Updated auto-docs

bio4j · Apr 18, 2014 · 262718e · 262718e
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diff --git a/scala-model/docs/src/main/scala/bio4j/model/edgeTypes.scala.md b/scala-model/docs/src/main/scala/bio4j/model/edgeTypes.scala.md
@@ -3,20 +3,22 @@
 package bio4j.model
 ```
 
-  Declares an Edge type. They are essentially classified by its label, a `String`.
 
-  Its source and target types are not bound here, as that would lead to an explosion of equally named but different objects. The goal is to be able to express any source and target type configurations through witnesses.
+Declares an Edge type. They are essentially classified by its label, a `String`.
+
+Its source and target types are not bound here, as that would lead to an explosion of equally named but different objects. The goal is to be able to express any source and target type configurations through witnesses.
 
 
 ```scala
 trait AnyEdgeType { val label: String }
 ```
 
-  A convenience class for declaring types as case objects; just do
 
-  ``` scala
-  case object Follows extends EdgeType
-  ```
+A convenience class for declaring types as case objects; just do
+
+``` scala
+case object Follows extends EdgeType
+```
 
 
 ```scala
@@ -26,15 +28,12 @@ object AnyEdgeType {
 
   implicit def edgeTypeOps[E <: AnyEdgeType](edgeType: E): EdgeTypeOps[E] = EdgeTypeOps(edgeType) 
 }
-```
-
 
-
-```scala
 case class EdgeTypeOps[E <: AnyEdgeType](val edgeType: E) {
 
   def has[P <: AnyProperty](property: P): (E EdgeTypeHasProperty P) = EdgeTypeHasProperty(edgeType, property)
 }
+
 ```
 
 
@@ -43,36 +42,40 @@ case class EdgeTypeOps[E <: AnyEdgeType](val edgeType: E) {
 ### Index
 
 + src
-  + test
-    + scala
-      + bio4j
-        + model
-          + [propertyTypes.scala][test/scala/bio4j/model/propertyTypes.scala]
-          + [vertices.scala][test/scala/bio4j/model/vertices.scala]
-          + [relationships.scala][test/scala/bio4j/model/relationships.scala]
-          + [vertexTypes.scala][test/scala/bio4j/model/vertexTypes.scala]
-          + [edgeTypes.scala][test/scala/bio4j/model/edgeTypes.scala]
   + main
     + scala
       + bio4j
         + model
-          + [properties.scala][main/scala/bio4j/model/properties.scala]
           + [edges.scala][main/scala/bio4j/model/edges.scala]
-          + [vertices.scala][main/scala/bio4j/model/vertices.scala]
+          + [edgeTypes.scala][main/scala/bio4j/model/edgeTypes.scala]
+          + [properties.scala][main/scala/bio4j/model/properties.scala]
           + [relationships.scala][main/scala/bio4j/model/relationships.scala]
           + [relationshipTypes.scala][main/scala/bio4j/model/relationshipTypes.scala]
           + [vertexTypes.scala][main/scala/bio4j/model/vertexTypes.scala]
-          + [edgeTypes.scala][main/scala/bio4j/model/edgeTypes.scala]
+          + [vertices.scala][main/scala/bio4j/model/vertices.scala]
+  + test
+    + scala
+      + bio4j
+        + model
+          + [edges.scala][test/scala/bio4j/model/edges.scala]
+          + [edgeTypes.scala][test/scala/bio4j/model/edgeTypes.scala]
+          + [properties.scala][test/scala/bio4j/model/properties.scala]
+          + [rels.scala][test/scala/bio4j/model/rels.scala]
+          + [relTypes.scala][test/scala/bio4j/model/relTypes.scala]
+          + [vertexTypes.scala][test/scala/bio4j/model/vertexTypes.scala]
+          + [vertices.scala][test/scala/bio4j/model/vertices.scala]
 
-[test/scala/bio4j/model/propertyTypes.scala]: ../../../../test/scala/bio4j/model/propertyTypes.scala.md
-[test/scala/bio4j/model/vertices.scala]: ../../../../test/scala/bio4j/model/vertices.scala.md
-[test/scala/bio4j/model/relationships.scala]: ../../../../test/scala/bio4j/model/relationships.scala.md
-[test/scala/bio4j/model/vertexTypes.scala]: ../../../../test/scala/bio4j/model/vertexTypes.scala.md
-[test/scala/bio4j/model/edgeTypes.scala]: ../../../../test/scala/bio4j/model/edgeTypes.scala.md
-[main/scala/bio4j/model/properties.scala]: properties.scala.md
 [main/scala/bio4j/model/edges.scala]: edges.scala.md
-[main/scala/bio4j/model/vertices.scala]: vertices.scala.md
+[main/scala/bio4j/model/edgeTypes.scala]: edgeTypes.scala.md
+[main/scala/bio4j/model/properties.scala]: properties.scala.md
 [main/scala/bio4j/model/relationships.scala]: relationships.scala.md
 [main/scala/bio4j/model/relationshipTypes.scala]: relationshipTypes.scala.md
 [main/scala/bio4j/model/vertexTypes.scala]: vertexTypes.scala.md
-[main/scala/bio4j/model/edgeTypes.scala]: edgeTypes.scala.md
+[main/scala/bio4j/model/vertices.scala]: vertices.scala.md
+[test/scala/bio4j/model/edges.scala]: ../../../../test/scala/bio4j/model/edges.scala.md
+[test/scala/bio4j/model/edgeTypes.scala]: ../../../../test/scala/bio4j/model/edgeTypes.scala.md
+[test/scala/bio4j/model/properties.scala]: ../../../../test/scala/bio4j/model/properties.scala.md
+[test/scala/bio4j/model/rels.scala]: ../../../../test/scala/bio4j/model/rels.scala.md
+[test/scala/bio4j/model/relTypes.scala]: ../../../../test/scala/bio4j/model/relTypes.scala.md
+[test/scala/bio4j/model/vertexTypes.scala]: ../../../../test/scala/bio4j/model/vertexTypes.scala.md
+[test/scala/bio4j/model/vertices.scala]: ../../../../test/scala/bio4j/model/vertices.scala.md
diff --git a/scala-model/docs/src/main/scala/bio4j/model/edges.scala.md b/scala-model/docs/src/main/scala/bio4j/model/edges.scala.md
@@ -8,41 +8,48 @@ trait AnyEdge {
 
   type EdgeType <: AnyEdgeType
   val edgeType: EdgeType
+```
+
+The raw underlying type representing this Edge
 
-  // the raw underlying type representing this Edge
+```scala
   type Rep
+```
+
+Tags `Rep` with this edge type
 
+```scala
   import shapeless.record._
+
+  type TaggedRep = FieldType[edge.type, Rep]
+  def ->>(e: Rep): FieldType[edge.type, Rep] = field[edge.type](e)
 ```
 
-Tags a Rep with this edge type
+Read a property from this representation
 
 ```scala
-  def ->>(v: Rep): FieldType[edge.type, Rep] = field[edge.type](v)
-
-  // read a property from this representation
   abstract case class ReadProperty[P <: AnyProperty](val p: P) {
-
-    def apply(edgeRep: FieldType[edge.type, Rep]): p.Rep
+    def apply(edgeRep: TaggedRep): p.Rep
   }
 
-
-  // this should go somewhere else
-  case class PropertyOps(val edgeRep: FieldType[edge.type, Rep]) {
+  // TODO: this should go somewhere else
+  case class PropertyOps(val edgeRep: TaggedRep) {
 
     import AnyEdgeTypeHasProperty.PropertyOf
 
-    def get[P <: AnyProperty]
-    (p: P)
-    (implicit 
-      witness: PropertyOf[edge.EdgeType]#is[P],
-      retrieve: ReadProperty[P]
-    ) = retrieve(edgeRep)
+    def get[P <: AnyProperty](p: P)
+      (implicit 
+        witness: PropertyOf[edge.EdgeType]#is[P],
+        retrieve: ReadProperty[P]
+      ) = retrieve(edgeRep)
   }
 
-  implicit def propertyOps[P <: AnyProperty]
-    (edgeRep: FieldType[edge.type, Rep]): edge.PropertyOps = PropertyOps(edgeRep)
+  implicit def propertyOps(edgeRep: TaggedRep): edge.PropertyOps = PropertyOps(edgeRep)
 }
+
+abstract class Edge[ET <: AnyEdgeType](val edgeType: ET)
+  extends AnyEdge { type EdgeType = ET }
+
 ```
 
 
@@ -51,36 +58,40 @@ Tags a Rep with this edge type
 ### Index
 
 + src
-  + test
-    + scala
-      + bio4j
-        + model
-          + [propertyTypes.scala][test/scala/bio4j/model/propertyTypes.scala]
-          + [vertices.scala][test/scala/bio4j/model/vertices.scala]
-          + [relationships.scala][test/scala/bio4j/model/relationships.scala]
-          + [vertexTypes.scala][test/scala/bio4j/model/vertexTypes.scala]
-          + [edgeTypes.scala][test/scala/bio4j/model/edgeTypes.scala]
   + main
     + scala
       + bio4j
         + model
-          + [properties.scala][main/scala/bio4j/model/properties.scala]
           + [edges.scala][main/scala/bio4j/model/edges.scala]
-          + [vertices.scala][main/scala/bio4j/model/vertices.scala]
+          + [edgeTypes.scala][main/scala/bio4j/model/edgeTypes.scala]
+          + [properties.scala][main/scala/bio4j/model/properties.scala]
           + [relationships.scala][main/scala/bio4j/model/relationships.scala]
           + [relationshipTypes.scala][main/scala/bio4j/model/relationshipTypes.scala]
           + [vertexTypes.scala][main/scala/bio4j/model/vertexTypes.scala]
-          + [edgeTypes.scala][main/scala/bio4j/model/edgeTypes.scala]
+          + [vertices.scala][main/scala/bio4j/model/vertices.scala]
+  + test
+    + scala
+      + bio4j
+        + model
+          + [edges.scala][test/scala/bio4j/model/edges.scala]
+          + [edgeTypes.scala][test/scala/bio4j/model/edgeTypes.scala]
+          + [properties.scala][test/scala/bio4j/model/properties.scala]
+          + [rels.scala][test/scala/bio4j/model/rels.scala]
+          + [relTypes.scala][test/scala/bio4j/model/relTypes.scala]
+          + [vertexTypes.scala][test/scala/bio4j/model/vertexTypes.scala]
+          + [vertices.scala][test/scala/bio4j/model/vertices.scala]
 
-[test/scala/bio4j/model/propertyTypes.scala]: ../../../../test/scala/bio4j/model/propertyTypes.scala.md
-[test/scala/bio4j/model/vertices.scala]: ../../../../test/scala/bio4j/model/vertices.scala.md
-[test/scala/bio4j/model/relationships.scala]: ../../../../test/scala/bio4j/model/relationships.scala.md
-[test/scala/bio4j/model/vertexTypes.scala]: ../../../../test/scala/bio4j/model/vertexTypes.scala.md
-[test/scala/bio4j/model/edgeTypes.scala]: ../../../../test/scala/bio4j/model/edgeTypes.scala.md
-[main/scala/bio4j/model/properties.scala]: properties.scala.md
 [main/scala/bio4j/model/edges.scala]: edges.scala.md
-[main/scala/bio4j/model/vertices.scala]: vertices.scala.md
+[main/scala/bio4j/model/edgeTypes.scala]: edgeTypes.scala.md
+[main/scala/bio4j/model/properties.scala]: properties.scala.md
 [main/scala/bio4j/model/relationships.scala]: relationships.scala.md
 [main/scala/bio4j/model/relationshipTypes.scala]: relationshipTypes.scala.md
 [main/scala/bio4j/model/vertexTypes.scala]: vertexTypes.scala.md
-[main/scala/bio4j/model/edgeTypes.scala]: edgeTypes.scala.md
+[main/scala/bio4j/model/vertices.scala]: vertices.scala.md
+[test/scala/bio4j/model/edges.scala]: ../../../../test/scala/bio4j/model/edges.scala.md
+[test/scala/bio4j/model/edgeTypes.scala]: ../../../../test/scala/bio4j/model/edgeTypes.scala.md
+[test/scala/bio4j/model/properties.scala]: ../../../../test/scala/bio4j/model/properties.scala.md
+[test/scala/bio4j/model/rels.scala]: ../../../../test/scala/bio4j/model/rels.scala.md
+[test/scala/bio4j/model/relTypes.scala]: ../../../../test/scala/bio4j/model/relTypes.scala.md
+[test/scala/bio4j/model/vertexTypes.scala]: ../../../../test/scala/bio4j/model/vertexTypes.scala.md
+[test/scala/bio4j/model/vertices.scala]: ../../../../test/scala/bio4j/model/vertices.scala.md
diff --git a/scala-model/docs/src/main/scala/bio4j/model/properties.scala.md b/scala-model/docs/src/main/scala/bio4j/model/properties.scala.md
@@ -3,14 +3,18 @@
 package bio4j.model
 ```
 
+
 Properties
 
+
 ```scala
 import shapeless.FieldOf
 ```
 
+
 this has a label!
 
+
 ```scala
 trait AnyProperty extends LiteralType {
 
@@ -23,8 +27,10 @@ class Property[V]() extends AnyProperty with FieldOf[V] {
 }
 ```
 
+
 witness for an Edge of type E having a property of type P
 
+
 ```scala
 trait AnyEdgeTypeHasProperty {
 
@@ -57,8 +63,10 @@ object AnyEdgeTypeHasProperty {
 }
 ```
 
+
 witness for a vertex type declaring a property of the given type
 
+
 ```scala
 trait AnyVertexTypeHasProperty {
 
@@ -97,36 +105,40 @@ object AnyVertexTypeHasProperty {
 ### Index
 
 + src
-  + test
-    + scala
-      + bio4j
-        + model
-          + [propertyTypes.scala][test/scala/bio4j/model/propertyTypes.scala]
-          + [vertices.scala][test/scala/bio4j/model/vertices.scala]
-          + [relationships.scala][test/scala/bio4j/model/relationships.scala]
-          + [vertexTypes.scala][test/scala/bio4j/model/vertexTypes.scala]
-          + [edgeTypes.scala][test/scala/bio4j/model/edgeTypes.scala]
   + main
     + scala
       + bio4j
         + model
-          + [properties.scala][main/scala/bio4j/model/properties.scala]
           + [edges.scala][main/scala/bio4j/model/edges.scala]
-          + [vertices.scala][main/scala/bio4j/model/vertices.scala]
+          + [edgeTypes.scala][main/scala/bio4j/model/edgeTypes.scala]
+          + [properties.scala][main/scala/bio4j/model/properties.scala]
           + [relationships.scala][main/scala/bio4j/model/relationships.scala]
           + [relationshipTypes.scala][main/scala/bio4j/model/relationshipTypes.scala]
           + [vertexTypes.scala][main/scala/bio4j/model/vertexTypes.scala]
-          + [edgeTypes.scala][main/scala/bio4j/model/edgeTypes.scala]
+          + [vertices.scala][main/scala/bio4j/model/vertices.scala]
+  + test
+    + scala
+      + bio4j
+        + model
+          + [edges.scala][test/scala/bio4j/model/edges.scala]
+          + [edgeTypes.scala][test/scala/bio4j/model/edgeTypes.scala]
+          + [properties.scala][test/scala/bio4j/model/properties.scala]
+          + [rels.scala][test/scala/bio4j/model/rels.scala]
+          + [relTypes.scala][test/scala/bio4j/model/relTypes.scala]
+          + [vertexTypes.scala][test/scala/bio4j/model/vertexTypes.scala]
+          + [vertices.scala][test/scala/bio4j/model/vertices.scala]
 
-[test/scala/bio4j/model/propertyTypes.scala]: ../../../../test/scala/bio4j/model/propertyTypes.scala.md
-[test/scala/bio4j/model/vertices.scala]: ../../../../test/scala/bio4j/model/vertices.scala.md
-[test/scala/bio4j/model/relationships.scala]: ../../../../test/scala/bio4j/model/relationships.scala.md
-[test/scala/bio4j/model/vertexTypes.scala]: ../../../../test/scala/bio4j/model/vertexTypes.scala.md
-[test/scala/bio4j/model/edgeTypes.scala]: ../../../../test/scala/bio4j/model/edgeTypes.scala.md
-[main/scala/bio4j/model/properties.scala]: properties.scala.md
 [main/scala/bio4j/model/edges.scala]: edges.scala.md
-[main/scala/bio4j/model/vertices.scala]: vertices.scala.md
+[main/scala/bio4j/model/edgeTypes.scala]: edgeTypes.scala.md
+[main/scala/bio4j/model/properties.scala]: properties.scala.md
 [main/scala/bio4j/model/relationships.scala]: relationships.scala.md
 [main/scala/bio4j/model/relationshipTypes.scala]: relationshipTypes.scala.md
 [main/scala/bio4j/model/vertexTypes.scala]: vertexTypes.scala.md
-[main/scala/bio4j/model/edgeTypes.scala]: edgeTypes.scala.md
+[main/scala/bio4j/model/vertices.scala]: vertices.scala.md
+[test/scala/bio4j/model/edges.scala]: ../../../../test/scala/bio4j/model/edges.scala.md
+[test/scala/bio4j/model/edgeTypes.scala]: ../../../../test/scala/bio4j/model/edgeTypes.scala.md
+[test/scala/bio4j/model/properties.scala]: ../../../../test/scala/bio4j/model/properties.scala.md
+[test/scala/bio4j/model/rels.scala]: ../../../../test/scala/bio4j/model/rels.scala.md
+[test/scala/bio4j/model/relTypes.scala]: ../../../../test/scala/bio4j/model/relTypes.scala.md
+[test/scala/bio4j/model/vertexTypes.scala]: ../../../../test/scala/bio4j/model/vertexTypes.scala.md
+[test/scala/bio4j/model/vertices.scala]: ../../../../test/scala/bio4j/model/vertices.scala.md