From 710a31531c9e4614ede203542c2146086d55a9ff Mon Sep 17 00:00:00 2001
From: Daniel Shapiro <d.shapiro@berkeley.edu>
Date: Fri, 21 Jun 2019 17:09:37 -0700
Subject: [PATCH] 1.1.2

handle paraphyly more gracefully
---
 build.sbt                                        |  2 +-
 src/main/scala/cladograms/WikiClade.scala        | 14 ++++++++++++--
 src/main/scala/cladograms/WikiPageClade.scala    | 11 ++---------
 src/main/scala/cladograms/WikiTaxoboxClade.scala |  8 --------
 4 files changed, 15 insertions(+), 20 deletions(-)

diff --git a/build.sbt b/build.sbt
index 2ca76f1..a99dcc0 100644
--- a/build.sbt
+++ b/build.sbt
@@ -1,6 +1,6 @@
 name := "wikiClade"
 
-version := "1.1.1"
+version := "1.1.2"
 
 scalaVersion := "2.12.8"
 
diff --git a/src/main/scala/cladograms/WikiClade.scala b/src/main/scala/cladograms/WikiClade.scala
index 87e97bc..a00acf1 100644
--- a/src/main/scala/cladograms/WikiClade.scala
+++ b/src/main/scala/cladograms/WikiClade.scala
@@ -15,7 +15,8 @@ abstract class WikiClade extends Clade {
 
   def priorityOverride: Double
 
-  case class WikiCladeMetadata(trueName: String, ancestors: List[Clade], path: Option[String], cladeType: String, docPriority: Double)
+  case class WikiCladeMetadata(trueName: String, ancestors: List[Clade], path: Option[String], cladeType: String,
+                               docPriority: Double, paraphyletic: Boolean = false)
 
   override def DOTDefinition: Option[String] = {
     val cladeTypeStr = if (meta.cladeType.isEmpty) "" else s"""<FONT POINT-SIZE=\"10\">${meta.cladeType}</FONT><br/>"""
@@ -23,15 +24,24 @@ abstract class WikiClade extends Clade {
       case None => ""
       case Some(p) => s"""href="${WikiClade.baseUrl}${p.replaceAll("&", "&amp;")}","""
     }
+    val asterisk = if (meta.paraphyletic) "*" else ""
     val dispname =
       if (meta.trueName == name) name
-      else s"${meta.trueName}<br/>($name)"
+      else s"${meta.trueName}<br/>($name)$asterisk"
     Some(s""""$name" [$hrefStr label=<$cladeTypeStr<B>$dispname</B>>]""")
   }
 
   def priority: Double = Math.min(
     Math.min(priorityOverride, meta.docPriority),
     if (WikiClade.importantCladeTypes contains meta.cladeType) 20 else 100)
+
+  def canEqual(obj: Any): Boolean = obj.isInstanceOf[WikiClade]
+  override def equals(obj: Any): Boolean = obj match {
+    case obj: WikiClade => obj.canEqual(this) && this.meta.trueName == obj.meta.trueName
+    case _ => false
+  }
+
+  override def hashCode(): Int = meta.trueName.hashCode
 }
 
 object WikiClade {
diff --git a/src/main/scala/cladograms/WikiPageClade.scala b/src/main/scala/cladograms/WikiPageClade.scala
index 3f25ddd..5afaf07 100644
--- a/src/main/scala/cladograms/WikiPageClade.scala
+++ b/src/main/scala/cladograms/WikiPageClade.scala
@@ -26,7 +26,8 @@ class WikiPageClade(val name: String, path: Option[String], val priorityOverride
       else WikiClade.newClade(details.name, Some(details.path))
     }
     val docPriority = priorityBasedOnDoc(docOpt)
-    WikiCladeMetadata(mydetails.name ,ancestors, path, WikiClade.sanitizeCladeType(mydetails.cladeType), docPriority)
+    WikiCladeMetadata(mydetails.name ,ancestors, path, WikiClade.sanitizeCladeType(mydetails.cladeType), docPriority,
+      mydetails.path.nonEmpty && !mydetails.cladeType.contains("pecies"))
   }
 
   private def extractTaxonomy(elems: Elements): List[TaxonDetails] = {
@@ -95,14 +96,6 @@ class WikiPageClade(val name: String, path: Option[String], val priorityOverride
     case None => 99
   }
 
-  def canEqual(obj: Any): Boolean = obj.isInstanceOf[WikiPageClade]
-  override def equals(obj: Any): Boolean = obj match {
-    case obj: WikiPageClade => obj.canEqual(this) && this.meta.trueName == obj.meta.trueName
-    case _ => false
-  }
-
-  override def hashCode(): Int = meta.trueName.hashCode
-
   private def taxonDetails(name: String, cladeType: String, path: String): TaxonDetails = {
     TaxonDetails(name, cladeType, false, path, "")
   }
diff --git a/src/main/scala/cladograms/WikiTaxoboxClade.scala b/src/main/scala/cladograms/WikiTaxoboxClade.scala
index 0e7495f..fb841a2 100644
--- a/src/main/scala/cladograms/WikiTaxoboxClade.scala
+++ b/src/main/scala/cladograms/WikiTaxoboxClade.scala
@@ -69,12 +69,4 @@ class WikiTaxoboxClade(val name: String, taxonomyPath: Option[String], details:
     }
     iter(elems.size() - 1, List())
   }
-
-  def canEqual(obj: Any): Boolean = obj.isInstanceOf[WikiTaxoboxClade]
-  override def equals(obj: Any): Boolean = obj match {
-    case obj: WikiTaxoboxClade => obj.canEqual(this) && this.meta.trueName == obj.meta.trueName
-    case _ => false
-  }
-
-  override def hashCode(): Int = meta.trueName.hashCode
 }