remove most inline functions in features

- exceptions are some single line functions - templated classes
shogun-toolbox · Sep 15, 2011 · 8b4ce6c · 8b4ce6c
1 parent 5fee0e6
commit 8b4ce6c
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Showing 33 changed files with 997 additions and 746 deletions.
diff --git a/src/shogun/features/Alphabet.cpp b/src/shogun/features/Alphabet.cpp
@@ -591,6 +591,11 @@ void CAlphabet::print_histogram()
 	}
 }
 
+SGVector<int64_t> CAlphabet::get_histogram()
+{
+	return SGVector<int64_t>(&histogram[0], 1 << (sizeof(uint8_t)*8));
+}
+
 bool CAlphabet::check_alphabet(bool print_error)
 {
 	bool result = true;
@@ -632,7 +637,9 @@ bool CAlphabet::check_alphabet_size(bool print_error)
 
 void CAlphabet::copy_histogram(CAlphabet* a)
 {
-	memcpy(histogram, a->get_histogram(), sizeof(histogram));
+	SGVector<int64_t> h=a->get_histogram();
+	ASSERT(h.vlen == sizeof(histogram));
+	memcpy(histogram, h.vector, sizeof(histogram));
 }
 
 const char* CAlphabet::get_alphabet_name(EAlphabet alphabet)

diff --git a/src/shogun/features/Alphabet.h b/src/shogun/features/Alphabet.h
@@ -198,24 +198,9 @@ class CAlphabet : public CSGObject
 
 		/** get histogram
 		 *
-		 * @param h where the histogram will be stored
-		 * @param len length of histogram
+		 * @return histogram
 		 */
-		inline void get_hist(int64_t** h, int32_t* len)
-		{
-			int32_t hist_size=(1 << (sizeof(uint8_t)*8));
-			ASSERT(h && len);
-			*h= SG_MALLOC(int64_t, hist_size);
-			*len=hist_size;
-			ASSERT(*len);
-			memcpy(*h, &histogram[0], sizeof(int64_t)*hist_size);
-		}
-
-		/// get pointer to histogram
-		inline const int64_t* get_histogram()
-		{
-			return &histogram[0];
-		}
+		SGVector<int64_t> get_histogram();
 
 		/** check whether symbols in histogram are valid in alphabet
 		 * e.g. for DNA if only letters ACGT appear

diff --git a/src/shogun/features/AttributeFeatures.cpp b/src/shogun/features/AttributeFeatures.cpp
@@ -18,6 +18,73 @@ CAttributeFeatures::CAttributeFeatures()
 {
 }
 
+CFeatures* CAttributeFeatures::get_attribute(char* attr_name)
+{
+	int32_t idx=find_attr_index(attr_name);
+	if (idx>=0)
+	{
+		CFeatures* f=features[idx].attr_obj;
+		SG_REF(f);
+		return f;
+	}
+
+	return NULL;
+}
+
+void CAttributeFeatures::get_attribute_by_index(int idx, const char* &attr_name, CFeatures* &attr_obj)
+{
+		T_ATTRIBUTE a= features.get_element_safe(idx);
+		attr_name= a.attr_name;
+		attr_obj= a.attr_obj;
+		SG_REF(a.attr_obj);
+}
+
+bool CAttributeFeatures::set_attribute(char* attr_name, CFeatures* attr_obj)
+{
+	int32_t idx=find_attr_index(attr_name);
+	if (idx==-1)
+		idx=features.get_num_elements();
+
+	T_ATTRIBUTE a;
+	a.attr_name=strdup(attr_name);
+	a.attr_obj=attr_obj;
+
+	SG_REF(attr_obj);
+
+	return features.set_element(a, idx);
+}
+
+bool CAttributeFeatures::del_attribute(char* attr_name)
+{
+	int32_t idx=find_attr_index(attr_name);
+
+	if (idx>=0)
+	{
+		T_ATTRIBUTE a= features[idx];
+		SG_FREE(a.attr_name);
+		SG_UNREF(a.attr_obj);
+		return true;
+	}
+	return false;
+}
+
+int32_t CAttributeFeatures::get_num_attributes()
+{
+	return features.get_num_elements();
+}
+
+int32_t CAttributeFeatures::find_attr_index(char* attr_name)
+{
+	int32_t n=features.get_num_elements();
+	for (int32_t i=0; i<n; i++)
+	{
+		if (!strcmp(features[n].attr_name, attr_name))
+			return i;
+	}
+
+	return -1;
+}
+
 CAttributeFeatures::~CAttributeFeatures()
 {
 	int32_t n=features.get_num_elements();

diff --git a/src/shogun/features/AttributeFeatures.h b/src/shogun/features/AttributeFeatures.h
@@ -58,82 +58,36 @@ class CAttributeFeatures : public CFeatures
 	 * @param attr_name attribute name
 	 * @return feature object
 	 */
-	CFeatures* get_attribute(char* attr_name)
-	{
-		int32_t idx=find_attr_index(attr_name);
-		if (idx>=0)
-		{
-			CFeatures* f=features[idx].attr_obj;
-			SG_REF(f);
-			return f;
-		}
-
-		return NULL;
-	}
+	CFeatures* get_attribute(char* attr_name);
 
 	/** return the feature object at index
 	 *
 	 * @param idx index of attribute
 	 * @param attr_name attribute name (returned by reference)
 	 * @param attr_obj attribute object (returned by reference)
 	 */
-	inline void get_attribute_by_index(int idx, const char* &attr_name, CFeatures* &attr_obj)
-	{
-		T_ATTRIBUTE a= features.get_element_safe(idx);
-		attr_name= a.attr_name;
-		attr_obj= a.attr_obj;
-		SG_REF(a.attr_obj);
-	}
+	void get_attribute_by_index(int idx, const char* &attr_name, CFeatures* &attr_obj);
 
 	/** set the feature object for attribute name
 	 *
 	 * @param attr_name attribute name
 	 * @param attr_obj feature object to set
 	 * @return true on success
 	 */
-	inline bool set_attribute(char* attr_name, CFeatures* attr_obj)
-	{
-		int32_t idx=find_attr_index(attr_name);
-		if (idx==-1)
-			idx=features.get_num_elements();
-
-		T_ATTRIBUTE a;
-		a.attr_name=strdup(attr_name);
-		a.attr_obj=attr_obj;
-
-		SG_REF(attr_obj);
-
-		return features.set_element(a, idx);
-	}
+	bool set_attribute(char* attr_name, CFeatures* attr_obj);
 
 	/** delete the attribute matching attribute name
 	 *
 	 * @param attr_name attribute name
 	 * @return true on success
 	 */
-	inline bool del_attribute(char* attr_name)
-	{
-		int32_t idx=find_attr_index(attr_name);
-
-		if (idx>=0)
-		{
-			T_ATTRIBUTE a= features[idx];
-			SG_FREE(a.attr_name);
-			SG_UNREF(a.attr_obj);
-			return true;
-		}
-		return false;
-	}
-
+	bool del_attribute(char* attr_name);
 
 	/** get number of attributes
 	 *
 	 * @return number of attributes
 	 */
-	inline int32_t get_num_attributes()
-	{
-		return features.get_num_elements();
-	}
+	int32_t get_num_attributes();
 
 	/** @return object name */
 	inline virtual const char* get_name() const { return "AttributeFeatures"; }
@@ -184,18 +138,7 @@ class CAttributeFeatures : public CFeatures
 	 * @param attr_name attribute name
 	 * @return index (if found), otherwise -1
 	 */
-	inline int32_t find_attr_index(char* attr_name)
-	{
-		int32_t n=features.get_num_elements();
-		for (int32_t i=0; i<n; i++)
-		{
-			if (!strcmp(features[n].attr_name, attr_name))
-				return i;
-		}
-
-		return -1;
-	}
-
+	inline int32_t find_attr_index(char* attr_name);
 
 protected:
 	///list of attributes (sorted)

diff --git a/src/shogun/features/CombinedDotFeatures.cpp b/src/shogun/features/CombinedDotFeatures.cpp
@@ -15,17 +15,6 @@
 
 using namespace shogun;
 
-void
-CCombinedDotFeatures::init(void)
-{
-	m_parameters->add(&num_dimensions, "num_dimensions",
-					  "Total number of dimensions.");
-	m_parameters->add(&num_vectors, "num_vectors",
-					  "Total number of vectors.");
-	m_parameters->add((CSGObject**) &feature_list,
-					  "feature_list", "Feature list.");
-}
-
 CCombinedDotFeatures::CCombinedDotFeatures() : CDotFeatures()
 {
 	init();
@@ -240,6 +229,109 @@ void CCombinedDotFeatures::add_to_dense_vec(float64_t alpha, int32_t vec_idx1, f
 	}
 }
 
+void* CCombinedDotFeatures::get_feature_iterator(int32_t vector_index)
+{
+	combined_feature_iterator* it=SG_MALLOC(combined_feature_iterator, 1);
+
+	it->current=NULL;
+	it->f=get_first_feature_obj(it->current);
+	it->iterator=it->f->get_feature_iterator(vector_index);
+	it->vector_index=vector_index;
+	return it;
+}
+
+bool CCombinedDotFeatures::get_next_feature(int32_t& index, float64_t& value, void* iterator)
+{
+	ASSERT(iterator);
+	combined_feature_iterator* it = (combined_feature_iterator*) iterator;
+
+	while (it->f)
+	{
+		if (it->f->get_next_feature(index, value, it->iterator))
+		{
+			value*=get_combined_feature_weight();
+			return true;
+		}
+
+		it->f->free_feature_iterator(it->iterator);
+		it->f=get_next_feature_obj(it->current);
+		if (it->f)
+			it->iterator=it->f->get_feature_iterator(it->vector_index);
+		else
+			it->iterator=NULL;
+	}
+	return false;
+}
+
+void CCombinedDotFeatures::free_feature_iterator(void* iterator)
+{
+	if (iterator)
+	{
+		combined_feature_iterator* it = (combined_feature_iterator*) iterator;
+		if (it->iterator && it->f)
+			it->f->free_feature_iterator(it->iterator);
+		SG_FREE(it);
+	}
+}
+
+CDotFeatures* CCombinedDotFeatures::get_first_feature_obj()
+{
+	return (CDotFeatures*) feature_list->get_first_element();
+}
+
+CDotFeatures* CCombinedDotFeatures::get_first_feature_obj(CListElement*& current)
+{
+	return (CDotFeatures*) feature_list->get_first_element(current);
+}
+
+CDotFeatures* CCombinedDotFeatures::get_next_feature_obj()
+{
+	return (CDotFeatures*) feature_list->get_next_element();
+}
+
+CDotFeatures* CCombinedDotFeatures::get_next_feature_obj(CListElement*& current)
+{
+	return (CDotFeatures*) feature_list->get_next_element(current);
+}
+
+CDotFeatures* CCombinedDotFeatures::get_last_feature_obj()
+{
+	return (CDotFeatures*) feature_list->get_last_element();
+}
+
+bool CCombinedDotFeatures::insert_feature_obj(CDotFeatures* obj)
+{
+	ASSERT(obj);
+	bool result=feature_list->insert_element(obj);
+	update_dim_feature_space_and_num_vec();
+	return result;
+}
+
+bool CCombinedDotFeatures::append_feature_obj(CDotFeatures* obj)
+{
+	ASSERT(obj);
+	bool result=feature_list->append_element(obj);
+	update_dim_feature_space_and_num_vec();
+	return result;
+}
+
+bool CCombinedDotFeatures::delete_feature_obj()
+{
+	CDotFeatures* f=(CDotFeatures*) feature_list->delete_element();
+	if (f)
+	{
+		SG_UNREF(f);
+		update_dim_feature_space_and_num_vec();
+		return true;
+	}
+	else
+		return false;
+}
+
+int32_t CCombinedDotFeatures::get_num_feature_obj()
+{
+	return feature_list->get_num_elements();
+}
 
 int32_t CCombinedDotFeatures::get_nnz_features_for_vector(int32_t num)
 {
@@ -296,3 +388,14 @@ void CCombinedDotFeatures::set_subfeature_weights(
 		i++;
 	}
 }
+
+void CCombinedDotFeatures::init()
+{
+	m_parameters->add(&num_dimensions, "num_dimensions",
+					  "Total number of dimensions.");
+	m_parameters->add(&num_vectors, "num_vectors",
+					  "Total number of vectors.");
+	m_parameters->add((CSGObject**) &feature_list,
+					  "feature_list", "Feature list.");
+}
+