Serialized Form

Package ubic.basecode.dataStructure

Class ubic.basecode.dataStructure.DoubleAddingMap

class DoubleAddingMap extends HashMap<K,Double> implements Serializable

serialVersionUID:

2L

Class ubic.basecode.dataStructure.StringToStringSetMap

class StringToStringSetMap extends HashMap<String,Set<String>> implements Serializable

serialVersionUID:

1L

Package ubic.basecode.dataStructure.matrix

Class ubic.basecode.dataStructure.matrix.AbstractMatrix

class 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

class 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

class CompressedSparseDoubleMatrix extends DoubleMatrix<R,C> implements Serializable

serialVersionUID:

5771918031750038719L

Class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix

class DenseDoubleMatrix extends DoubleMatrix<R,C> implements Serializable

serialVersionUID:

-239226762166912931L

Serialized Fields

matrix

DoubleMatrix2D matrix

Class ubic.basecode.dataStructure.matrix.DenseDoubleMatrix1D

class DenseDoubleMatrix1D extends DenseDoubleMatrix1D implements Serializable

serialVersionUID:

-5196826500179433512L

Class ubic.basecode.dataStructure.matrix.DoubleMatrix

class DoubleMatrix extends AbstractMatrix<R,C,Double> implements Serializable

serialVersionUID:

1L

Class ubic.basecode.dataStructure.matrix.FastRowAccessDoubleMatrix

class FastRowAccessDoubleMatrix extends DoubleMatrix<R,C> implements Serializable

serialVersionUID:

-5458302072944941517L

Serialized Fields

data

DoubleArrayList[] data

Class ubic.basecode.dataStructure.matrix.IntegerMatrix

class IntegerMatrix extends AbstractMatrix<R,C,Integer> implements Serializable

serialVersionUID:

-8413796057024940237L

Serialized Fields

matrix

ObjectMatrixImpl<R,C,Integer> matrix

Class ubic.basecode.dataStructure.matrix.ObjectMatrixImpl

class ObjectMatrixImpl extends AbstractMatrix<R,C,V> implements Serializable

serialVersionUID:

-902358802107186038L

Serialized Fields

matrix

DenseObjectMatrix2D matrix

Class ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D

class RCDoubleMatrix1D extends DoubleMatrix1D implements Serializable

serialVersionUID:

-5883440011745758929L

Serialized Fields

indexes

IntArrayList indexes

values

DoubleArrayList values

Class ubic.basecode.dataStructure.matrix.SparseDoubleMatrix

class SparseDoubleMatrix extends DoubleMatrix<R,C> implements Serializable

serialVersionUID:

-1651885517252689369L

Serialized Fields

matrix

SparseDoubleMatrix2D matrix

Class ubic.basecode.dataStructure.matrix.SparseRaggedDoubleMatrix

class 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

class StringMatrix extends AbstractMatrix<R,C,String> implements Serializable

serialVersionUID:

-7369003979104984162L

Serialized Fields

matrix

DenseObjectMatrix2D matrix

Package ubic.basecode.graphics

Class ubic.basecode.graphics.JGradientBar

class 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

class 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

class 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

Exception Class ubic.basecode.ontology.search.OntologySearchException

class OntologySearchException extends Exception implements Serializable

Serialized Fields

query

String query

Package ubic.basecode.ontology.simple

Class ubic.basecode.ontology.simple.AbstractOntologyResourceSimple

class AbstractOntologyResourceSimple extends Object implements Serializable

Serialized Fields

label

@Nullable String label

localName

@Nullable String localName

uri

@Nullable String uri

Class ubic.basecode.ontology.simple.OntologyIndividualSimple

class OntologyIndividualSimple extends AbstractOntologyResourceSimple implements Serializable

Serialized Fields

instanceOf

OntologyTermSimple instanceOf

Class ubic.basecode.ontology.simple.OntologyPropertySimple

class OntologyPropertySimple extends AbstractOntologyResourceSimple implements Serializable

Class ubic.basecode.ontology.simple.OntologyTermSimple

class OntologyTermSimple extends AbstractOntologyResourceSimple implements Serializable

Serialized Fields

comment

@Nullable String comment

obsolete

boolean obsolete