Serialized Form (baseCode 1.1.11 API)

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<K,V> colMap
```
    - colNames
```
List<E> colNames
```
    - lastColumnIndex
```
int lastColumnIndex
```
    - lastRowIndex
```
int lastRowIndex
```
    - rowMap
```
Map<K,V> rowMap
```
    - rowNames
```
List<E> rowNames
```
- Class ubic.basecode.dataStructure.matrix.CompressedBitMatrix extends AbstractMatrix<R,C,double[]> implements Serializable
  
  serialVersionUID:
  
  1775002416710933373L
  - Serialized Fields
    - matrix
```
no.uib.cipr.matrix.sparse.FlexCompRowMatrix[] matrix
```
    - rows
```
int rows
```
    - cols
```
int cols
```
    - 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,V> 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<E> 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<A,B> colorMatrix
```
    - m_isShowingStandardizedMatrix
```
boolean m_isShowingStandardizedMatrix
```
    - m_standardizedMatrix
```
ColorMatrix<A,B> m_standardizedMatrix
```
    - m_unstandardizedMatrix
```
ColorMatrix<A,B> m_unstandardizedMatrix
```
    - SCALE_BAR_ROOM
```
int SCALE_BAR_ROOM
```
    - 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_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_textSize
```
int m_textSize
```
Package ubic.basecode.math.linearmodels
- Class ubic.basecode.math.linearmodels.GenericAnovaResult extends AnovaResult implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - interactionEffects
```
Map<K,V> interactionEffects
```
    - mainEffects
```
Map<K,V> mainEffects
```
    - residual
```
AnovaEffect residual
```
- Class ubic.basecode.math.linearmodels.LinearModelSummary extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - adjRSquared
```
Double adjRSquared
```
    - anovaResult
```
GenericAnovaResult anovaResult
```
    - coefficients
```
Double[] coefficients
```
    - contrastCoefficients
```
DoubleMatrix<R,C> contrastCoefficients
```
    - denominatorDof
```
Integer denominatorDof
```
    - effects
```
Double[] effects
```
      AKA Qty
    - factorNames
```
List<E> factorNames
```
    - factorValueNames
```
Map<K,V> factorValueNames
```
    - formula
```
String formula
```
    - fStat
```
Double fStat
```
    - key
```
String key
```
      Name for this summary e.g. probe identifier
    - numeratorDof
```
Integer numeratorDof
```
    - priorDof
```
Double priorDof
```
      Only if ebayes has been applied
    - residuals
```
Double[] residuals
```
    - rSquared
```
Double rSquared
```
    - shrunken
```
boolean shrunken
```
      True = ebayes has been applied
    - sigma
```
Double sigma
```
    - stdevUnscaled
```
Double[] stdevUnscaled
```
    - term2CoefficientNames
```
Map<K,V> term2CoefficientNames
```
Package ubic.basecode.ontology.model
- Class ubic.basecode.ontology.model.AbstractOntologyResource extends Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class ubic.basecode.ontology.model.DatatypePropertyImpl extends OntologyPropertyImpl implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - type
```
Class<T> type
```
    - resource
```
com.hp.hpl.jena.ontology.DatatypeProperty resource
```
- Class ubic.basecode.ontology.model.ObjectPropertyImpl extends OntologyPropertyImpl implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - resource
```
com.hp.hpl.jena.ontology.ObjectProperty resource
```
- Class ubic.basecode.ontology.model.OntologyCardinalityRestrictionImpl extends OntologyRestrictionImpl implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - cardinality
```
int cardinality
```
    - cardType
```
OntologyCardinalityRestriction.CardinalityType cardType
```
- Class ubic.basecode.ontology.model.OntologyClassRestrictionImpl extends OntologyRestrictionImpl implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - value
```
com.hp.hpl.jena.rdf.model.RDFNode value
```
    - restrictedTo
```
OntologyTerm restrictedTo
```
- Class ubic.basecode.ontology.model.OntologyDatatypeRestrictionImpl extends OntologyRestrictionImpl implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - type
```
Class<T> type
```
- Class ubic.basecode.ontology.model.OntologyIndividualImpl extends AbstractOntologyResource implements Serializable
  
  serialVersionUID:
  
  -6164561945940667693L
  - Serialized Fields
    - ind
```
com.hp.hpl.jena.ontology.Individual ind
```
    - uri
```
String uri
```
- Class ubic.basecode.ontology.model.OntologyPropertyImpl extends AbstractOntologyResource implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - isFunctional
```
boolean isFunctional
```
- Class ubic.basecode.ontology.model.OntologyRestrictionImpl extends OntologyTermImpl implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - restrictionOn
```
OntologyProperty restrictionOn
```
- Class ubic.basecode.ontology.model.OntologyTermImpl extends AbstractOntologyResource implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - label
```
String label
```
    - localName
```
String localName
```
- Class ubic.basecode.ontology.model.OntologyTermSimple extends OntologyTermImpl implements Serializable
  
  serialVersionUID:
  
  -2589717267279872909L
  - Serialized Fields
    - description
```
String description
```
    - obsolete
```
boolean obsolete
```
    - term
```
String term
```
    - uri
```
String uri
```
Package ubic.basecode.ontology.search
- Class ubic.basecode.ontology.search.OntologySearchException extends Exception implements Serializable
  - Serialized Fields
    - query
```
String query
```
- Class ubic.basecode.ontology.search.OntologySearchJenaException extends OntologySearchException implements Serializable
  - Serialized Fields
    - cause
```
com.hp.hpl.jena.shared.JenaException cause
```
- Class ubic.basecode.ontology.search.RetryWithoutWildcardFailedException extends OntologySearchJenaException implements Serializable
  - Serialized Fields
    - firstAttemptCause
```
com.hp.hpl.jena.shared.JenaException firstAttemptCause
```
Package ubic.basecode.util.r.type
- Class ubic.basecode.util.r.type.AnovaEffect extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - degreesOfFreedom
```
Double degreesOfFreedom
```
    - effectName
```
String effectName
```
    - fStatistic
```
Double fStatistic
```
    - isInteraction
```
boolean isInteraction
```
    - meanSq
```
Double meanSq
```
    - pValue
```
Double pValue
```
    - ssQ
```
Double ssQ
```

Serialized Form

Package ubic.basecode.dataStructure

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

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

Package ubic.basecode.dataStructure.matrix

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

Serialized Fields

colMap

colNames

lastColumnIndex

lastRowIndex

rowMap

rowNames

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

Serialized Fields

matrix

rows

cols

totalBitsPerItem

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

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

Serialized Fields

matrix

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

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

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

Serialized Fields

data

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

Serialized Fields

matrix

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

Serialized Fields

matrix

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

Serialized Fields

indexes

values

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

Serialized Fields

matrix

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

Serialized Fields

columns

isDirty

matrix

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

Serialized Fields

matrix

Package ubic.basecode.graphics

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

Serialized Fields

gradient

m_max

m_min

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

Serialized Fields

colorMatrix

m_isShowingStandardizedMatrix

m_standardizedMatrix

m_unstandardizedMatrix

SCALE_BAR_ROOM

m_cellSize

m_columnLabelHeight

m_defaultResolution

m_fontGutter

m_fontSize

m_isShowLabels

m_isShowScale

m_labelFont

m_labelGutter

m_maxColumnLength

m_maxFontSize

m_ratioWidth

m_resolution

m_rowLabelWidth

m_textSize

Package ubic.basecode.math.linearmodels

Class ubic.basecode.math.linearmodels.GenericAnovaResult extends AnovaResult implements Serializable

Serialized Fields