include unit tests

.gitignore

@@ -30,3 +30,4 @@
 .dirstamp
 topo
 topo_dbg
+unittest

.travis.yml

@@ -13,3 +13,5 @@ before_install:
 
 script:
   - make
+  - make unittest
+  - ./unittest

Makefile

@@ -4,14 +4,23 @@ FLAGS = -O3 -g -std=c++0x -DVERSION=\"${VERSION}\"
 SOURCE = all_gene_topo.cpp
 
 .PHONY: all
-all: clean_all topo topo_dbg
+all: topo topo_dbg
 
-topo:
+topo: all_gene_topo.hpp all_gene_topo.cpp main.cpp
 	${COMPILER} ${FLAGS} -DNDEBUG -o topo ${SOURCE} main.cpp
 
-topo_dbg:
+topo_dbg: all_gene_topo.hpp all_gene_topo.cpp main.cpp
 	${COMPILER} ${FLAGS} -o topo_dbg ${SOURCE} main.cpp
 
+# Tester flags
+unittests_CXXFLAGS = -DUNITTEST -DNDEBUG -std=c++0x -DVERSION=\"${VERSION}\"
+unittests_LDADD = -lcppunit -ldl
+
+test_src = test_topo.cpp  ${SOURCE}
+
+unittest: all_gene_topo.hpp all_gene_topo.cpp test_runner.cpp  test_topo.cpp
+	${COMPILER} ${unittests_CXXFLAGS} ${test_src} test_runner.cpp -o unittest ${unittests_LDADD}
+
 .PHONY: clean
 clean:
 	rm -f topo topo_dbg

README

@@ -0,0 +1 @@
+README.md

README.md

@@ -0,0 +1,4 @@
+A simple program for enumerating all possible binary tree Newick strings from given taxon names. This program is part of the program hybrid-coal.
+USEAGE:
+
+    $ ./topo a b c d e

all_gene_topo.cpp

@@ -1,11 +1,11 @@
 /*
- * hybrid-Lambda is used to simulate gene trees given species network under 
+ * hybrid-Lambda is used to simulate gene trees given species network under
  * coalescent process.
- * 
- * Copyright (C) 2010 -- 2014 Sha (Joe) Zhu
- * 
+ *
+ * Copyright (C) 2010 -- 2015 Sha (Joe) Zhu
+ *
  * This file is part of hybrid-Lambda.
- * 
+ *
  * hybrid-Lambda is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
  * the Free Software Foundation, either version 3 of the License, or
@@ -23,13 +23,18 @@
 /*! \file all_gene_topo.cpp
  *     \brief  Enumerate all possible tree topologies for given number of taxon */
 
-#include"all_gene_topo.hpp"
+#include "all_gene_topo.hpp"
 
 //GeneTopoList::GeneTopoList( string tree_str ){
 GeneTopoList::GeneTopoList( vector < string > &TipLabels_in ){
     this->TipLabels = TipLabels_in;
     //this->extract_TipLabels_from_TreeStr ( tree_str );
     assert ( this->TipLabels.size() >= 2 ) ;
+    this->run();
+}
+
+
+void GeneTopoList::run(){
     this->init();
     this->core();
     this->finalize();

all_gene_topo.hpp

@@ -1,11 +1,11 @@
 /*
- * hybrid-Lambda is used to simulate gene trees given species network under 
+ * hybrid-Lambda is used to simulate gene trees given species network under
  * coalescent process.
- * 
- * Copyright (C) 2010 -- 2014 Sha (Joe) Zhu
- * 
+ *
+ * Copyright (C) 2010 -- 2015 Sha (Joe) Zhu
+ *
  * This file is part of hybrid-Lambda.
- * 
+ *
  * hybrid-Lambda is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
  * the Free Software Foundation, either version 3 of the License, or
@@ -49,6 +49,7 @@ using namespace std;
 class GeneTopoList {
     friend class HybridCoal;
     friend class TopoApp;
+    friend class TestGeneTopoList;
     //deque < string > TreeList;
     vector < string > TreeList;
     vector < string > TipLabels;
@@ -59,7 +60,8 @@ class GeneTopoList {
     string add_new_taxa_at_int(string &in_str, size_t i, string &newly_added );
     string add_new_taxa_at_tip(string &in_str, size_t i, string &newly_added, string added_to );
     string extract_label( string &in_str, size_t i);
-
+
+    void run();
     void init();
     void core();
     void extract_TipLabels_from_TreeStr ( string &tree_str );
@@ -88,7 +90,7 @@ class TopoApp {
 
     void parse(){
         if ( argc_ == 1 ){
-            cout << "print help "<<endl;
+            cout << "USEAGE: ./topo a b c d e "<<endl;
             return;
         }
 
@@ -100,9 +102,11 @@ class TopoApp {
     }
 
     void finalize(){
-        if ( topo_list_->TreeList.size() > 1 ) 
-            topo_list_ ->init();
-        topo_list_ ->core();
+        if ( topo_list_->TipLabels.size() > 1 ) {
+            topo_list_ ->run();
+        } {
+            cout << " Please provide at least two taxon names." <<endl;
+        }
         for ( size_t i = 0; i < topo_list_->TreeList.size(); i++){
             cout << topo_list_->TreeList[i] << endl;
         }

main.cpp

@@ -1,3 +1,25 @@
+/*
+ * hybrid-Lambda is used to simulate gene trees given species network under
+ * coalescent process.
+ *
+ * Copyright (C) 2010 -- 2015 Sha (Joe) Zhu
+ *
+ * This file is part of hybrid-Lambda.
+ *
+ * hybrid-Lambda is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
 #include "all_gene_topo.hpp"
 
 int main ( int argc, char *argv[] ) {

test_runner.cpp

@@ -0,0 +1,34 @@
+/*
+ * Execute this program to run the test suite.
+ *
+ * Usually there's no need to change anything in here.
+ */
+#include <cppunit/TestResult.h>
+#include <cppunit/TestResultCollector.h>
+#include <cppunit/TestRunner.h>
+#include <cppunit/extensions/TestFactoryRegistry.h>
+#include <cppunit/BriefTestProgressListener.h>
+#include <cppunit/CompilerOutputter.h>
+
+using namespace CppUnit;
+
+int main(void) {
+	TestResult controller;
+
+	TestResultCollector result;
+	controller.addListener(&result);
+
+	BriefTestProgressListener progress;
+	controller.addListener(&progress);
+
+	TestRunner runner;
+	runner.addTest( TestFactoryRegistry::getRegistry().makeTest() );
+	runner.run(controller);
+
+	CompilerOutputter outputter(&result, std::cerr);
+	outputter.write();
+
+	return result.wasSuccessful() ? 0 : 1;
+}
+
+// EOF

test_topo.cpp

@@ -0,0 +1,62 @@
+#include <cppunit/TestCase.h>
+#include <cppunit/extensions/HelperMacros.h>
+#include "all_gene_topo.hpp"
+
+#pragma GCC diagnostic ignored "-Wwrite-strings"
+
+class TestGeneTopoList : public CppUnit::TestCase {
+
+  CPPUNIT_TEST_SUITE( TestGeneTopoList );
+  CPPUNIT_TEST ( testConstructor );
+  CPPUNIT_TEST ( testExtract );
+  CPPUNIT_TEST_SUITE_END();
+ private:
+
+ public:
+  void setUp() {
+        return;
+    }
+
+    void tearDown() {
+        return;
+    }
+
+    void testConstructor(){
+        const char *vinit3[] = {"a", "b", "c"};
+        std::vector<std::string> v3(vinit3, end(vinit3));
+        GeneTopoList testList3(v3);
+        CPPUNIT_ASSERT (  testList3.TipLabels.size() == (unsigned)3 );
+        CPPUNIT_ASSERT (  testList3.TreeList.size() == (unsigned)3 );
+
+        const char *vinit4[] = {"a", "b", "c", "d"};
+        std::vector<std::string> v4(vinit4, end(vinit4));
+        GeneTopoList testList4(v4);
+        CPPUNIT_ASSERT (  testList4.TipLabels.size() == (unsigned)4 );
+        CPPUNIT_ASSERT (  testList4.TreeList.size() == (unsigned)15 );
+
+        const char *vinit5[] = {"a", "b", "c", "d", "e"};
+        std::vector<std::string> v5(vinit5, end(vinit5));
+        GeneTopoList testList5(v5);
+        CPPUNIT_ASSERT (  testList5.TipLabels.size() == (unsigned)5 );
+        CPPUNIT_ASSERT (  testList5.TreeList.size() == (unsigned)105 );
+
+        const char *vinit6[] = {"a", "b", "c", "1", "2", "3"};
+        std::vector<std::string> v6(vinit6, end(vinit6));
+        GeneTopoList testList6(v6);
+        CPPUNIT_ASSERT (  testList6.TipLabels.size() == (unsigned)6 );
+        CPPUNIT_ASSERT (  testList6.TreeList.size() == (unsigned)945 );
+
+    }
+
+    void testExtract(){
+        GeneTopoList testList;
+        string tree = "(((A,B),C),D);";
+        CPPUNIT_ASSERT_NO_THROW(testList.extract_TipLabels_from_TreeStr(tree));
+        CPPUNIT_ASSERT (  testList.TipLabels.size() == (unsigned)4 );
+        CPPUNIT_ASSERT_NO_THROW(testList.init());
+        CPPUNIT_ASSERT_NO_THROW(testList.core());
+        CPPUNIT_ASSERT (  testList.TreeList.size() == (unsigned)15 );
+    }
+};
+
+CPPUNIT_TEST_SUITE_REGISTRATION( TestGeneTopoList );