Serialized Form

Package ubic.basecode.dataStructure

Class ubic.basecode.dataStructure.DoubleAddingMap extends HashMap<K,Double> implements Serializable

serialVersionUID:

2L

Class ubic.basecode.dataStructure.StringToStringSetMap extends HashMap<String,Set<String>> implements Serializable

serialVersionUID:

1L

Package ubic.basecode.dataStructure.matrix

Class ubic.basecode.dataStructure.matrix.AbstractMatrix extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

colMap

Map<C,Integer> colMap

colNames

List<C> colNames

lastColumnIndex

int lastColumnIndex

lastRowIndex

int lastRowIndex

rowMap

Map<R,Integer> rowMap

rowNames

List<R> rowNames

Class ubic.basecode.dataStructure.matrix.CompressedBitMatrix extends AbstractMatrix<R,C,double[]> implements Serializable

serialVersionUID:

1775002416710933373L

Serialized Fields

cols

int cols

matrix

no.uib.cipr.matrix.sparse.FlexCompRowMatrix[] matrix

rows

int rows

totalBitsPerItem

int totalBitsPerItem

Class ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix extends DoubleMatrix<R,C> implements Serializable

serialVersionUID:

5771918031750038719L

Class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix extends DoubleMatrix<R,C> implements Serializable

serialVersionUID:

-239226762166912931L

Serialized Fields

matrix

cern.colt.matrix.DoubleMatrix2D matrix

Class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix1D extends cern.colt.matrix.impl.DenseDoubleMatrix1D implements Serializable

serialVersionUID:

-5196826500179433512L

Class ubic.basecode.dataStructure.matrix.DoubleMatrix extends AbstractMatrix<R,C,Double> implements Serializable

serialVersionUID:

1L

Class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix extends DoubleMatrix<R,C> implements Serializable

serialVersionUID:

-5458302072944941517L

Serialized Fields

data

cern.colt.list.DoubleArrayList[] data

Class ubic.basecode.dataStructure.matrix.IntegerMatrix extends AbstractMatrix<R,C,Integer> implements Serializable

serialVersionUID:

-8413796057024940237L

Serialized Fields

matrix

ObjectMatrixImpl<R,C,Integer> matrix

Class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl extends AbstractMatrix<R,C,V> implements Serializable

serialVersionUID:

-902358802107186038L

Serialized Fields

matrix

cern.colt.matrix.impl.DenseObjectMatrix2D matrix

Class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D extends cern.colt.matrix.DoubleMatrix1D implements Serializable

serialVersionUID:

-5883440011745758929L

Serialized Fields

indexes

cern.colt.list.IntArrayList indexes

values

cern.colt.list.DoubleArrayList values

Class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix extends DoubleMatrix<R,C> implements Serializable

serialVersionUID:

-1651885517252689369L

Serialized Fields

matrix

cern.colt.matrix.impl.SparseDoubleMatrix2D matrix

Class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix extends DoubleMatrix<R,C> implements Serializable

serialVersionUID:

-8911689395488681312L

Serialized Fields

columns

int columns

isDirty

boolean isDirty

matrix

Vector<List<Double>> matrix

Class ubic.basecode.dataStructure.matrix.StringMatrix extends AbstractMatrix<R,C,String> implements Serializable

serialVersionUID:

-7369003979104984162L

Serialized Fields

matrix

cern.colt.matrix.impl.DenseObjectMatrix2D matrix

Package ubic.basecode.graphics

Class ubic.basecode.graphics.JGradientBar extends JPanel implements Serializable

serialVersionUID:

6668982782351006998L

Serialized Fields

gradient

ubic.basecode.graphics.JGradientLabel gradient

m_max

ubic.basecode.graphics.JNumberLabel m_max

m_min

ubic.basecode.graphics.JNumberLabel m_min

Class ubic.basecode.graphics.MatrixDisplay extends JPanel implements Serializable

serialVersionUID:

-8078532270193813539L

Serialized Fields

colorMatrix

ColorMatrix<R,C> colorMatrix

m_cellSize

Dimension m_cellSize

m_columnLabelHeight

int m_columnLabelHeight

m_defaultResolution

int m_defaultResolution

m_fontGutter

int m_fontGutter

m_fontSize

int m_fontSize

m_isShowingStandardizedMatrix

boolean m_isShowingStandardizedMatrix

m_isShowLabels

boolean m_isShowLabels

m_isShowScale

boolean m_isShowScale

m_labelFont

Font m_labelFont

m_labelGutter

int m_labelGutter

m_maxColumnLength

int m_maxColumnLength

m_maxFontSize

int m_maxFontSize

m_ratioWidth

int m_ratioWidth

m_resolution

int m_resolution

m_rowLabelWidth

int m_rowLabelWidth

m_standardizedMatrix

ColorMatrix<R,C> m_standardizedMatrix

m_textSize

int m_textSize

m_unstandardizedMatrix

ColorMatrix<R,C> m_unstandardizedMatrix

SCALE_BAR_ROOM

int SCALE_BAR_ROOM

Package ubic.basecode.math.linearmodels

Class ubic.basecode.math.linearmodels.AnovaEffect extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

dof

double dof

effectName

String effectName

fStat

double fStat

isInteraction

boolean isInteraction

isResiduals

boolean isResiduals

meanSq

double meanSq

pValue

double pValue

ssQ

double ssQ

Package ubic.basecode.ontology.search

Class ubic.basecode.ontology.search.OntologySearchException extends Exception implements Serializable

Serialized Fields

query

String query

Package ubic.basecode.ontology.simple

Class ubic.basecode.ontology.simple.AbstractOntologyResourceSimple extends Object implements Serializable

Serialized Fields

label

String label

uri

String uri

Class ubic.basecode.ontology.simple.OntologyIndividualSimple extends AbstractOntologyResourceSimple implements Serializable

Serialized Fields

instanceOf

OntologyTermSimple instanceOf

Class ubic.basecode.ontology.simple.OntologyPropertySimple extends AbstractOntologyResourceSimple implements Serializable

Class ubic.basecode.ontology.simple.OntologyTermSimple extends AbstractOntologyResourceSimple implements Serializable

Serialized Fields

comment

String comment

label

String label

obsolete

boolean obsolete

uri

String uri