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, DSDemandResultSet, DSGSEAResultDataSet, DSHierClusterDataSet, DSMasterRagulatorResultSet<T>, DSMasterRegulatorTableResultSet, DSMatrixReduceSet, DSMicroarraySet, DSPCADataSet, DSProbeIntensityArray, DSProteinStructure, DSSequenceSet<T>, DSSignificanceResultSet<T>, DSSOMClusterDataSet, DSTTestResultSet<T>
All Known Implementing Classes:
AdjacencyMatrixDataSet, AracneResult, CSAlignmentResultSet, CSAncillaryDataSet, CSAnovaResultSet, CSClassifier, CSDataSet, CSDemandResultSet, CSGSEAResultDataSet, CSHierClusterDataSet, CSMasterRegulatorResultSet, CSMasterRegulatorTableResultSet, CSMatrixReduceSet, CSMicroarraySet, CSPCADataSet, CSProbeIntensityArray, CSProteinStructure, CSSequenceSet, CSSignificanceResultSet, CSSOMClusterDataSet, CSTTestResultSet, CSVisualClassifier, EdgeListDataSet, FoldChangeResult, GoAnalysisResult, IdeaResultDataSet, ImageData, KMeansResult, KMeansResultMarkers, LincsDataSet, MarkUsResultDataSet, MedusaDataSet, MindyDataSet, NetBoostDataSet, PatternResult, PudgeResultSet, SamResultData, SelectorResult, SkybaseResultSet, SkyLineResultDataSet, SVMResultSet

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.Class<?> objectType, java.lang.Object anObject)
          Stores an arbitrary object by type.
 java.util.ArrayList<java.lang.Integer> getColumnOrder()
           
 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.Class<?> objectType)
          Gets an object by the specified type.
 boolean isActive()
          Gets the activation status of the data set.
 void setColumnOrder(java.util.ArrayList<java.lang.Integer> columnOrder)
           
 void setExperimentInformation(java.lang.String experimentInformation)
          Sets the experiment information.
 void setFile(java.io.File file)
           
 void writeToFile(java.lang.String fileName)
          Writes the data set to the provided filename.
 
Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSDescribable
getDescription, setDescription
 
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
 
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.Class<?> 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.Class<?> 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.

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.

getColumnOrder

java.util.ArrayList<java.lang.Integer> getColumnOrder()

setColumnOrder

void setColumnOrder(java.util.ArrayList<java.lang.Integer> columnOrder)