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Public Member Functions
AdDataSet Class Reference

#import <AdunDataSet.h>

Inheritance diagram for AdDataSet:
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List of all members.

Public Member Functions

(id) - init
(id) - initWithName:
(id) - initWithName:inputReferences:
(id) - initWithName:inputReferences:dataGenerator:
(id) - initWithName:inputReferences:dataGeneratorName:dataGeneratorVersion:
(BOOL) - containsDataMatrix:
(BOOL) - containsDataMatrixWithName:
(void) - addDataMatrix:
(void) - removeDataMatrix:
(BOOL) - removeDataMatrixWithName:
(NSArray *) - dataMatrices
(AdDataMatrix *) - dataMatrixWithName:
(NSString *) - dataGeneratorID
(NSString *) - dataGeneratorName
(double) - dataGeneratorVersion
(NSArray *) - dataMatrixNames
(NSEnumerator *) - dataMatrixEnumerator
(NSEnumerator *) - nameEnumerator
(NSString *) - attributeFileFromMatrix:attributeColumn:residueColumn:atomColumn:name:matchMode:
- Public Member Functions inherited from AdModelObject
(BOOL) - archiveToDirectory:
(BOOL) - archiveToFile:
(NSString *) - identification
(NSString *) - archivePathExtension
(id) - creator
(id) - created
(NSString *) - name
(NSString *) - type
(id) - keywords
(NSDictionary *) - reference
(NSString *) - database
(NSString *) - schema
(NSDictionary *) - properties
(NSDictionary *) - systemMetadata
(NSDictionary *) - userMetadata
(NSDictionary *) - metadata
(NSDictionary *) - combinedMetadata
(NSDictionary *) - allMetadata
(id) - valueForMetadataKey:
(void) - setValue:forMetadataKey:
(void) - setValue:forMetadataKey:inDomain:
(void) - removeMetadataKey:
(AdMetadataDomain- domainForMetadataKey:
(void) - setDomain:forMetadataKey:
(void) - updateMetadata:
(void) - updateMetadata:inDomains:
(id) - valueForVolatileMetadataKey:
(void) - setValue:forVolatileMetadataKey:
(void) - removeVolatileMetadataKey:
(NSArray *) - inputReferencesToObjectsOfClass:
(NSArray *) - inputReferences
(void) - addInputReference:
(void) - addInputReferenceToObject:
(void) - addInputReferenceToObjectWithID:ofType:
(void) - removeInputReferenceToObject:
(void) - removeInputReferenceToObjectWithID:ofType:
(NSArray *) - outputReferencesToObjectsOfClass:
(NSArray *) - outputReferences
(void) - addOutputReferenceToObject:
(void) - addOutputReferenceToObjectWithID:ofType:
(void) - removeOutputReferenceToObject:
(void) - removeOutputReferenceToObjectWithID:ofType:
(void) - removeOutputReferenceToObjectWithID:
(void) - removeAllOutputReferences
(void) - copyMetadataInDomains:fromObject:
(void) - copyInputReferencesFromObject:
(void) - copyOutputReferencesFromObject:

Additional Inherited Members

- Static Public Member Functions inherited from AdModelObject
(id) + unarchiveFromFile:

Detailed Description

AdDataSet objects hold a collection of related AdDataMatrix instances along with information on how they were generated i.e. who they were generated from and how. AdDataSet is the basic class for transmitting and storing information in both AdunKernel and ULFramework.

Todo:
Refactor - Implement mutable and immutable classes, AdDataSet, AdMutableDataSet.

Member Function Documentation

- (void) addDataMatrix: (AdDataMatrix*)  aDataMatrix

Adds aDataMatrix to the data set

- (NSString *) attributeFileFromMatrix: (NSString*)  matrix
attributeColumn: (NSString*)  attributeColName
residueColumn: (NSString*)  residueColName
atomColumn: (NSString*)  atomColName
name: (NSString*)  name
matchMode: (NSString*)  matchMode 

Creates a chimera attribute file string from the data in matrix Assumes each row in matrix contains data related to a protein residue or atom.

Parameters:
matrixThe matrix in the receiver to create the attribute file from.
residueColNameThe name of the column in the receiver which contains the residue index each row relates too. If 'Numbered' is passed then it is assumed the residue index is equivalent to the row index. Cannot be nil.
atomColNameThe name of the column in the receiver which contains the name of the atom each row relates to. Can be nil in which case the attribute is a residue attribute.
attributeColNameThe name of the column in the receiver containing the attribute data
nameThe name of the attribute
matchModeTells chimera how to match attributes to atoms. The valid values are
  • Any: Every atom/residue that matches the specification is given the attribute
  • 1-to-1: Each attribute can only match one atom
  • Non-zero: Each attribute must match something.
- (BOOL) containsDataMatrix: (AdDataMatrix*)  aDataMatrix

Returns YES if aDataMatrix is part of the data set. Returns NO otherwise.

- (BOOL) containsDataMatrixWithName: (NSString*)  aString

Returns YES the object contains a matrix called aString. Returns NO otherwise.

- (NSString*) dataGeneratorID

Returns the id of the plugin that generated the data - usually pluginName_pluginVersion.

- (NSString *) dataGeneratorName

Returns the name of the plugin that generated the data. This is "Unknown" if no name was supplied on creation.

- (double) dataGeneratorVersion

Returns the version number of the plugin that generated the data or "1.0" if none was supplied on creation.

- (NSArray*) dataMatrices

Returns an array containing all the AdDataMatrix objects in the data set.

- (NSEnumerator *) dataMatrixEnumerator

Returns an enumerator over the data matrices

- (NSArray *) dataMatrixNames

Returns an array containining the names of all the data matrix names

- (AdDataMatrix *) dataMatrixWithName: (NSString*)  aString

Returns the AdDataMatrix instance with name aString . Returns nil if no matrix with name aString is present. If there is more than one AdDataMatrix object with name aString it returns the first one found.

- (id) init
- (id) initWithName: (NSString*)  aString

As initWithName:inputReferences: passing nil for aDict.

- (id) initWithName: (NSString*)  name
inputReferences: (NSDictionary*)  aDict 

As initWithName:inputReferences:dataGeneratorName:dataGeneratorVersion: passing nil for aDict, stringTwo and aNumber.

- (id) initWithName: (NSString*)  aString
inputReferences: (NSDictionary*)  aDict
dataGenerator: (NSBundle*)  aBundle 

As initWithName:inputReferences:dataGeneratorName:dataGeneratorVersion: with stringTwo being set to [aBundle bundleIdentifier] and aNumber given by the value for "PluginVersion" in aBundles info dictionary.

- (id) initWithName: (NSString*)  stringOne
inputReferences: (NSDictionary*)  aDict
dataGeneratorName: (NSString*)  stringTwo
dataGeneratorVersion: (NSString*)  aNumber 

Creates a new AdDataSet instance for data generated from the objects referenced by aDict by the plugin aBundle.

Parameters:
aStringThe name of the new object. If nil defaults to "None".
aDictA dictionary whose keys are class types and whose values are NSDictionaries. The keys of these dictionaries are object idents. The values are also NSDictionaries with the following keys, "Identification", "Class", "Schema" and "Database". If nil no references are set.
dataGeneratorNameThe name of the plugin that generated the data. If nil this defaults to "Unknown".
dataGeneratorVersionThe version of the plugin that generated the data as a NSString. If nil this defaults to "1"
Note:
Simplfy input references arguement e.g. pass an array of dictionaries with each dictionary containing an object reference.
- (NSEnumerator *) nameEnumerator

Returns an enumerator over the matrix names

- (void) removeDataMatrix: (AdDataMatrix*)  aDataMatrix

Removes the matrix aDataMatrix from the data set. Does nothing if aDataMatrix is not part of the data set or if it is nil.

- (BOOL) removeDataMatrixWithName: (NSString*)  aString

Removes the AdDataMatrix object with name aString from the data set returning YES on success. If no data matrix with name aString is present or it is nil this method return NO. If there is more than one AdDataMatrix instance with name aString the first one found is removed.