Partial updates to the class diagrams of the project.

src/main/paradox/developers-guide/class-diagrams.md

@@ -8,7 +8,7 @@ which produces all the expected arithmetic operations on coefficients.
 way as is main-stream in the persistent homology library ecosystem finite field
 arithmetic with lookup tables for inverses.
 
-```mermaid
+```
 classDiagram
     class FiniteField {
         val p: Int
@@ -52,11 +52,11 @@ boundary() Chain[AbstractSimplex[VertexT],CoefficientT]
 
 ## How do we describe a Simplicial Complex?
 
-```mermaid
+```
 classDiagram
     `Cell[CellT]` --> `Simplex[VertexT]`
     class `Cell[CellT]` {
-<<interface Typeclass>>
+<<interface>>
 boundary() Chain[CellT, CoefficientT]
 }
 class `Simplex[VertexT]` {
@@ -105,4 +105,226 @@ apply(metricSpace, maxFiltrationValue, maxDimension) Seq[AbstractSimplex[VertexT
 `CliqueFinder[VertexT]` --> BronKerbosch : implements
 `CliqueFinder[VertexT]` --> ZomorodianIncremental : implements
 `CliqueFinder[VertexT]` --> SymmetricZomorodianIncremental : implements
+```
+
+
+## Revision 2024-09-18
+
+```mermaid
+classDiagram
+    namespace Barcode_scala {
+        class BarcodeEndpoint
+        class PositiveInfinity
+        class NegativeInfinity
+        class OpenEndpoint
+        class ClosedEndpoint
+        class PersistenceBar {
+            dim : int
+            lower : BarcodeEndpoint
+            upper : BarcodeEndpoint
+            annotation : Option[AnnotationT]
+            toString()
+        }
+        class BarcodeContext {
+            FiltrationT bc FiltrationT : PersistenceBar
+            FiltrationT clcl FiltrationT : PersistenceBar
+            FiltrationT clop FiltrationT : PersistenceBar
+            FiltrationT opcl FiltrationT : PersistenceBar
+            FiltrationT opop FiltrationT : PersistenceBar
+            clinf FiltrationT : PersistenceBar
+            opinf FiltrationT : PersistenceBar
+            infcl FiltrationT : PersistenceBar
+            infop FiltrationT : PersistenceBar
+        }
+        class Barcode {
+            isMap(List~PersistenceBar~, List~PersistenceBar~, RealMatrix) bool
+            imageMatrix(List~PersistenceBar~, List~PersistenceBar~, RealMatrix) RealMatrix
+            image(List~PersistenceBar~, List~PersistenceBar~, RealMatrix) List~PersistenceBar~
+            kernel(List~PersistenceBar~, List~PersistenceBar~, RealMatrix) List~PersistenceBar~
+            cokernelMatrix(List~PersistenceBar~, List~PersistenceBar~, RealMatrix) RealMatrix
+            cokernel(List~PersistenceBar~, List~PersistenceBar~, RealMatrix) List~PersistenceBar~
+            reduceMatrix(RealMatrix) RealMatrix
+        }
+    }
+    BarcodeEndpoint --|> PositiveInfinity
+    BarcodeEndpoint --|> NegativeInfinity
+    BarcodeEndpoint --|> OpenEndpoint
+    BarcodeEndpoint --|> ClosedEndpoint
+```
+
+```mermaid
+classDiagram
+    namespace Chain_scala {
+        class HasBoundary {
+            type Self : Ordering
+            extension Self.boundary[CoefficientT : Fractional] : Chain[Self, CoefficientT]
+        }
+        class HasDimension {
+            type Self
+            extension Self.dim : Int
+        }
+        class Cell
+        class OrderedCell
+        class given_Ordering~OrderedCell~
+        class OrderedBasis {
+            type Self
+            extension Self.leadingTerm: Tuple[Option[CellT], CoefficientT]
+            extension Self.leadingCoefficient : CoefficientT
+            extension Self.leadingCell : Option[CellT]
+        }
+        class Chain~CellT, CoefficientT~ {
+            private entries : mutable.PriorityQueue[Tuple[CellT, CoefficientT]]
+            collapseHead()
+            collapseAll()
+            isZero() bool
+            items : Seq[Tuple[CellT, CoefficientT]]
+            chainBoundary() Chain~CellT, CoefficientT~ 
+        }
+        class object_Chain {
+            apply(cs : vararg Tuple[CellT, CoefficientT]) Chain~CellT, CoefficientT~
+            apply(c : CellT) Chain~CellT, CoefficientT~
+            from(cs : Seq[Tuple[CellT, CoefficientT]]) Chain~CellT, CoefficientT~ 
+        }
+        class given_Chain_is_OrderedBasis
+        class ChainOps~CellT, CoefficientT~
+    }
+    HasBoundary --|> Cell
+    HasDimension --|> Cell
+    Cell --|> OrderedCell
+    RingModule --|> ChainOps
+
+```
+
+```mermaid
+classDiagram
+    namespace Cube_scala {
+        class ElementaryInterval {
+            n : int
+        }
+        class DegenerateInterval
+        class FullInterval
+        class given_Ordering_ElementaryInterval
+        class given_ElementaryInterval_is_OrderedCell
+        class ElementaryCube {
+            intervals : List[ElementaryInterval]
+        }
+    }
+    ElementaryInterval --|> DegenerateInterval
+    ElementaryInterval --|> FullInterval
+```
+
+```mermaid
+classDiagram
+    namespace FiniteField_scala {
+        class FiniteField {
+            p : int
+            type Fp
+            given Fp_is_Fractional
+        }
+    }
+```
+
+```mermaid
+classDiagram
+    namespace FiniteMetricSpace_scala {
+        class FiniteMetricSpace {
+            distance(vertex, vertex) Double
+            size : int
+            elements : Iterable[VertexT]
+            contains(vertex) bool
+            minimumEnclosingRadius : lazy Double
+        }
+        class MaximumDistanceFiltrationValue
+        class ExplicitMetricSpace
+        class EuclideanMetricSpace
+    }
+    FiniteMetricSpace --|> ExplicitMetricSpace
+    FiniteMetricSpace --|> EuclideanMetricSpace
+```
+
+```mermaid
+classDiagram
+    namespace Homology_scala {
+        class HomologyState {
+            cycles : mutable.Map[CellT, Chain[CellT, CoefficientT]]
+            cyclesBornBy : mutable.Map[CellT, CellT]
+            boundaries : mutable.Map[CellT, Chain[CellT, CoefficientT]]
+            boundariesBornBy : mutable.Map[CellT, CellT]
+            coboundaries : mutable.Map[CellT, Chain[CellT, CoefficientT]]
+            stream : CellStream[CellT, FiltrationT]
+            current : FiltrationT
+            barcode : mutable.ArrayDeque[Tuple[Int, FiltrationT, FiltrationT, Chain[CellT, CoefficientT]]
+            diagramAt(f : FiltrationT) List[Tuple[Int,FiltrationT,FiltrationT]]
+            barcodeAt(f : FiltrationT) List[PersistenceBar]
+            advanceOne()
+            advanceTo(f: FiltrationT)
+            advanceAll()
+        }
+    }
+```
+
+```mermaid
+classDiagram
+    namespace RingModule_scala {
+        class RingModule {
+            zero : T
+            isZero(t : T) bool
+            plus(s : T, t: T) T
+            minus(s : T, t: T) T
+            negate(t: T) T
+            scale(r : R, t : T) T
+            extension T.+
+            extension T.-
+            extension T.unary_-
+            extension infix T.mul
+            extension R.⊠
+            extension infix R.scale
+        }
+    }
+```
+
+```mermaid
+classDiagram
+    namespace Simplex_scala {
+        class Simplex {
+            vertices : SortedSet[VertexT]
+            union(other : Simplex) Simplex
+        }
+        class given_Ordering_Simplex
+        class given_Simplex_is_OrderedCell
+        class object_Simplex {
+            apply(vertices : vararg VertexT) Simplex
+            from(vertices : Seq[VertexT]) Simplex
+            empty() Simplex
+            ∆(vertices : vararg VertexT) Simplex
+        }
+    }
+```
+
+```mermaid
+classDiagram
+    namespace SimplexStream_scala {
+        class SimplexStream
+    }
+```
+
+```mermaid
+classDiagram
+    namespace SymmetryGroup_scala {
+        class SymmetryGroup
+    }
+```
+
+```mermaid
+classDiagram
+    namespace UnionFind_scala {
+        class UnionFind
+    }
+```
+
+```mermaid
+classDiagram
+    namespace VietorisRips_scala {
+        class VietorisRips
+    }
 ```