org.geworkbench.bison.datastructure.biocollections.microarrays
Interface DSMicroarraySet<T extends DSMicroarray>

All Superinterfaces:

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

All Known Implementing Classes:

CSExprMicroarraySet, CSMicroarraySet

public interface DSMicroarraySet<T extends DSMicroarray>
extends DSMatrixDataSet<T>, DSDataSet<T>

Defines a generic set of Microarrays.

DSDataSet. The objects in a matrix dataset will themselves contain vectors of values. -- AM todo - watkin - this should have two generic type variables, one for microarray, one for marker. Currently, it is just generic for microarrays.

Field Summary

static int	affyTxtType
static int	alleleType
static int	chipChipType
static int	expPvalueType
static int	geneExpType
static int	genepixGPRType
static int	snpType

Method Summary

DSMicroarraySet<T>	clone(java.lang.String newLabel, int newMarkerNo, int newChipNo)
DSMicroarraySet<T>	deepCopy() Creates a deep copy of the current microarray set (creating fresh copies for all markers, marker values and microarrays in the microarray set).
DSItemList<DSGeneMarker>	getMarkers() get the marker list
double	getMeanValue(DSGeneMarker marker, int maIndex)
int	getPlatformType() Return the platform type (Affy, Genepix, etc) of the arrays contained in this array set.
double[]	getRow(DSGeneMarker marker)
int	getType() The type of the array can be gene expression or genotype This should be replaced by two separate classes with the same interface
double	getValue(DSGeneMarker marker, int maIndex)
void	initialize(int maNo, int mrkNo)
void	mergeMicroarraySet(DSMicroarraySet<T> newMaSet) Merges another MicroarraySet into this one
void	parse(DSMutableMarkerValue marker, java.lang.String value)
void	readFromFile(java.io.File file)
void	resetStatistics()
void	setCompatibilityLabel(java.lang.String compatibilityLabel)

Methods inherited from interface org.geworkbench.bison.datastructure.biocollections.DSMatrixDataSet

getRow, getValue

Methods inherited from interface org.geworkbench.bison.datastructure.biocollections.DSDataSet

addObject, getCompatibilityLabel, getDataSetName, getExperimentInformation, getFile, getObject, getPath, isActive, readFromResource, removeResource, setAbsPath, setExperimentInformation, setFile, setResource, writeToFile, writeToResource

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

Field Detail

geneExpType

static final int geneExpType

See Also:

Constant Field Values

snpType

static final int snpType

See Also:

Constant Field Values

alleleType

static final int alleleType

See Also:

Constant Field Values

expPvalueType

static final int expPvalueType

See Also:

Constant Field Values

chipChipType

static final int chipChipType

See Also:

Constant Field Values

genepixGPRType

static final int genepixGPRType

See Also:

Constant Field Values

affyTxtType

static final int affyTxtType

See Also:

Constant Field Values

Method Detail

getType

int getType()

The type of the array can be gene expression or genotype This should be replaced by two separate classes with the same interface

clone

DSMicroarraySet<T> clone(java.lang.String newLabel,
                         int newMarkerNo,
                         int newChipNo)

getValue

double getValue(DSGeneMarker marker,
                int maIndex)

getMeanValue

double getMeanValue(DSGeneMarker marker,
                    int maIndex)

getRow

double[] getRow(DSGeneMarker marker)

resetStatistics

void resetStatistics()

parse

void parse(DSMutableMarkerValue marker,
           java.lang.String value)

mergeMicroarraySet

void mergeMicroarraySet(DSMicroarraySet<T> newMaSet)
                        throws java.lang.Exception

Merges another MicroarraySet into this one

Parameters:

newMaSet - MicroarraySet

Throws:

java.lang.Exception

getMarkers

DSItemList<DSGeneMarker> getMarkers()

get the marker list

Returns:

DSItemList todo - watkin - this should not be DSGeneMarker, but a generic variable.

deepCopy

DSMicroarraySet<T> deepCopy()

Creates a deep copy of the current microarray set (creating fresh copies for all markers, marker values and microarrays in the microarray set).

Returns:

The new microarray set copy.

getPlatformType

int getPlatformType()

Return the platform type (Affy, Genepix, etc) of the arrays contained in this array set.

Returns:

setCompatibilityLabel

void setCompatibilityLabel(java.lang.String compatibilityLabel)

readFromFile

void readFromFile(java.io.File file)

initialize

void initialize(int maNo,
                int mrkNo)