org.geworkbench.bison.datastructure.biocollections.microarrays
Class CSMicroarraySet

java.lang.Object
  extended by java.util.AbstractCollection<E>
      extended by java.util.AbstractList<E>
          extended by java.util.ArrayList<T>
              extended by org.geworkbench.bison.datastructure.complex.panels.CSItemList<T>
                  extended by org.geworkbench.bison.datastructure.complex.panels.CSSequentialItemList<T>
                      extended by org.geworkbench.bison.datastructure.biocollections.CSDataSet<DSMicroarray>
                          extended by org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<DSMicroarray>, java.util.Collection<DSMicroarray>, java.util.List<DSMicroarray>, java.util.RandomAccess, DSDataSet<DSMicroarray>, DSMicroarraySet, DSItemList<DSMicroarray>, DSDescribable, DSExtendable, DSIdentifiable, DSNamed

public final class CSMicroarraySet
extends CSDataSet<DSMicroarray>
implements DSMicroarraySet

Title: caWorkbench

Description: Modular Application Framework for Gene Expession, Sequence and Genotype Analysis

Copyright: Copyright (c) 2003 -2004

Company: Columbia University

Version:
$Id: CSMicroarraySet.java 8761 2012-01-25 17:34:14Z zji $
Author:
Adam Margolin
See Also:
Serialized Form

Field Summary
 
Fields inherited from class org.geworkbench.bison.datastructure.biocollections.CSDataSet
columnOrder, compatibilityLabel, dataSetProperties, description, experimentInfo, extend, file, label
 
Fields inherited from class java.util.AbstractList
modCount
 
Fields inherited from interface org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet
affyTxtType, DO_NOT_CREATE_VALUE_OBJECT, expPvalueType, genepixGPRType
 
Constructor Summary
CSMicroarraySet()
           
 
Method Summary
 java.lang.String getAnnotationFileName()
           
 java.lang.String getDescription()
          Get all available descriptions in the form of an array of strings.
 CSMarkerVector getMarkers()
          get the marker list
 double getMeanValue(DSGeneMarker marker, int maIndex)
           
 DSMicroarray getMicroarrayWithId(java.lang.String string)
           
 int[] getNewMarkerOrder()
           
 double[] getRow(DSGeneMarker marker)
           
 java.lang.String getSelectorMarkerOrder()
           
 double getValue(DSGeneMarker marker, int maIndex)
           
 double getValue(int markerIndex, int maIndex)
           
 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 writeToFile(java.lang.String fileName)
          Writes the data set to the provided filename.
 void writeToTabDelimFile(java.lang.String fileName)
           
 
Methods inherited from class org.geworkbench.bison.datastructure.biocollections.CSDataSet
addNameValuePair, addObject, allowMultipleValues, clearName, forceUniqueValue, getColumnOrder, getCompatibilityLabel, getDataSetName, getExperimentInformation, getFile, getID, getLabel, getObject, getValuesForName, isActive, isUniqueValue, setColumnOrder, setDescription, setExperimentInformation, setFile, setID, setLabel, toString
 
Methods inherited from class org.geworkbench.bison.datastructure.complex.panels.CSSequentialItemList
add, add, remove
 
Methods inherited from class org.geworkbench.bison.datastructure.complex.panels.CSItemList
addAll, clear, equals, get, hashCode, set, setLabel
 
Methods inherited from class java.util.ArrayList
addAll, clone, contains, ensureCapacity, get, indexOf, isEmpty, lastIndexOf, remove, removeRange, size, toArray, toArray, trimToSize
 
Methods inherited from class java.util.AbstractList
iterator, listIterator, listIterator, subList
 
Methods inherited from class java.util.AbstractCollection
containsAll, removeAll, retainAll
 
Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface org.geworkbench.bison.datastructure.biocollections.DSDataSet
addObject, getColumnOrder, getCompatibilityLabel, getDataSetName, getExperimentInformation, getFile, getObject, isActive, setColumnOrder, setExperimentInformation, setFile
 
Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSDescribable
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
 

Constructor Detail

CSMicroarraySet

public CSMicroarraySet()
Method Detail

getDescription

public java.lang.String getDescription()
Description copied from class: CSDataSet
Get all available descriptions in the form of an array of strings.

Specified by:
getDescription in interface DSDescribable
Overrides:
getDescription in class CSDataSet<DSMicroarray>
Returns:
an array containing all descriptions.

getValue

public double getValue(DSGeneMarker marker,
                       int maIndex)
Specified by:
getValue in interface DSMicroarraySet

getMeanValue

public double getMeanValue(DSGeneMarker marker,
                           int maIndex)
Specified by:
getMeanValue in interface DSMicroarraySet

getValue

public double getValue(int markerIndex,
                       int maIndex)
Specified by:
getValue in interface DSMicroarraySet

getRow

public double[] getRow(DSGeneMarker marker)
Specified by:
getRow in interface DSMicroarraySet

setCompatibilityLabel

public void setCompatibilityLabel(java.lang.String compatibilityLabel)
Specified by:
setCompatibilityLabel in interface DSMicroarraySet

getMarkers

public CSMarkerVector getMarkers()
Description copied from interface: DSMicroarraySet
get the marker list

Specified by:
getMarkers in interface DSMicroarraySet
Returns:
DSItemList

mergeMicroarraySet

public void mergeMicroarraySet(DSMicroarraySet newMaSet)
Description copied from interface: DSMicroarraySet
Merges another MicroarraySet into this one

Specified by:
mergeMicroarraySet in interface DSMicroarraySet
Parameters:
newMaSet - MicroarraySet

getMicroarrayWithId

public DSMicroarray getMicroarrayWithId(java.lang.String string)

writeToFile

public void writeToFile(java.lang.String fileName)
Description copied from interface: DSDataSet
Writes the data set to the provided filename.

Specified by:
writeToFile in interface DSDataSet<DSMicroarray>
Overrides:
writeToFile in class CSDataSet<DSMicroarray>
Parameters:
fileName - the filename (path) to which to write this file.

writeToTabDelimFile

public void writeToTabDelimFile(java.lang.String fileName)
Specified by:
writeToTabDelimFile in interface DSMicroarraySet

initializeMarkerVector

public void initializeMarkerVector(int markerCount)
Specified by:
initializeMarkerVector in interface DSMicroarraySet

getAnnotationFileName

public java.lang.String getAnnotationFileName()
Specified by:
getAnnotationFileName in interface DSMicroarraySet
Returns:
the annotationFileName

setAnnotationFileName

public void setAnnotationFileName(java.lang.String annotationFileName)
Specified by:
setAnnotationFileName in interface DSMicroarraySet
Parameters:
annotationFileName - the annotationFileName to set

getNewMarkerOrder

public int[] getNewMarkerOrder()
Specified by:
getNewMarkerOrder in interface DSMicroarraySet

sortMarkers

public void sortMarkers(int mrkNo)
Specified by:
sortMarkers in interface DSMicroarraySet

getSelectorMarkerOrder

public java.lang.String getSelectorMarkerOrder()
Specified by:
getSelectorMarkerOrder in interface DSMicroarraySet

setSelectorMarkerOrder

public void setSelectorMarkerOrder(java.lang.String order)
Specified by:
setSelectorMarkerOrder in interface DSMicroarraySet