enable major/minor string finding over 2 snp feature objects

src/shogun/features/SNPFeatures.cpp

@@ -208,7 +208,7 @@ void CSNPFeatures::add_to_dense_vec(float64_t alpha, int32_t vec_idx1, float64_t
 	strings->free_feature_vector(vec, vec_idx1, free_vec1);
 }
 
-void CSNPFeatures::obtain_base_strings()
+void CSNPFeatures::find_minor_major_strings(uint8_t* minor, uint8_t* major)
 {
 	for (int32_t i=0; i<num_strings; i++)
 	{
@@ -217,29 +217,37 @@ void CSNPFeatures::obtain_base_strings()
 		uint8_t* vec = ((CStringFeatures<uint8_t>*) strings)->get_feature_vector(i, len, free_vec);
 		ASSERT(string_length==len);
 
-		if (i==0)
-		{
-			size_t tlen=(len+1)*sizeof(uint8_t);
-			m_str_min=(uint8_t*) SG_MALLOC(tlen);
-			m_str_maj=(uint8_t*) SG_MALLOC(tlen);
-			memset(m_str_min, 0, tlen);
-			memset(m_str_maj, 0, tlen);
-		}
-
 		for (int32_t j=0; j<len; j++)
 		{
 			// skip sequencing errors
 			if (vec[j]=='0')
 				continue;
 
-			if (m_str_min[j]==0)
-				m_str_min[j]=vec[j];
-            else if (m_str_maj[j]==0 && vec[j]!=m_str_min[j])
-				m_str_maj[j]=vec[j];
+			if (minor[j]==0)
+				minor[j]=vec[j];
+            else if (major[j]==0 && vec[j]!=minor[j])
+				major[j]=vec[j];
 		}
 
 		((CStringFeatures<uint8_t>*) strings)->free_feature_vector(vec, i, free_vec);
 	}
+}
+
+void CSNPFeatures::obtain_base_strings(CSNPFeatures* snp)
+{
+	SG_FREE(m_str_min);
+	SG_FREE(m_str_maj);
+	size_t tlen=(string_length+1)*sizeof(uint8_t);
+
+	m_str_min=(uint8_t*) SG_MALLOC(tlen);
+	m_str_maj=(uint8_t*) SG_MALLOC(tlen);
+	memset(m_str_min, 0, tlen);
+	memset(m_str_maj, 0, tlen);
+
+	find_minor_major_strings(m_str_min, m_str_maj);
+
+	if (snp)
+		snp->find_minor_major_strings(m_str_min, m_str_maj);
 
 	for (int32_t j=0; j<string_length; j++)
 	{

src/shogun/features/SNPFeatures.h

@@ -212,9 +212,12 @@ class CSNPFeatures : public CDotFeatures
 			return (char*) m_str_maj;
 		}
 
-		/** compute the basee strings from current strings */
-		void obtain_base_strings();
-
+		/** compute the base strings from current strings optionally taking
+		 * into account snp
+		 *
+		 * @param snp optionally compute base string for snp too
+		 */
+		void obtain_base_strings(CSNPFeatures* snp=NULL);
 
 		/** @return object name */
 		inline virtual const char* get_name() const { return "SNPFeatures"; }
@@ -228,6 +231,15 @@ class CSNPFeatures : public CDotFeatures
 		 */
 		static SGMatrix<float64_t> get_2x3_table(CSNPFeatures* pos, CSNPFeatures* neg);
 
+	private:
+		/** determine minor and major base strings from current strings
+		 * @arg minor - array of string_length inited with zero that will
+		 *              contain the minor base string
+		 * @arg major - array of string_length inited with zero that will
+		 *              contain the major base string
+		 */
+		void find_minor_major_strings(uint8_t* minor, uint8_t* major);
+
 	protected:
 		/** stringfeatures the wdfeatures are based on*/
 		CStringFeatures<uint8_t>* strings;