From 8257b7287b84cad607887769195dbbc9601ea852 Mon Sep 17 00:00:00 2001
From: pnrobinson <annas0ph1e>
Date: Wed, 13 Dec 2017 16:49:29 -0800
Subject: [PATCH] adding function existsPath together with test

---
 .../ontology/data/ImmutableOntology.java      | 24 +++++++++++++++----
 .../ontolib/ontology/data/Ontology.java       |  7 ++++--
 .../ontology/data/ImmutableOntologyTest.java  | 23 ++++++++++++++++++
 3 files changed, 48 insertions(+), 6 deletions(-)

diff --git a/ontolib-core/src/main/java/com/github/phenomics/ontolib/ontology/data/ImmutableOntology.java b/ontolib-core/src/main/java/com/github/phenomics/ontolib/ontology/data/ImmutableOntology.java
index cd2559b..99f6b2f 100644
--- a/ontolib-core/src/main/java/com/github/phenomics/ontolib/ontology/data/ImmutableOntology.java
+++ b/ontolib-core/src/main/java/com/github/phenomics/ontolib/ontology/data/ImmutableOntology.java
@@ -1,9 +1,6 @@
 package com.github.phenomics.ontolib.ontology.data;
 
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
 
 import com.github.phenomics.ontolib.graph.algo.BreadthFirstSearch;
 import com.github.phenomics.ontolib.graph.algo.VertexVisitor;
@@ -188,6 +185,25 @@ public Set<TermId> getObsoleteTermIds() {
     return obsoleteTermIds;
   }
 
+  @Override
+  public boolean existsPath(final TermId sourceID, TermId destID){
+    // special case -- a term cannot have a path to itself in an ontology (DAG)
+    if (sourceID.equals(destID)) return false;
+    List<TermId> visited = new ArrayList<>();
+    BreadthFirstSearch<TermId, ImmutableEdge<TermId>> bfs = new BreadthFirstSearch<>();
+    bfs.startFromForward(graph, sourceID, new VertexVisitor<TermId, ImmutableEdge<TermId>>() {
+        @Override
+        public boolean visit(DirectedGraph<TermId, ImmutableEdge<TermId>> g, TermId termId) {
+          visited.add(termId);
+          return true;
+        }});
+    return visited.contains(destID);
+  }
+
+
+
+
+
   @Override
   public Ontology<T, R> subOntology(TermId subOntologyRoot) {
     final Set<TermId> childTermIds = OntologyTerms.childrenOf(subOntologyRoot, this);
diff --git a/ontolib-core/src/main/java/com/github/phenomics/ontolib/ontology/data/Ontology.java b/ontolib-core/src/main/java/com/github/phenomics/ontolib/ontology/data/Ontology.java
index 60efcad..bc11c79 100644
--- a/ontolib-core/src/main/java/com/github/phenomics/ontolib/ontology/data/Ontology.java
+++ b/ontolib-core/src/main/java/com/github/phenomics/ontolib/ontology/data/Ontology.java
@@ -42,7 +42,7 @@ default TermId getPrimaryTermId(TermId termId) {
 
   /**
    * Return all the {@link TermId}s of all ancestors from {@code termId}.
-   * 
+   *
    * @param termId The {@link TermId} to query ancestor {@link TermId}s for.
    * @param includeRoot Whether or not to include the root.
    * @return {@link Set} of {@link TermId}s of the ancestors of {@code termId} (including itself),
@@ -52,7 +52,7 @@ default TermId getPrimaryTermId(TermId termId) {
 
   /**
    * Return all the {@link TermId}s of all ancestors from {@code termId}, including root.
-   * 
+   *
    * @param termId The {@link TermId} to query ancestor {@link TermId}s for.
    * @return {@link Set} of {@link TermId}s of the ancestors of {@code termId} (including itself),
    *         including root.
@@ -97,6 +97,9 @@ default Set<TermId> getParentTermIds(TermId termId) {
     return result;
   }
 
+  public boolean existsPath(final TermId sourceID, TermId destID);
+
+
   /**
    * Construct and return sub ontology, starting from {@code subOntologyRoot}.
    *
diff --git a/ontolib-core/src/test/java/com/github/phenomics/ontolib/ontology/data/ImmutableOntologyTest.java b/ontolib-core/src/test/java/com/github/phenomics/ontolib/ontology/data/ImmutableOntologyTest.java
index 28aa8f6..9783dd2 100644
--- a/ontolib-core/src/test/java/com/github/phenomics/ontolib/ontology/data/ImmutableOntologyTest.java
+++ b/ontolib-core/src/test/java/com/github/phenomics/ontolib/ontology/data/ImmutableOntologyTest.java
@@ -1,6 +1,7 @@
 package com.github.phenomics.ontolib.ontology.data;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 
 import org.junit.Test;
@@ -36,4 +37,26 @@ public void test() {
         ontology.getParentTermIds(id1).toString());
   }
 
+
+  /** The example graph has id1->id2, id1->id3, id1->id4, id2->id5, id4->id5 */
+  @Test
+  public void testPathExists() {
+    assertTrue(ontology.existsPath(id1,id2));
+    assertFalse(ontology.existsPath(id2,id1));
+    assertTrue(ontology.existsPath(id1,id3));
+    assertFalse(ontology.existsPath(id3,id1));
+    assertTrue(ontology.existsPath(id1,id4));
+    assertFalse(ontology.existsPath(id4,id1));
+    assertTrue(ontology.existsPath(id1,id5));
+    assertFalse(ontology.existsPath(id5,id1));
+    assertTrue(ontology.existsPath(id2,id5));
+    assertFalse(ontology.existsPath(id5,id2));
+    assertTrue(ontology.existsPath(id4,id5));
+    assertFalse(ontology.existsPath(id5,id4));
+  // test that a term cannot have a path to itself.
+    assertFalse(ontology.existsPath(id5,id5));
+
+  }
+
+
 }