org.geworkbench.bison.datastructure.biocollections
Interface DSDataSet<T extends DSBioObject>

All Superinterfaces:

java.util.Collection<T>, DSDescribable, DSExtendable, DSIdentifiable, DSItemList<T>, DSNamed, java.lang.Iterable<T>, java.util.List<T>, java.io.Serializable

All Known Subinterfaces:

DSAlignmentResultSet, DSAncillaryDataSet<T>, DSAnovaResultSet<T>, DSClusterDataSet, DSGSEAResultDataSet, DSHierClusterDataSet, DSMasterRagulatorResultSet<T>, DSMatrixReduceSet, DSMicroarraySet<T>, DSPCADataSet, DSProbeIntensityArray, DSProteinStructure, DSPrtAnnotResultSet, DSPrtDBResultSet, DSSequenceSet<T>, DSSignificanceResultSet<T>, DSSOMClusterDataSet, DSTTestResultSet<T>

All Known Implementing Classes:

AdjacencyMatrixDataSet, CSAlignmentResultSet, CSAncillaryDataSet, CSAnovaResultSet, CSChipchipSet, CSClassifier, CSDataSet, CSExprMicroarraySet, CSGSEAResultDataSet, CSHierClusterDataSet, CSMasterRegulatorResultSet, CSMatrixReduceSet, CSMicroarraySet, CSPCADataSet, CSProbeIntensityArray, CSProteinStructure, CSPrtAnnotResultSet, CSPrtDBResultSet, CSSequenceSet, CSSignificanceResultSet, CSSOMClusterDataSet, CSTTestResultSet, CSVisualClassifier, EdgeListDataSet, GoAnalysisResult, ImageData, MarkUsResultDataSet, MedusaDataSet, MindyDataSet, NetBoostDataSet, PatternDB, PudgeResultSet, SkyLineResultDataSet, SoapParmsDataSet

public interface DSDataSet<T extends DSBioObject>
extends DSDescribable, DSNamed, java.io.Serializable, DSExtendable, DSItemList<T>

Implementing classes store sets of biological data (such as a set of microarrays or sequences).

Method Summary

void	addObject(java.lang.Object objectType, java.lang.Object anObject) Stores an arbitrary object by type.
java.lang.String	getCompatibilityLabel() Gets a string describing the compatibility of this data set.
java.lang.String	getDataSetName() The name of data set.
java.lang.String	getExperimentInformation() Returns the experiment information associated with the data set.
java.io.File	getFile() The underlying file associated with this data set.
java.lang.Object	getObject(java.lang.Object objectType) Gets an object by the specified type.
java.lang.String	getPath() Gets the path to the file associated with this data set.
boolean	isActive() Gets the activation status of the data set.
void	readFromResource() Reads from the resource associated with this data set.
void	removeResource(Resource resource) Disassociates the specified resource from this data set.
void	setAbsPath(java.lang.String absPath) Sets the path to the absolute path given.
void	setExperimentInformation(java.lang.String experimentInformation) Sets the experiment information.
void	setFile(java.io.File file)
void	setResource(Resource resource) Associates the given resource with this data set.
void	writeToFile(java.lang.String fileName) Writes the data set to the provided filename.
void	writeToResource() Writes to the resource associated with this data set.

Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSDescribable

addDescription, getDescriptions, removeDescription

Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSNamed

getLabel, setLabel

Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSExtendable

addNameValuePair, allowMultipleValues, clearName, forceUniqueValue, getValuesForName, isUniqueValue

Methods inherited from interface org.geworkbench.bison.datastructure.complex.panels.DSItemList

get, get, rename

Methods inherited from interface java.util.List

add, add, addAll, addAll, clear, contains, containsAll, equals, get, hashCode, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, retainAll, set, size, subList, toArray, toArray

Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSIdentifiable

getID, setID

Method Detail

getDataSetName

java.lang.String getDataSetName()

The name of data set.

Returns:

the data set name.

getFile

java.io.File getFile()

The underlying file associated with this data set.

Returns:

the file for this data set.

setFile

void setFile(java.io.File file)

writeToFile

void writeToFile(java.lang.String fileName)

Writes the data set to the provided filename.

Parameters:

fileName - the filename (path) to which to write this file.

getObject

java.lang.Object getObject(java.lang.Object objectType)

Gets an object by the specified type.

Parameters:

objectType - the object specifying the type of the required object.

Returns:

the requested object

addObject

void addObject(java.lang.Object objectType,
               java.lang.Object anObject)

Stores an arbitrary object by type.

Parameters:

objectType - the object specifying the type.

anObject - the object to store.

isActive

boolean isActive()

Gets the activation status of the data set.

Returns:

true if active, true otherwise.

getCompatibilityLabel

java.lang.String getCompatibilityLabel()

Gets a string describing the compatibility of this data set.

Returns:

the compatibility label.

getPath

java.lang.String getPath()

Gets the path to the file associated with this data set.

Returns:

the path as a String.

setAbsPath

void setAbsPath(java.lang.String absPath)

Sets the path to the absolute path given.

Parameters:

absPath - the absolute (non-relative) path.

setResource

void setResource(Resource resource)

Associates the given resource with this data set.

Parameters:

resource - the resource to associate with this data set.

removeResource

void removeResource(Resource resource)

Disassociates the specified resource from this data set.

Parameters:

resource - the resource to remove.

readFromResource

void readFromResource()

Reads from the resource associated with this data set.

writeToResource

void writeToResource()

Writes to the resource associated with this data set.

getExperimentInformation

java.lang.String getExperimentInformation()

Returns the experiment information associated with the data set. What constitutes "experiment information" varies, depending on the input source where the data set came from. E.g., for Affy input files it is the file preamble (the part just before the data lines which provides various experiment execution parameters) that becomes the experiment information.

Returns:

the experiment information string.

setExperimentInformation

void setExperimentInformation(java.lang.String experimentInformation)

Sets the experiment information.

Parameters:

experimentInformation - the experiment information.