Serialized Form

Package bsh
- Class bsh.BSHFormalComment extends bsh.SimpleNode implements Serializable
  - Serialized Fields
    - text
```
java.lang.String text
```
- Class bsh.BshMethod extends java.lang.Object implements Serializable
  - Serialized Fields
    - declaringNameSpace
```
bsh.NameSpace declaringNameSpace
```
    - modifiers
```
bsh.Modifiers modifiers
```
    - name
```
java.lang.String name
```
    - creturnType
```
java.lang.Class<T> creturnType
```
    - paramNames
```
java.lang.String[] paramNames
```
    - numArgs
```
int numArgs
```
    - cparamTypes
```
java.lang.Class<T>[] cparamTypes
```
    - methodBody
```
bsh.BSHBlock methodBody
```
    - javaMethod
```
java.lang.reflect.Method javaMethod
```
    - javaObject
```
java.lang.Object javaObject
```
- Class bsh.BSHPackageDeclaration extends bsh.SimpleNode implements Serializable
- Class bsh.Capabilities.Unavailable extends bsh.UtilEvalError implements Serializable
- Class bsh.ClassPathException extends bsh.UtilEvalError implements Serializable
- Class bsh.DelayedEvalBshMethod extends bsh.BshMethod implements Serializable
  - Serialized Fields
    - returnTypeDescriptor
```
java.lang.String returnTypeDescriptor
```
    - returnTypeNode
```
bsh.BSHReturnType returnTypeNode
```
    - paramTypeDescriptors
```
java.lang.String[] paramTypeDescriptors
```
    - paramTypesNode
```
bsh.BSHFormalParameters paramTypesNode
```
- Class bsh.EvalError extends java.lang.Exception implements Serializable
  - Serialized Fields
    - node
```
bsh.SimpleNode node
```
    - message
```
java.lang.String message
```
    - callstack
```
bsh.CallStack callstack
```
- Class bsh.ExternalNameSpace extends bsh.NameSpace implements Serializable
  - Serialized Fields
    - externalMap
```
java.util.Map<K,V> externalMap
```
- Class bsh.Interpreter extends java.lang.Object implements Serializable
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream arg0)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      Throws:
      
      java.io.IOException
      
      java.lang.ClassNotFoundException
  - Serialized Fields
    - strictJava
```
boolean strictJava
```
    - globalNameSpace
```
bsh.NameSpace globalNameSpace
```
    - console
```
bsh.ConsoleInterface console
```
    - parent
```
bsh.Interpreter parent
```
    - sourceFileInfo
```
java.lang.String sourceFileInfo
```
    - exitOnEOF
```
boolean exitOnEOF
```
    - evalOnly
```
boolean evalOnly
```
    - interactive
```
boolean interactive
```
    - showResults
```
boolean showResults
```
- Class bsh.InterpreterError extends java.lang.RuntimeException implements Serializable
- Class bsh.Modifiers extends java.lang.Object implements Serializable
  - Serialized Fields
    - modifiers
```
java.util.Hashtable<K,V> modifiers
```
- Class bsh.NameSpace extends java.lang.Object implements Serializable
  - Serialization Methods
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream arg0)
                  throws java.io.IOException
```
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - nsName
```
java.lang.String nsName
```
    - parent
```
bsh.NameSpace parent
```
    - variables
```
java.util.Hashtable<K,V> variables
```
    - methods
```
java.util.Hashtable<K,V> methods
```
    - importedClasses
```
java.util.Hashtable<K,V> importedClasses
```
    - importedPackages
```
java.util.Vector<E> importedPackages
```
    - importedCommands
```
java.util.Vector<E> importedCommands
```
    - importedObjects
```
java.util.Vector<E> importedObjects
```
    - importedStatic
```
java.util.Vector<E> importedStatic
```
    - packageName
```
java.lang.String packageName
```
    - thisReference
```
bsh.This thisReference
```
    - names
```
java.util.Hashtable<K,V> names
```
    - callerInfoNode
```
bsh.SimpleNode callerInfoNode
```
    - isMethod
```
boolean isMethod
```
    - isClass
```
boolean isClass
```
    - classStatic
```
java.lang.Class<T> classStatic
```
    - classInstance
```
java.lang.Object classInstance
```
    - nameSourceListeners
```
java.util.Vector<E> nameSourceListeners
```
- Class bsh.ParseException extends bsh.EvalError implements Serializable
  - Serialized Fields
    - sourceFile
```
java.lang.String sourceFile
```
    - specialConstructor
```
boolean specialConstructor
```
    - currentToken
```
bsh.Token currentToken
```
    - expectedTokenSequences
```
int[][] expectedTokenSequences
```
    - tokenImage
```
java.lang.String[] tokenImage
```
    - eol
```
java.lang.String eol
```
- Class bsh.PlexInterpreter extends bsh.Interpreter implements Serializable
  
  serialVersionUID:
  
  0L
- Class bsh.Primitive extends java.lang.Object implements Serializable
  - Serialized Fields
    - value
```
java.lang.Object value
```
- Class bsh.TargetError extends bsh.EvalError implements Serializable
  - Serialized Fields
    - target
```
java.lang.Throwable target
```
    - inNativeCode
```
boolean inNativeCode
```
- Class bsh.This extends java.lang.Object implements Serializable
  - Serialized Fields
    - namespace
```
bsh.NameSpace namespace
```
- Class bsh.Token extends java.lang.Object implements Serializable
  - Serialized Fields
    - kind
```
int kind
```
    - beginLine
```
int beginLine
```
    - beginColumn
```
int beginColumn
```
    - endLine
```
int endLine
```
    - endColumn
```
int endColumn
```
    - image
```
java.lang.String image
```
    - next
```
bsh.Token next
```
    - specialToken
```
bsh.Token specialToken
```
- Class bsh.TokenMgrError extends java.lang.Error implements Serializable
  - Serialized Fields
    - errorCode
```
int errorCode
```
- Class bsh.UtilEvalError extends java.lang.Exception implements Serializable
- Class bsh.UtilTargetError extends bsh.UtilEvalError implements Serializable
  - Serialized Fields
    - t
```
java.lang.Throwable t
```
- Class bsh.Variable extends java.lang.Object implements Serializable
  - Serialized Fields
    - name
```
java.lang.String name
```
    - type
```
java.lang.Class<T> type
```
    - typeDescriptor
```
java.lang.String typeDescriptor
```
    - value
```
java.lang.Object value
```
    - modifiers
```
bsh.Modifiers modifiers
```
    - lhs
```
bsh.LHS lhs
```
- Class bsh.XThis extends bsh.This implements Serializable
  - Serialized Fields
    - interfaces
```
java.util.Hashtable<K,V> interfaces
```
    - invocationHandler
```
java.lang.reflect.InvocationHandler invocationHandler
```

Package edu.stanford.math.plex

Class edu.stanford.math.plex.BCPlot extends javax.swing.JPanel implements Serializable

serialVersionUID:: 1L

Serialized Fields

plotTypeScatter
```
boolean plotTypeScatter
```
fixedRuler
```
BCPlot.Ruler fixedRuler
```
barcodePane
```
BCPlot.DrawingPane barcodePane
```
fileSaveMenuHandler
```
javax.swing.Action fileSaveMenuHandler
```

baseRegionUsedForPlotLegendRulerLabels

java.awt.Rectangle baseRegionUsedForPlotLegendRulerLabels

heightOfBaseRegionUsedForPlotLegendRulerLabels

int heightOfBaseRegionUsedForPlotLegendRulerLabels

widthOfSideRegionUsedForPlotLegendRulerLabels

int widthOfSideRegionUsedForPlotLegendRulerLabels

leftMargin
```
int leftMargin
```
rightMargin
```
int rightMargin
```
legendMajorString
```
java.lang.String legendMajorString
```
legendMinorString
```
java.lang.String legendMinorString
```
fullVisualizationWidth
```
int fullVisualizationWidth
```
gridWidth
```
int gridWidth
```
gridHeight
```
int gridHeight
```
fullVisualizationHeight
```
int fullVisualizationHeight
```
plotValue
```
double[][] plotValue
```
plotUpperBound
```
double plotUpperBound
```
gridRulerFontColor
```
java.awt.Color gridRulerFontColor
```
tickUpperBoundColor
```
java.awt.Color tickUpperBoundColor
```
gridTickMinorColor
```
java.awt.Color gridTickMinorColor
```
gridTickMajorColor
```
java.awt.Color gridTickMajorColor
```
upperBoundFontColor
```
java.awt.Color upperBoundFontColor
```
labelFontColor
```
java.awt.Color labelFontColor
```
legendMinorFontColor
```
java.awt.Color legendMinorFontColor
```
legendMajorFontColor
```
java.awt.Color legendMajorFontColor
```
fixedRulerBorderColor
```
java.awt.Color fixedRulerBorderColor
```
fixedRulerColor
```
java.awt.Color fixedRulerColor
```
barcodeBarColor
```
java.awt.Color barcodeBarColor
```
fixedRulerFontColor
```
java.awt.Color fixedRulerFontColor
```
fixedRulerMinorTickColor
```
java.awt.Color fixedRulerMinorTickColor
```
fixedRulerMajorTickColor
```
java.awt.Color fixedRulerMajorTickColor
```
labelFont
```
java.awt.Font labelFont
```
legendMinorFont
```
java.awt.Font legendMinorFont
```
legendMajorFont
```
java.awt.Font legendMajorFont
```
gridRulerFont
```
java.awt.Font gridRulerFont
```
fixedRulerFont
```
java.awt.Font fixedRulerFont
```

legendMinorFontMetrics

java.awt.FontMetrics legendMinorFontMetrics

legendMajorFontMetrics

java.awt.FontMetrics legendMajorFontMetrics

fixedRulerFontMetrics

java.awt.FontMetrics fixedRulerFontMetrics

labelFontMetrics
```
java.awt.FontMetrics labelFontMetrics
```

gridRulerFontMetrics

java.awt.FontMetrics gridRulerFontMetrics

upperMargin
```
int upperMargin
```
barcodeBarHeight
```
int barcodeBarHeight
```
barcodeBarSpacing
```
int barcodeBarSpacing
```
gridIsVisible
```
java.lang.Boolean gridIsVisible
```
plotBeingSaved
```
java.lang.Boolean plotBeingSaved
```
unitsPerPixel
```
double unitsPerPixel
```
pixelsPerUnit
```
double pixelsPerUnit
```
tickMajorPlacement
```
int tickMajorPlacement
```
tickGap
```
int tickGap
```

bufferedImage

java.awt.image.BufferedImage bufferedImage

thereIsaBackgroundImage

java.lang.Boolean thereIsaBackgroundImage

backgroundImageName
```
java.lang.String backgroundImageName
```

Class edu.stanford.math.plex.BCPlot.DrawingPane extends javax.swing.JPanel implements Serializable

serialVersionUID:

1L
Class edu.stanford.math.plex.BCPlot.fileSaveMenuHandler extends javax.swing.AbstractAction implements Serializable

serialVersionUID:

1L
Class edu.stanford.math.plex.BCPlot.Ruler extends javax.swing.JComponent implements Serializable

serialVersionUID:

1L
- Serialized Fields
  - dp
```
BCPlot.DrawingPane dp
```

Package edu.stanford.math.plex4.graph
- Class edu.stanford.math.plex4.graph.UndirectedListGraph extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -6877203803491057242L
  - Serialized Fields
    - adjacencySets
```
gnu.trove.TIntObjectHashMap<V> adjacencySets
```
      This is the adjacency set structure
    - degrees
```
gnu.trove.TIntIntHashMap degrees
```
    - numVertices
```
int numVertices
```
      Stores the number of vertices in the graph - must be prespecified
- Class edu.stanford.math.plex4.graph.UndirectedWeightedListGraph extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -4885036152039543245L
  - Serialized Fields
    - adjacencySets
```
gnu.trove.TIntObjectHashMap<V> adjacencySets
```
    - numVertices
```
int numVertices
```
    - degrees
```
gnu.trove.TIntIntHashMap degrees
```
Package edu.stanford.math.plex4.graph.random
- Class edu.stanford.math.plex4.graph.random.BAGraph extends GraphInstanceGenerator implements Serializable
  
  serialVersionUID:
  
  -2891811948996610346L
  - Serialized Fields
    - nParam
```
int nParam
```
    - mParam
```
int mParam
```
- Class edu.stanford.math.plex4.graph.random.BinaryHierarchicalGraph extends GraphInstanceGenerator implements Serializable
  
  serialVersionUID:
  
  830228704317022605L
  - Serialized Fields
    - probabilities
```
double[] probabilities
```
      Stores the probabilities that govern edge creation at each hierarchy level.
    - numNodes
```
int numNodes
```
    - k
```
int k
```
    - maxProbability
```
double maxProbability
```
    - debugFlag
```
boolean debugFlag
```
- Class edu.stanford.math.plex4.graph.random.BinaryTreeGraph extends GraphInstanceGenerator implements Serializable
  
  serialVersionUID:
  
  379015239255681800L
  - Serialized Fields
    - n
```
int n
```
- Class edu.stanford.math.plex4.graph.random.CircleGraph extends GraphInstanceGenerator implements Serializable
  
  serialVersionUID:
  
  -3618903660728579100L
  - Serialized Fields
    - numNodes
```
int numNodes
```
    - numNeighbors
```
int numNeighbors
```
    - rewiringProbability
```
double rewiringProbability
```
    - numRewired
```
int numRewired
```
- Class edu.stanford.math.plex4.graph.random.ClusteredERGraph extends GraphInstanceGenerator implements Serializable
  
  serialVersionUID:
  
  -1685211333671788823L
  - Serialized Fields
    - clusterSizes
```
int[] clusterSizes
```
    - clusterParams
```
double[] clusterParams
```
    - srcClusters
```
java.util.List<E> srcClusters
```
    - destClusters
```
java.util.List<E> destClusters
```
    - edgeCounts
```
java.util.List<E> edgeCounts
```
    - n
```
int n
```
- Class edu.stanford.math.plex4.graph.random.ErdosRenyiGraph extends GraphInstanceGenerator implements Serializable
  
  serialVersionUID:
  
  8667419683575090941L
  - Serialized Fields
    - n
```
int n
```
    - p
```
double p
```
- Class edu.stanford.math.plex4.graph.random.ForestFireGraph extends GraphInstanceGenerator implements Serializable
  
  serialVersionUID:
  
  -872184123268309649L
  - Serialized Fields
    - forwardBurningProbability
```
double forwardBurningProbability
```
    - backwardBurningProbability
```
double backwardBurningProbability
```
    - randomEngine
```
cern.jet.random.engine.RandomEngine randomEngine
```
    - uniformGenerator
```
cern.jet.random.Uniform uniformGenerator
```
    - nodeCount
```
int nodeCount
```
- Class edu.stanford.math.plex4.graph.random.GraphInstanceGenerator extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  6049123403450474191L
  - Serialized Fields
    - implementationType
```
GraphInstanceGenerator.ImplementationType implementationType
```
    - graphImplementation
```
AbstractUndirectedGraph graphImplementation
```
- Class edu.stanford.math.plex4.graph.random.HierarchicalERGraph extends BinaryHierarchicalGraph implements Serializable
  
  serialVersionUID:
  
  3491552989916440763L
  - Serialized Fields
    - rootedGraphSize
```
int rootedGraphSize
```
    - hgLeafCount
```
int hgLeafCount
```
    - erParameter
```
double erParameter
```
- Class edu.stanford.math.plex4.graph.random.KNearestNeighborsGraph extends ManifoldGraph implements Serializable
  
  serialVersionUID:
  
  8103387342329387307L
- Class edu.stanford.math.plex4.graph.random.ManifoldGraph extends GraphInstanceGenerator implements Serializable
  
  serialVersionUID:
  
  -5873098569927731498L
  - Serialized Fields
    - points
```
double[][] points
```
    - size
```
int size
```
    - dimension
```
int dimension
```
    - k
```
int k
```
- Class edu.stanford.math.plex4.graph.random.PrescribedDegrees extends GraphInstanceGenerator implements Serializable
  
  serialVersionUID:
  
  -5243083558152110213L
  - Serialized Fields
    - degreeSequence
```
int[] degreeSequence
```
    - numNodes
```
int numNodes
```
- Class edu.stanford.math.plex4.graph.random.RandomGeometricGraph extends GraphInstanceGenerator implements Serializable
  
  serialVersionUID:
  
  -6990717409349574954L
  - Serialized Fields
    - numNodes
```
int numNodes
```
    - dimension
```
int dimension
```
    - radius
```
double radius
```
- Class edu.stanford.math.plex4.graph.random.SphereGraph extends ManifoldGraph implements Serializable
  
  serialVersionUID:
  
  2433480265430826207L
- Class edu.stanford.math.plex4.graph.random.StochasticBlockmodel extends GraphInstanceGenerator implements Serializable
  
  serialVersionUID:
  
  -4992866715916257875L
  - Serialized Fields
    - probabilityMatrix
```
double[][] probabilityMatrix
```
    - n
```
int n
```
- Class edu.stanford.math.plex4.graph.random.TorusGraph extends ManifoldGraph implements Serializable
  
  serialVersionUID:
  
  101044478862814881L
Package edu.stanford.math.plex4.homology.barcodes
- Class edu.stanford.math.plex4.homology.barcodes.Interval extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -3434702188482864510L
  - Serialized Fields
    - start
```
java.lang.Comparable<T> start
```
    - end
```
java.lang.Comparable<T> end
```
    - isLeftClosed
```
boolean isLeftClosed
```
    - isRightClosed
```
boolean isRightClosed
```
    - isLeftInfinite
```
boolean isLeftInfinite
```
    - isRightInfinite
```
boolean isRightInfinite
```
Package edu.stanford.math.plex4.visualization
- Class edu.stanford.math.plex4.visualization.AbstractVisualizer extends PAppletSplitscreen implements Serializable
  - Serialized Fields
    - doubleArrayReaderWriter
```
DoubleArrayReaderWriter doubleArrayReaderWriter
```
    - fileName
```
java.lang.String fileName
```
    - pointsViz
```
float[][] pointsViz
```
    - pointsComp
```
double[][] pointsComp
```
    - metricSpace
```
AbstractSearchableMetricSpace<T> metricSpace
```
    - stream
```
VietorisRipsStream<T> stream
```
    - fc
```
FiltrationConverter fc
```
    - scale3D
```
int scale3D
```
    - r
```
float r
```
      Drawing parameters
    - fillTriangles
```
boolean fillTriangles
```
    - pointSize
```
int pointSize
```
    - topMargin
```
int topMargin
```
    - leftMargin
```
int leftMargin
```
    - rightMargin
```
int rightMargin
```
    - infinityMargin
```
int infinityMargin
```
    - maxBarSpacing
```
float maxBarSpacing
```
    - imgWidth
```
int imgWidth
```
    - lineHeight
```
int lineHeight
```
    - font
```
java.lang.String font
```
    - dims
```
edu.stanford.math.plex4.visualization.AbstractVisualizer.Dimensions dims
```
      State variables
    - plottype
```
edu.stanford.math.plex4.visualization.AbstractVisualizer.PlotType plottype
```
    - filtrationValue
```
double filtrationValue
```
    - stepSize
```
java.lang.Double stepSize
```
    - maxFiltrationValue
```
java.lang.Double maxFiltrationValue
```
    - incrementFiltrationValue
```
java.lang.Double incrementFiltrationValue
```
- Class edu.stanford.math.plex4.visualization.HomologyGeneratorVisualizer extends AbstractVisualizer implements Serializable
  - Serialized Fields
    - diagramToGenerators
```
java.util.Map<K,V> diagramToGenerators
```
    - visibleGenerators
```
java.util.List<E> visibleGenerators
```
    - visibleGeneratorCoordinates
```
java.util.List<E> visibleGeneratorCoordinates
```
    - genColors
```
java.lang.String[] genColors
```
    - intervals
```
AnnotatedBarcodeCollection<T extends java.lang.Comparable<T>,G> intervals
```
- Class edu.stanford.math.plex4.visualization.HomologyVisualizer extends AbstractVisualizer implements Serializable
  - Serialized Fields
    - intervals
```
BarcodeCollection<T extends java.lang.Comparable<T>> intervals
```
- Class edu.stanford.math.plex4.visualization.PAppletSplitscreen extends processing.core.PApplet implements Serializable
  - Serialized Fields
    - rotX
```
float rotX
```
      Global variables to enable rotation and zoom of 3D image
    - rotY
```
float rotY
```
      Global variables to enable rotation and zoom of 3D image
    - distX
```
float distX
```
    - distY
```
float distY
```
    - lastX
```
int lastX
```
    - lastY
```
int lastY
```
    - zoomZ
```
float zoomZ
```

Serialized Form

Package bsh

Class bsh.BSHFormalComment extends bsh.SimpleNode implements Serializable

Serialized Fields

text

Class bsh.BshMethod extends java.lang.Object implements Serializable

Serialized Fields

declaringNameSpace

modifiers

name

creturnType

paramNames

numArgs

cparamTypes

methodBody

javaMethod

javaObject

Class bsh.BSHPackageDeclaration extends bsh.SimpleNode implements Serializable

Class bsh.Capabilities.Unavailable extends bsh.UtilEvalError implements Serializable

Class bsh.ClassPathException extends bsh.UtilEvalError implements Serializable

Class bsh.DelayedEvalBshMethod extends bsh.BshMethod implements Serializable

Serialized Fields

returnTypeDescriptor

returnTypeNode

paramTypeDescriptors

paramTypesNode

Class bsh.EvalError extends java.lang.Exception implements Serializable

Serialized Fields

node

message

callstack

Class bsh.ExternalNameSpace extends bsh.NameSpace implements Serializable

Serialized Fields

externalMap

Class bsh.Interpreter extends java.lang.Object implements Serializable

Serialization Methods

readObject

Serialized Fields

strictJava

globalNameSpace

console

parent

sourceFileInfo

exitOnEOF

evalOnly

interactive

showResults

Class bsh.InterpreterError extends java.lang.RuntimeException implements Serializable

Class bsh.Modifiers extends java.lang.Object implements Serializable

Serialized Fields

modifiers

Class bsh.NameSpace extends java.lang.Object implements Serializable

Serialization Methods

writeObject

Serialized Fields

nsName

parent

variables

methods

importedClasses

importedPackages

importedCommands

importedObjects

importedStatic

packageName

thisReference

names

callerInfoNode

isMethod

isClass

classStatic

classInstance

nameSourceListeners

Class bsh.ParseException extends bsh.EvalError implements Serializable

Serialized Fields

sourceFile

specialConstructor

currentToken

expectedTokenSequences

tokenImage