Serialized Form (baseCode 1.1.19 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<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.GenericAnovaResult extends AnovaResult implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - interactionEffects
      
      Map<ubic.basecode.math.linearmodels.GenericAnovaResult.InteractionFactor,AnovaEffect> interactionEffects
    - mainEffects
      
      Map<String,AnovaEffect> 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<String,String> contrastCoefficients
    - denominatorDof
      
      Integer denominatorDof
    - effects
      
      Double[] effects
      
      AKA Qty
    - factorNames
      
      List<String> factorNames
    - factorValueNames
      
      Map<String,List<String>> 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<String,Collection<String>> term2CoefficientNames
Package ubic.basecode.ontology.model
- Class ubic.basecode.ontology.model.OntologyTermSimple extends Object 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
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

cols

matrix

rows

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_cellSize

m_columnLabelHeight

m_defaultResolution

m_fontGutter

m_fontSize

m_isShowingStandardizedMatrix

m_isShowLabels

m_isShowScale

m_labelFont

m_labelGutter

m_maxColumnLength

m_maxFontSize

m_ratioWidth

m_resolution

m_rowLabelWidth

m_standardizedMatrix

m_textSize

m_unstandardizedMatrix

SCALE_BAR_ROOM

Package ubic.basecode.math.linearmodels

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

Serialized Fields

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

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

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

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

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

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

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

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

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

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