some cleanup, documentation, begin() and end() methods

diff --git a/src/geneorder.cpp b/src/geneorder.cpp
index 994137d288a025e788eaf99d2b79b4272bc7d96a..5915524644e32ee84c76de09ebbcfac6932d3fb1 100644 (file)
--- a/src/geneorder.cpp
+++ b/src/geneorder.cpp
@@ -18,13 +18,13 @@
  *   51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA          *
  ***************************************************************************/
 
-#include <geneorder.h>
-
 #include <algorithm>
+#include <stdexcept>
 #include <cstdlib>
-
 using namespace std;
 
+#include "geneorder.h"
+
 /**
  * \file GeneOrder.cpp
  * Implements the GeneOrder class
@@ -33,7 +33,6 @@ using namespace std;
  */
 
 
-
 GeneOrder::GeneOrder(const GeneOrder& go){
        _geneorder = go._geneorder;
 }
@@ -45,7 +44,7 @@ void GeneOrder::pad(){
                _geneorder.push_back(_geneorder.size());
 }
 
-struct test{
+struct Abs{
        Gene operator()(Gene x) const{
                return abs(x);
        }
@@ -53,11 +52,12 @@ struct test{
 
 void GeneOrder::verify(){
        if(_geneorder[0] != 0)
-               throw std::invalid_argument("Permutation doesn't start with 0");
+               throw invalid_argument("Permutation doesn't start with 0");
        if ( _geneorder.back() != static_cast<Gene>(_geneorder.size() - 1))
-               throw std::invalid_argument("Permutation doesn't end with n+1");
+               throw invalid_argument("Permutation doesn't end with n+1");
+
        GeneList genes(_geneorder);
-       transform(genes.begin(),genes.end(),genes.begin(),test());
+       transform(genes.begin(),genes.end(),genes.begin(),Abs());
        sort(genes.begin(),genes.end());
        if (unique(genes.begin(),genes.end()) != genes.end())
                throw std::invalid_argument("Not all genes are present exactly 1 time");
@@ -77,14 +77,23 @@ const GeneOrder& GeneOrder::operator=(const GeneOrder& go){
  */
 const Gene& GeneOrder::operator[](size_type i) const{
        if (i < 0 || i >= _geneorder.size())
-               throw out_of_range("Index is not in valid range");
+               throw out_of_range("Indexis not in valid range");
        return _geneorder[i];
 }
 
-int GeneOrder::size() const{
+GeneOrder::size_type GeneOrder::size() const{
        return _geneorder.size();
 }
 
 const GeneOrder::GeneList& GeneOrder::list() const{
        return _geneorder;
 }
+
+
+GeneOrder::iterator GeneOrder::begin() const{
+       return _geneorder.begin();
+}
+
+GeneOrder::iterator GeneOrder::end() const{
+       return _geneorder.end();
+}

diff --git a/src/geneorder.h b/src/geneorder.h
index ebc427a9c4c0f49bb770de0af27a3c8c795c80de..b29a1acc2ceefc15d700f9720f09a2ad9f22568a 100644 (file)
--- a/src/geneorder.h
+++ b/src/geneorder.h
@@ -33,8 +33,9 @@
 class GeneOrder{
        public:
 
-               typedef std::vector<long> GeneList;
+               typedef std::vector<Gene> GeneList;
                typedef GeneList::size_type size_type;
+               typedef GeneList::const_iterator iterator;
 
                /**
                 * Creates a copy of the given gene order
@@ -42,9 +43,20 @@ class GeneOrder{
                GeneOrder(const GeneOrder& go);
 
                /**
-                * Creates a gene order from a given list.
+                * Creates a gene order from a given list, using STL-type iterators.
                 *
-                * \throws invalid_argument if the list is not a valid permutation.
+                * The given permutation needs to contain all genes 1 to n, if 0 is
+                * included it has to be the first item, if it is not present it will
+                * be added automatically. Similarily, if n is not the last item, then
+                * n+1 will be added to the end.
+                *
+                * \param begin iterator to the first element in the list, from begin()
+                * on stl collections and pointer to first item on plain arrays.
+                *
+                * \param end iterator to the element behind the last, from end() in
+                * stl collections or pointer to first element+size on plain arrays.
+                *
+                * \throws std::invalid_argument if the list is not a valid permutation.
                 */
                template<class T>
                GeneOrder(T begin, T end);
@@ -62,20 +74,36 @@ class GeneOrder{
                /**
                 * Returns the gene at the given index.
                 *
-                * \throws out_of_range if i is smaller than 0 or too big.
+                * \throws std::out_of_range if i is smaller than 0 or bigger than n.
                 */
                const Gene& operator[](size_type i) const;
 
                /**
                 * Returns the size of the permutation.
                 */
-               int size() const;
+               size_type size() const;
 
                /**
                 * Returns the vector containing the gene order permutation.
                 */
                const GeneList& list() const;
 
+               /**
+                * Returns the start iterator for the permutation.
+                * To be used with STL style functions.
+                *
+                * \see end
+                */
+               iterator begin() const;
+
+               /**
+                * Returns the end iterator for the permutation.
+                * To be used with STL style functions.
+                *
+                * \see begin
+                */
+               iterator end() const;
+
 
        private:
                GeneList _geneorder;

diff --git a/src/test/geneordertest.cpp b/src/test/geneordertest.cpp
index 0d37456450a0521d1195a37a3f932fe220754150..8583b3b7731fe164776f5034c510995c8ad478ae 100644 (file)
--- a/src/test/geneordertest.cpp
+++ b/src/test/geneordertest.cpp
@@ -58,17 +58,17 @@ protected:
        void testCopyCreate (){
                GeneOrder go(_bigvalidPerm.begin(),_bigvalidPerm.end());
                GeneOrder go2(go);
-               CPPUNIT_ASSERT(equal(go.list().begin(),go.list().end(),go2.list().begin()));
+               CPPUNIT_ASSERT(equal(go.begin(),go.end(),go2.begin()));
                GeneOrder go3(_validPerm.begin(),_validPerm.end());
-               CPPUNIT_ASSERT(!equal(go3.list().begin(),go3.list().end(),go2.list().begin()));
+               CPPUNIT_ASSERT(!equal(go3.begin(),go3.end(),go2.begin()));
        }
        void testAssign (){
                GeneOrder go(_bigvalidPerm.begin(),_bigvalidPerm.end());
                GeneOrder go2(_validPerm.begin(),_validPerm.end());
                go2 = go;
-               CPPUNIT_ASSERT(equal(go.list().begin(),go.list().end(),go2.list().begin()));
+               CPPUNIT_ASSERT(equal(go.begin(),go.end(),go2.begin()));
                GeneOrder go3(_validPerm.begin(),_validPerm.end());
-               CPPUNIT_ASSERT(!equal(go3.list().begin(),go3.list().end(),go2.list().begin()));
+               CPPUNIT_ASSERT(!equal(go3.begin(),go3.end(),go2.begin()));
        }
 };