Merge branch 'master' of github.com:OpenTreeOfLife/reference-taxonomy

Author: mtholder

org/opentreeoflife/smasher/AlignmentByName.java

@@ -239,7 +239,8 @@ Map<Taxon, String> getCandidates(Taxon node) {
         Map<Taxon, String> candidateMap = new HashMap<Taxon, String>();
         getCandidatesViaName(node, "C", candidateMap); // canonical
         for (Synonym syn : node.getSynonyms())
-            getCandidatesViaName(syn, "S", candidateMap);
+            if (!syn.type.equals("common name"))
+                getCandidatesViaName(syn, "S", candidateMap);
         if (candidateMap.size() == 0)
             getCandidatesViaGender(node, candidateMap);
         return candidateMap;

org/opentreeoflife/taxa/InterimFormat.java

@@ -488,17 +488,18 @@ else if (losers == 10)
 
                     if (type.equals("type material")) // NCBI
                         continue;
-                    if (type.equals("authority")) // NCBI
+                    else if (type.equals("authority")) // NCBI
                         continue;
-                    if (type.endsWith("common name")) // NCBI
+                    else if (type.endsWith("common name")) { // NCBI
+                        if (!type.equals("common name")) // NCBI
+                            continue;
+                    } else if (type.equals("blast name")) // NCBI
                         continue;
-                    if (type.equals("blast name")) // NCBI
+                    else if (type.equals("in-part")) // NCBI
                         continue;
-                    if (type.equals("in-part")) // NCBI
+                    else if (type.equals("valid")) // IRMNG - redundant - ?
                         continue;
-                    if (type.equals("valid")) // IRMNG - redundant - ?
-                        continue;
-                    if (type.equals("") || type.equals("None"))
+                    else if (type.equals("") || type.equals("None"))
                         type = "synonym";
 
                     Node syn = node.addSynonym(name, type, sid);

org/opentreeoflife/taxa/Synonym.java

@@ -4,7 +4,7 @@ public class Synonym extends Node {
 
     // name inherited from class Node
 
-    String type;                 // synonym, authority, common name, etc.
+    public String type;                 // synonym, authority, common name, etc.
 
     public Synonym(String name, String kind, Taxon taxon) {
         super(name);