org.geworkbench.bison.datastructure.biocollections.microarrays
Interface DSMicroarraySet

All Superinterfaces:
java.util.Collection<DSMicroarray>, DSDataSet<DSMicroarray>, DSDescribable, DSExtendable, DSIdentifiable, DSItemList<DSMicroarray>, DSNamed, java.lang.Iterable<DSMicroarray>, java.util.List<DSMicroarray>, java.io.Serializable
All Known Implementing Classes:
CSMicroarraySet

public interface DSMicroarraySet
extends DSDataSet<DSMicroarray>

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.

Version:
$Id: DSMicroarraySet.java 8491 2011-11-04 20:01:11Z youmi $

Field Summary
static int affyTxtType
           
static int DO_NOT_CREATE_VALUE_OBJECT
           
static int expPvalueType
           
static int genepixGPRType
           
 
Method Summary
 java.lang.String getAnnotationFileName()
           
 DSItemList<DSGeneMarker> getMarkers()
          get the marker list
 double getMeanValue(DSGeneMarker marker, int maIndex)
           
 int[] getNewMarkerOrder()
           
 double[] getRow(DSGeneMarker marker)
           
 java.lang.String getSelectorMarkerOrder()
           
 double getValue(DSGeneMarker marker, int maIndex)
           
 double getValue(int markerIndex, int microarrayIndex)
           
 void initializeMarkerVector(int markerCount)
           
 void mergeMicroarraySet(DSMicroarraySet newMaSet)
          Merges another MicroarraySet into this one
 void setAnnotationFileName(java.lang.String annotationFileName)
           
 void setCompatibilityLabel(java.lang.String compatibilityLabel)
           
 void setSelectorMarkerOrder(java.lang.String order)
           
 void sortMarkers(int mrkNo)
           
 void writeToTabDelimFile(java.lang.String fileName)
           
 
Methods inherited from interface org.geworkbench.bison.datastructure.biocollections.DSDataSet
addObject, getColumnOrder, getCompatibilityLabel, getDataSetName, getExperimentInformation, getFile, getObject, isActive, setColumnOrder, setExperimentInformation, setFile, writeToFile
 
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
 

Field Detail

DO_NOT_CREATE_VALUE_OBJECT

static final int DO_NOT_CREATE_VALUE_OBJECT
See Also:
Constant Field Values

expPvalueType

static final int expPvalueType
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

getValue

double getValue(int markerIndex,
                int microarrayIndex)

getValue

double getValue(DSGeneMarker marker,
                int maIndex)

getMeanValue

double getMeanValue(DSGeneMarker marker,
                    int maIndex)

getRow

double[] getRow(DSGeneMarker marker)

mergeMicroarraySet

void mergeMicroarraySet(DSMicroarraySet 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

setCompatibilityLabel

void setCompatibilityLabel(java.lang.String compatibilityLabel)

initializeMarkerVector

void initializeMarkerVector(int markerCount)

getAnnotationFileName

java.lang.String getAnnotationFileName()

setAnnotationFileName

void setAnnotationFileName(java.lang.String annotationFileName)

sortMarkers

void sortMarkers(int mrkNo)

getNewMarkerOrder

int[] getNewMarkerOrder()

getSelectorMarkerOrder

java.lang.String getSelectorMarkerOrder()

setSelectorMarkerOrder

void setSelectorMarkerOrder(java.lang.String order)

writeToTabDelimFile

void writeToTabDelimFile(java.lang.String fileName)