Autogenerated literator docs for v0.2.0

bio4j · Nov 9, 2016 · 8b77689 · 8b77689
1 parent 43d347c
commit 8b77689
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Showing 3 changed files with 60 additions and 35 deletions.
diff --git a/docs/src/main/scala/uniref.scala.md b/docs/src/main/scala/uniref.scala.md
@@ -5,11 +5,17 @@ package com.bio4j.data.uniref
 trait AnyCluster extends Any {
 
   def ID: String
-  def seedID: Option[String]
-  def representativeID: Option[String]
-  def nonRepresentativeMemberIDs: Seq[String]
+  def seed: ClusterMember
+  def representative: ClusterMember
+  def nonRepresentativeMembers: Seq[ClusterMember]
 }
 
+sealed trait ClusterMember extends Any {
+  def id: String
+}
+case class UniProtProtein(val id: String) extends ClusterMember
+case class UniParcProtein(val id: String) extends ClusterMember
+
 ```
 
 

diff --git a/docs/src/main/scala/xml/entry.scala.md b/docs/src/main/scala/xml/entry.scala.md
@@ -17,42 +17,49 @@ case class Entry(val xml: Elem) extends AnyVal with AnyCluster {
   def ID: String =
     xml \ "@id" text
 
-  def representativeID: Option[String] =
-    (xml \ "representativeMember" \ "dbReference" \ "property" )
-      .filter( isUniProtAccessionProperty )
-      .map( _ \ "@value" text )
-      .headOption
-
-  def nonRepresentativeMemberIDs: Seq[String] =
-    nonRepresentativeMembers
-      .flatMap( dbRef =>
-        (dbRef \ "property").filter(isUniProtAccessionProperty)
-        .map(_ \ "@value" text)
+  def representative: ClusterMember =
+    dbRefToClusterMember(representativedbRef)
+
+  def seed: ClusterMember =
+    if(dbRefIsSeed(representativedbRef))
+      representative
+    else
+      dbRefToClusterMember(
+        nonRepresentativeMembersdbRefs
+          .filter(dbRefIsSeed)
+          .head
       )
 
-  def seedID: Option[String] =
-    if( (xml \ "representativeMember" \ "dbReference" \ "property") exists isSeed  )
-      representativeID
+  def nonRepresentativeMembers: Seq[ClusterMember] =
+    nonRepresentativeMembersdbRefs map dbRefToClusterMember
+
+  private def dbRefToClusterMember(dbRef: Node): ClusterMember = {
+
+    val id = dbRef \ "@id" text
+
+    if(isUniProtDBReference(dbRef))
+      UniProtProtein(id)
     else
-      nonRepresentativeMembers
-        .filter( member => (member \ "property") exists isSeed )
-        .headOption
-        .flatMap(accession)
+      UniParcProtein(id)
+  }
 
   private def isUniProtDBReference(dbRef: Node): Boolean =
     (dbRef \ "@type" text) == "UniProtKB ID"
 
-  private def isUniProtAccessionProperty(property: Node): Boolean =
-    (property \ "@type" text) == "UniProtKB accession"
+  private def isUniParcDBReference(dbRef: Node): Boolean =
+    (dbRef \ "@type" text) == "UniParc ID"
+
+  private def dbRefIsSeed(dbRef: Node): Boolean =
+    (dbRef \ "property") exists isSeed
 
   private def isSeed(property: Node): Boolean =
     (property \ "@type" text) == "isSeed"
 
-  private def nonRepresentativeMembers =
-    (xml \ "member" \ "dbReference") filter isUniProtDBReference
+  private def representativedbRef: Node =
+    xml \ "representativeMember" \ "dbReference" head
 
-  private def accession(dbRef: Node): Option[String] =
-    (dbRef \ "property").filter(isUniProtAccessionProperty).headOption.map(_.text)
+  private def nonRepresentativeMembersdbRefs =
+    (xml \ "member" \ "dbReference")
 }
 
 ```

diff --git a/docs/src/test/scala/ParseUniRef50.scala.md b/docs/src/test/scala/ParseUniRef50.scala.md
@@ -18,10 +18,16 @@ class ParseUniRef50 extends FunSuite {
 
     xml.entries.fromLines(lines) foreach { e =>
 
-      val ID = e.ID
-      val seedID = e.seedID
-      val representativeID = e.representativeID
-      val nonRepresentativeMemberIDs = e.nonRepresentativeMemberIDs
+      val id = e.ID
+
+      val seed    = e.seed
+      val seedID  = seed.id
+
+      val representative    = e.representative
+      val representativeID  = representative.id
+
+      val nonRepresentativeMembers    = e.nonRepresentativeMembers
+      val nonRepresentativeMembersIDs = nonRepresentativeMembers map { _.id }
     }
   }
 
@@ -30,10 +36,16 @@ class ParseUniRef50 extends FunSuite {
 
     xml.entries.fromLines(bigLines) foreach { e =>
 
-      val ID = e.ID
-      val seedID = e.seedID
-      val representativeID = e.representativeID
-      val nonRepresentativeMemberIDs = e.nonRepresentativeMemberIDs
+      val id = e.ID
+
+      val seed    = e.seed
+      val seedID  = seed.id
+
+      val representative    = e.representative
+      val representativeID  = representative.id
+
+      val nonRepresentativeMembers    = e.nonRepresentativeMembers
+      val nonRepresentativeMembersIDs = nonRepresentativeMembers map { _.id }
     }
   }