Changed some protected to internal.

Not sure if this is the right encapsulation, but we can go over these later.

src/commonMain/kotlin/org/appliedtopology/tda4j/Sets.kt

@@ -2,7 +2,7 @@ package org.appliedtopology.tda4j
 
 open class ArrayMutableSortedSetBaseWith<T>(capacity: Int = 8, val comparator: Comparator<T>) {
     @Suppress("ktlint:standard:property-naming")
-    protected val _set: ArrayList<T> = ArrayList(capacity)
+    internal val _set: ArrayList<T> = ArrayList(capacity)
 
     fun add(element: T): Boolean {
         val index = _set.binarySearch(element, comparator)
@@ -79,7 +79,7 @@ open class ArrayMutableSortedMapWith<K, V>(
     val defaultValue: V? = null,
 ) :
     ArrayMutableSortedSetBaseWith<K>(capacity, comparator), MutableMap<K, V> {
-    protected val _values: ArrayList<V> = ArrayList(capacity)
+    internal val _values: ArrayList<V> = ArrayList(capacity)
 
     override fun containsKey(key: K): Boolean = _set.binarySearch(key, comparator) >= 0
 

src/commonMain/kotlin/org/appliedtopology/tda4j/Simplex.kt

@@ -4,7 +4,7 @@ import arrow.core.padZip
 
 open class AbstractSimplexWith<VertexT>(val vertexComparator: Comparator<VertexT>) : Set<VertexT> {
     @Suppress("ktlint:standard:property-naming")
-    protected val _simplex: MutableSortedSetWith<VertexT> = MutableSortedSetWith(comparator = vertexComparator)
+    internal val _simplex: MutableSortedSetWith<VertexT> = MutableSortedSetWith(comparator = vertexComparator)
 
     constructor(vertexComparator: Comparator<VertexT>, elements: HashSet<VertexT>) : this(vertexComparator) {
         _simplex.addAll(elements)

src/commonMain/kotlin/org/appliedtopology/tda4j/SimplexStream.kt

@@ -13,7 +13,7 @@ abstract class SimplexStream<VertexT : Comparable<VertexT>, FiltrationT : Compar
 
 open class ExplicitStream<VertexT : Comparable<VertexT>, FiltrationT : Comparable<FiltrationT>> :
     SimplexStream<VertexT, FiltrationT>(), MutableMap<AbstractSimplex<VertexT>, FiltrationT> {
-    protected val filtrationValues: MutableMap<AbstractSimplex<VertexT>, FiltrationT> = HashMap()
+    internal val filtrationValues: MutableMap<AbstractSimplex<VertexT>, FiltrationT> = HashMap()
 
     override fun filtrationValue(simplex: AbstractSimplex<VertexT>): FiltrationT? = filtrationValues[simplex]