with MultiMap[String, KBEntry]

The root data structure implementing this in-memory knowledge base.
def toResolutions(entry: KBEntry): Resolutions

Wrap the given KB entry in a new singleton-sequence of resolutions formed from this KB and the given KB entry.
def toString(): String

Definition Classes
AnyRef → Any
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( ... )

Related Doc: package grounding

class InMemoryKB extends Speciated with ReachKBKeyTransforms

Instance Constructors

new InMemoryKB(namespace: String, hasSpeciesInfo: Boolean, metaInfo: IMKBMetaInfo)

new InMemoryKB(hasSpeciesInfo: Boolean = false, metaInfo: IMKBMetaInfo = new IMKBMetaInfo())

Type Members

type KeyTransforms = Seq[(String) ⇒ String]

type SpeciesNameSet = Set[String]

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

def SpeciesNameSet(xs: String*): Set[String]

def addEntry(entry: KBEntry): HashMap[String, Set[KBEntry]] with MultiMap[String, KBEntry]

def applyTransforms(text: String, transformFns: KeyTransforms): Seq[String]

final def asInstanceOf[T0]: T0

def clone(): AnyRef

def containsHumanNsId(nsIdSeq: Seq[String]): Boolean

def containsHumanSpecies(speciesSeq: Seq[String]): Boolean

def entries: Seq[KBEntry]

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def finalize(): Unit

final def getClass(): Class[_]

def hasHumanNsId(nsId: String): Boolean

val hasSpeciesInfo: Boolean

def hashCode(): Int

def hyphenatedProteinKey(text: String): String

def isHumanSpecies(species: String): Boolean

final def isInstanceOf[T0]: Boolean

def isMemberOf(species: String, speciesSet: SpeciesNameSet): Boolean

def lookupAll(key: String): Resolutions

def lookupByASpecies(key: String, species: String): Resolutions

def lookupBySpecies(key: String, speciesSet: SpeciesNameSet): Resolutions

def lookupHuman(key: String): Resolutions

def lookupNoSpecies(key: String): Resolutions

def lookupsAll(allKeys: Seq[String]): Resolutions

def lookupsByASpecies(allKeys: Seq[String], species: String): Resolutions

def lookupsBySpecies(allKeys: Seq[String], speciesSet: SpeciesNameSet): Resolutions

def lookupsHuman(allKeys: Seq[String]): Resolutions

def lookupsNoSpecies(allKeys: Seq[String]): Resolutions

def makeCanonicalKey(text: String): String

def makeResolution(entry: Option[KBEntry]): Option[KBResolution]

val metaInfo: IMKBMetaInfo

final def ne(arg0: AnyRef): Boolean

def newResolution(entry: KBEntry): KBResolution

def newResolutions(entries: Option[Seq[KBEntry]]): Resolutions

final def notify(): Unit

final def notifyAll(): Unit

def reachAlternateKeys(text: String, transformFns: KeyTransforms): Seq[String]

def stripFamilySuffixes(text: String): String

def stripMutantProtein(text: String): String

def stripOrganCellTypeSuffixes(text: String): String

def stripPTMPrefixes(text: String): String

def stripProteinSuffixes(text: String): String

def stripSuffixes(suffixes: Seq[String], text: String): String

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

val theKB: HashMap[String, Set[KBEntry]] with MultiMap[String, KBEntry]

def toResolutions(entry: KBEntry): Resolutions

def toString(): String

final def wait(): Unit

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

final def wait(arg0: Long): Unit

Inherited from ReachKBKeyTransforms

Inherited from KBKeyTransforms

Inherited from Speciated

Inherited from AnyRef

Inherited from Any

Ungrouped