ReachKBKeyTransforms

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

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
val HyphenatedNamePat: Regex

Pattern matching 2 text strings separated by a hyphen, case insensitive.
val OrganSuffixPat: Regex

Trailing context strings for organ phrases, case insensitive.
val PTMPrefixPat: Regex

Match protein names beginning with special PTM-related prefix characters.
val PhosphorMutationPat: Regex

Match phosphorylation mutation phrases, case insensitive.
val TrailingMutationPat: Regex

Match mutation string at end of text string, case insensitive.
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( ... )
final def eq(arg0: AnyRef): Boolean

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

Definition Classes
AnyRef → Any
val familyKeyTransforms: Seq[(String) ⇒ String]

List of transform methods to apply for alternate Protein Family lookups.
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 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
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
def isProteinDomain(domain: String): Boolean
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
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
val organCellTypeKeyTransforms: Seq[(String) ⇒ String]

List of transform methods to apply for alternate Organ-CellType lookups.
val proteinDomainSuffixes: Set[String]

Set of protein domain suffixes.
val proteinKeyTransforms: Seq[(String) ⇒ String]

List of transform methods to apply for alternate Protein lookups.
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
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 Docs: trait ReachKBKeyTransforms | package grounding

object ReachKBKeyTransforms extends ReachKBKeyTransforms

Type Members

type KeyTransforms = Seq[(String) ⇒ String]

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

val HyphenatedNamePat: Regex

val OrganSuffixPat: Regex

val PTMPrefixPat: Regex

val PhosphorMutationPat: Regex

val TrailingMutationPat: Regex

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

final def asInstanceOf[T0]: T0

def clone(): AnyRef

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

val familyKeyTransforms: Seq[(String) ⇒ String]

def finalize(): Unit

final def getClass(): Class[_]

def hashCode(): Int

def hyphenatedProteinKey(text: String): String

final def isInstanceOf[T0]: Boolean

def isProteinDomain(domain: String): Boolean

def makeCanonicalKey(text: String): String

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

val organCellTypeKeyTransforms: Seq[(String) ⇒ String]

val proteinDomainSuffixes: Set[String]

val proteinKeyTransforms: Seq[(String) ⇒ String]

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

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 AnyRef

Inherited from Any

Ungrouped