Major update: Column aliases. Columns are now identified in the context

of a view by an alias that can be modified.

src/hashtable.c

@@ -0,0 +1,197 @@
+/****************************************************************************
+ * Hash table source file	                                                *
+ ****************************************************************************/
+
+/**
+ * @file hashtable.c
+ * @author Celine Mercier
+ * @date July 26th 2016
+ * @brief Source file for hash table functions.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include "string.h"
+
+#include "murmurhash2.h"
+#include "hashtable.h"
+
+
+// Create a new hashtable
+hashtable_p ht_create(size_t size)
+{
+	hashtable_p hashtable = NULL;
+	size_t		i;
+
+	// Allocate the table
+	hashtable = malloc(sizeof(hashtable_t));
+	if (hashtable == NULL)
+		return NULL;
+
+	// Allocate the head nodes
+	hashtable->table = malloc(size * sizeof(entry_p));
+	if (hashtable->table == NULL)
+		return NULL;
+
+	// Initialize the head nodes
+	for (i=0; i<size; i++)
+		hashtable->table[i] = NULL;
+
+	hashtable->size = size;
+
+	return hashtable;
+}
+
+
+// Create an entry
+entry_p ht_new_entry(const char* key, void* value)
+{
+	entry_p new_entry;
+
+	new_entry = malloc(sizeof(entry_t));
+	if (new_entry == NULL)
+		return NULL;
+
+	new_entry->key = strdup(key);
+	if (new_entry->key == NULL)
+		return NULL;
+
+	new_entry->value = value;
+
+	new_entry->next = NULL;
+
+	return new_entry;
+}
+
+
+// Delete an entry
+int ht_delete_entry(hashtable_p hashtable, const char* key)
+{
+	entry_p last  = NULL;
+	entry_p entry = NULL;
+	size_t  bin   = 0;
+
+	bin = murmurhash2(key, strlen(key), SEED);
+	bin = bin % hashtable->size;
+
+	// Step through the bin looking for the value
+	entry = hashtable->table[bin];
+
+	while ((entry != NULL) && (strcmp(key, entry->key ) != 0))
+	{
+		last = entry;
+		entry = entry->next;
+	}
+
+	if (entry == NULL)	// key not found
+		return -1;
+
+	// Link the entries before and after the entry
+	if (last != NULL)	// If not head node
+		last->next = entry->next;
+	else	// If head node
+		hashtable->table[bin] = entry->next;
+
+	// Free the entry
+	free(entry->key);
+	free(entry->value);
+	free(entry);
+
+	return 0;
+}
+
+
+// Set a new entry in the hash table. If the key is already in the table, the value is replaced by the new one
+int ht_set(hashtable_p hashtable, const char* key, void* value)
+{
+	size_t  bin       = 0;
+	entry_p new_entry = NULL;
+	entry_p next      = NULL;
+	entry_p last      = NULL;
+
+	if ((key == NULL) || (value == NULL))
+		return -1;
+
+	bin = murmurhash2(key, strlen(key), SEED);
+	bin = bin % hashtable->size;
+
+	next = hashtable->table[bin];
+
+	while ((next != NULL) && (strcmp(key, next->key) != 0))
+	{
+		last = next;
+		next = next->next;
+	}
+
+	// If the key is already in the table, the value is replaced
+	if ((next != NULL) && (strcmp(key, next->key) == 0))
+		new_entry->value = value;
+
+	// Else, create the new entry and link it at the end of the list
+	else
+	{
+		// Create the new entry
+		new_entry = ht_new_entry(key, value);
+		if (new_entry == NULL)
+			return -1;
+
+		// If it is the first entry of that bin, we're at the head node of the list, and we replace it with the new entry
+		if (last == NULL)
+			hashtable->table[bin] = new_entry;
+
+		// Else link the new entry at the end of the list
+		else
+			last->next = new_entry;
+	}
+	return 0;
+}
+
+
+// Retrieve a value from a hash table
+void* ht_get(hashtable_p hashtable, const char* key)
+{
+	size_t  bin = 0;
+	entry_p entry;
+
+	bin = murmurhash2(key, strlen(key), SEED);
+	bin = bin % hashtable->size;
+
+	// Step through the bin looking for the value
+	entry = hashtable->table[bin];
+
+	while ((entry != NULL) && (strcmp(key, entry->key ) != 0))
+		entry = entry->next;
+
+	if (entry == NULL)
+		return NULL;
+
+	else
+		return entry->value;
+}
+
+
+// Free the hash table
+void ht_free(hashtable_p hashtable)
+{
+	size_t  i;
+	entry_p entry;
+	entry_p next;
+
+	for (i=0; i < hashtable->size; i++)
+	{
+		next = hashtable->table[i];
+		while (next != NULL)
+		{
+			entry = next;
+			free(entry->key);
+			next = entry->next;
+			free(entry);
+		}
+	}
+	free(hashtable->table);
+	free(hashtable);
+}
+
+

src/hashtable.h

@@ -0,0 +1,123 @@
+/****************************************************************************
+ * Hash table header file	                                                *
+ ****************************************************************************/
+
+/**
+ * @file hashtable.h
+ * @author Celine Mercier
+ * @date July 26th 2016
+ * @brief Header file for hash table functions.
+ */
+
+
+#ifndef HASHTABLE_H_
+#define HASHTABLE_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+
+
+#define SEED (0x9747b28c)   		/**< The seed used by the hash function.
+                                	 */
+
+
+/**
+ * @brief Structure for an entry.
+ */
+typedef struct entry_s {
+	char*           key;		/**< Key used to refer to the entry.
+	 	 	 	 	 	 	 	 */
+	void*           value;		/**< Pointer on the value to be stored.
+	 	 	 	 	 	 	 	 */
+	struct entry_s* next;		/**< Pointer on the next entry in the bin.
+	 	 	 	 	 	 	 	 */
+} entry_t, *entry_p;
+
+
+/**
+ * @brief Structure for a hash table.
+ */
+typedef struct hashtable {
+	size_t size;			/**< Number of bins in the table.
+	 	 	 	 	 	 	 */
+	entry_p* table;			/**< Table of bins.
+	 	 	 	 	 	 	 */
+} hashtable_t, *hashtable_p;
+
+
+/**
+ * @brief Creates a new hashtable.
+ *
+ * @param size The number of bins in the hash table.
+ *
+ * @returns A pointer to the newly created hash table.
+ * @retval NULL if an error occurred.
+ *
+ * @since July 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+hashtable_p ht_create(size_t size);
+
+
+/**
+ * @brief Inserts a new entry in the hash table.
+ * 		  If the key is already in the table, the value is replaced by the new one.
+ *
+ * @param hashtable A pointer on the hash table structure.
+ * @param key The key.
+ * @param value A pointer on the value associated with the key.
+ *
+ * @retval 0 if the entry was correctly set.
+ * @retval -1 if an error occurred.
+ *
+ * @since July 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int ht_set(hashtable_p hashtable, const char* key, void* value);
+
+
+/**
+ * @brief Retrieves a value from a hash table.
+ *
+ * @param hashtable A pointer on the hash table structure.
+ * @param key The key.
+ *
+ * @returns A pointer on the value associated with the key.
+ * @retval NULL if the key was not found.
+ *
+ * @since July 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+void* ht_get(hashtable_p hashtable, const char* key);
+
+
+/**
+ * @brief Deletes an entry.
+ *
+ * @param hashtable A pointer on the hash table structure.
+ * @param key The key.
+ *
+ * @retval 0 if the entry was correctly deleted.
+ * @retval -1 if an error occurred.
+ *
+ * @since July 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int ht_delete_entry(hashtable_p hashtable, const char* key);
+
+
+/**
+ * @brief Frees a hash table.
+ *
+ * @param hashtable A pointer on the hash table structure.
+ *
+ * @since July 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+void ht_free(hashtable_p hashtable);
+
+
+#endif /* HASHTABLE_H_ */
+

src/obiview.c

@@ -30,6 +30,7 @@
 #include "obierrno.h"
 #include "obidebug.h"
 #include "obilittlebigman.h"
+#include "hashtable.h"
 #include "utils.h"
 
 
@@ -42,6 +43,16 @@
  *
  **************************************************************************/
 
+/**
+ * Internal function calculating the size of the file where the informations about an obiview are stored.
+ *
+ * @returns The size of the file in bytes.
+ *
+ * @since June 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+size_t get_platform_view_file_size();
+
 
 /**
  * Internal function building the file name where the informations about an obiview are stored.
@@ -82,6 +93,14 @@ int create_obiview_file(OBIDMS_p dms, const char* view_name);
  * The column references stored in the mapped view infos structures are updated
  * to match the columns opened in the opened view structure.
  *
+ * @warning The column pointer array should be up to date before using this function.
+ * @warning Aliases are not updated by this function and have to be edited separately.
+ * 			This function simply reads the column pointer array associated with the view
+ * 			and fills the column names and versions in the column reference array accordingly,
+ * 			without touching the alias.
+ *          That means that for example if there is a shift in the column pointer array, this
+ *          function should not be used.
+ *
  * @param view A pointer on the view.
  *
  * @since June 2016
@@ -90,6 +109,69 @@ int create_obiview_file(OBIDMS_p dms, const char* view_name);
 void update_column_refs(Obiview_p view);
 
 
+/**
+ * @brief Internal function creating the column dictionary associated with a view.
+ *
+ * The column dictionary is built from the column references array, and associates each column alias
+ * with the pointer on the column.
+ *
+ * @warning The column reference array and the column pointer array should be up to date before using this function.
+ *
+ * @param view A pointer on the view.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since July 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int create_column_dict(Obiview_p view);
+
+
+/**
+ * @brief Internal function updating the column dictionary associated with a view.
+ *
+ * The column dictionary is built from the column references array, and associates each column alias
+ * with the pointer on the column.
+ *
+ * @warning The column reference array and the column pointer array should be up to date before using this function.
+ *
+ * @param view A pointer on the view.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since July 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int update_column_dict(Obiview_p view);
+
+
+/**
+ * @brief Internal function updating the column reference array and the column dictionary associated with a view.
+ *
+ * The column reference array is updated from the column pointer array, then the column dictionary that
+ * and associates each column alias with the pointer on the column is updated from the column reference array.
+ *
+ * @warning The column pointer array should be up to date before using this function.
+ * @warning Aliases are not updated by this function and have to be edited separately.
+ * 			This function simply reads the column pointer array associated with the view
+ * 			and fills the column names and versions in the column reference array accordingly,
+ * 			without touching the alias.
+ *          That means that for example if there is a shift in the column pointer array, this
+ *          function should not be used.
+ *
+ * @param view A pointer on the view.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since July 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int update_column_refs_and_dict(Obiview_p view);
+
+
 /**
  * @brief Internal function to update the line count in the context of a view.
  *
@@ -368,19 +450,72 @@ int create_obiview_file(OBIDMS_p dms, const char* view_name)
 }
 
 
-
 void update_column_refs(Obiview_p view)
 {
 	int i;
 
 	for (i=0; i < (view->infos)->column_count; i++)
 	{
-		strcpy((((view->infos)->column_references)+i)->column_name, (((view->columns)[i])->header)->name);
-		(((view->infos)->column_references)+i)->version = (((view->columns)[i])->header)->version;
+		strcpy(((((view->infos)->column_references)[i]).column_refs).column_name, (((view->columns)[i])->header)->name);
+		((((view->infos)->column_references)[i]).column_refs).version = (((view->columns)[i])->header)->version;
 	}
 }
 
 
+int create_column_dict(Obiview_p view)
+{
+	int i;
+
+	view->column_dict = ht_create(MAX_NB_OPENED_COLUMNS);
+	if (view->column_dict == NULL)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError creating a column dictionary");
+		return -1;
+	}
+
+	// Rebuild the dictionary from the column references and the column pointer array associated with the view
+	for (i=0; i < (view->infos)->column_count; i++)
+	{
+		// Check that each alias is unique
+		if (ht_get(view->column_dict, (((view->infos)->column_references)[i]).alias) != NULL)
+		{
+			obi_set_errno(OBIVIEW_ERROR);
+			obidebug(1, "\nError: the name/alias identifying a column in a view is not unique");
+			return -1;
+		}
+
+		if (ht_set(view->column_dict, (((view->infos)->column_references)[i]).alias, (view->columns)[i]) < 0)
+		{
+			obi_set_errno(OBIVIEW_ERROR);
+			obidebug(1, "\nError adding a column in a column dictionary");
+			return -1;
+		}
+	}
+
+	return 0;
+}
+
+
+int update_column_dict(Obiview_p view)
+{
+	// Re-initialize the dictionary to rebuild it from scratch
+	ht_free(view->column_dict);
+
+	if (create_column_dict(view) < 0)
+		return -1;
+
+	return 0;
+}
+
+
+int update_column_refs_and_dict(Obiview_p view)
+{
+	update_column_refs(view);
+	return update_column_dict(view);
+}
+
+
 int update_lines(Obiview_p view, index_t line_count)
 {
 	int i;
@@ -408,6 +543,7 @@ OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name)
 	OBIDMS_column_p current_line_selection = NULL;
 	OBIDMS_column_p column = NULL;
 	OBIDMS_column_p column_buffer;
+	bool found;
 
 	// Check that the view is not read-only
 	if (view->read_only)
@@ -422,9 +558,10 @@ OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name)
 	else
 		current_line_selection = view->line_selection;
 
+	found = false;
 	for (i=0; i<((view->infos)->column_count); i++)
 	{
-		if ((current_line_selection != NULL) || (!(strcmp((((view->columns)[i])->header)->name, column_name))))
+		if ((current_line_selection != NULL) || (!strcmp((((view->infos)->column_references)[i]).alias, column_name)))
 		{ // Clone with the right line selection and replace (for all columns if there is a line selection)
 
 			// Save pointer to close column after cloning
@@ -442,7 +579,7 @@ OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name)
 			// Close old cloned column
 			obi_close_column(column_buffer);
 
-			if (!(strcmp((((view->columns)[i])->header)->name, column_name)))
+			if (!strcmp((((view->infos)->column_references)[i]).alias, column_name))
 			{	// Found the column to return
 				column = (view->columns)[i];
 			}
@@ -464,8 +601,8 @@ OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name)
 		view->new_line_selection = NULL;
 	}
 
-	// Update column references in view infos
-	update_column_refs(view);
+	// Update column refs and dict
+	update_column_refs_and_dict(view);
 
 	return column;
 }
@@ -473,7 +610,8 @@ OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name)
 
 int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* column_pp, index_t* line_nb_p)
 {
-	char* column_name;
+	int   i;
+	char* column_name = NULL;
 
 	// Check that the view is not read-only
 	if (view->read_only)
@@ -491,22 +629,25 @@ int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* column_pp, i
 		if (view->line_selection != NULL)
 			(*line_nb_p) = *(((index_t*) ((view->line_selection)->data)) + (*line_nb_p));
 
-		column_name = (char*) malloc(strlen(((*column_pp)->header)->name) * sizeof(char));
+		// Get the name/alias of the column from the pointer
+		for (i=0; i<((view->infos)->column_count); i++)
+		{
+			if (obi_view_get_column(view, (((view->infos)->column_references)[i]).alias) == *column_pp)
+				column_name = (((view->infos)->column_references)[i]).alias;
+		}
 		if (column_name == NULL)
 		{
-			obi_set_errno(OBI_MALLOC_ERROR);
-			obidebug(1, "\nError trying to allocate memory for a column name");
+			obi_set_errno(OBIVIEW_ERROR);
+			obidebug(1, "\nError trying to clone a column in a view: column alias not found from pointer");
 			return -1;
 		}
-		strcpy(column_name, ((*column_pp)->header)->name);
+
 		(*column_pp) = clone_column_in_view(view, column_name);
 		if ((*column_pp) == NULL)
 		{
 			obidebug(1, "\nError trying to clone a column to modify it");
 			return -1;
 		}
-
-		free(column_name);
 	}
 
 	if (((*line_nb_p)+1) > (view->infos)->line_count)
@@ -797,6 +938,7 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 	}
 
 	view->dms = dms;
+	view->read_only = 0;
 
 	// Create view file
 	if (create_obiview_file(dms, view_name) < 0)
@@ -888,24 +1030,12 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 			(view->infos)->line_count = (view_to_clone->infos)->line_count;
 		}
 
-		for (i=0; i<((view_to_clone->infos)->column_count); i++)
-		{
-			(view->columns)[i] = obi_open_column(dms, (((view_to_clone->columns)[i])->header)->name, (((view_to_clone->columns)[i])->header)->version);
-			if ((view->columns)[i] == NULL)
-			{
-				if (view->line_selection != NULL)
-					obi_close_column(view->line_selection);
-				obi_view_unmap_file(view->dms, view->infos);
-				free(view);
-				return NULL;
-			}
-		}
-
-		(view->infos)->column_count = (view_to_clone->infos)->column_count;
+		// Fill informations
 		strcpy((view->infos)->view_type, (view_to_clone->infos)->view_type);
 		strcpy((view->infos)->created_from, (view_to_clone->infos)->name);
 		view->new_line_selection = NULL;
 	}
+
 	// Else, fill empty view structure
 	else
 	{
@@ -919,10 +1049,10 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 		//view->columns          = NULL;  // TODO
 	}
 
+	// Fill last informations
 	strcpy((view->infos)->name, view_name);
 	strcpy((view->infos)->comments, comments);
 	(view->infos)->creation_date = time(NULL);
-	view->read_only = 0;
 	view->nb_predicates = 0;
 	view->predicate_functions = NULL;
 
@@ -938,8 +1068,44 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 		((view->infos)->line_selection).version = ((view->line_selection)->header)->version;
 	}
 
-	// Store references for columns
-	update_column_refs(view);
+	// Create the column dictionary (hash table) associating column names (or aliases) to column pointers
+	if (create_column_dict(view) < 0)
+	{
+		obi_close_view(view);
+		return NULL;
+	}
+
+	// Once the view has been created with all its elements and informations, add the columns if the view is cloned from another view
+	// Add the columns from the view to clone in the new view
+	if (view_to_clone != NULL)
+	{
+		(view->infos)->column_count = 0;
+		for (i=0; i<((view_to_clone->infos)->column_count); i++)
+		{
+			if (obi_view_add_column(view,
+									(((view_to_clone->columns)[i])->header)->name,
+									(((view_to_clone->columns)[i])->header)->version,
+									(((view_to_clone->infos)->column_references)[i]).alias,
+									0,
+									(view->infos)->line_count,
+									0,
+									NULL,
+									NULL,
+									NULL,
+									-1,
+									NULL,
+									false)
+					< 0)
+			{
+				obidebug(1, "\nError adding a column in a new view from a view to clone");
+				if (view->line_selection != NULL)
+					obi_close_column(view->line_selection);
+				obi_view_unmap_file(view->dms, view->infos);
+				free(view);
+				return NULL;
+			}
+		}
+	}
 
 	return view;
 }
@@ -985,26 +1151,26 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
 	if (view_to_clone == NULL)
 	{
 		// Adding sequence column
-		if (obi_view_add_column(view, NUC_SEQUENCE_COLUMN, -1, OBI_SEQ, 0, 1, NUC_SEQUENCE_COLUMN, "", NULL, -1, "Nucleotide sequences", true) < 0)
+		if (obi_view_add_column(view, NUC_SEQUENCE_COLUMN, -1, NUC_SEQUENCE_COLUMN, OBI_SEQ, 0, 1, NUC_SEQUENCE_COLUMN, "", NULL, -1, "Nucleotide sequences", true) < 0)
 		{
 			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
 			return NULL;
 		}
 		// Adding id column
-		if (obi_view_add_column(view, ID_COLUMN, -1, OBI_STR, 0, 1, ID_COLUMN, "", NULL, -1, "Ids", true) < 0)
+		if (obi_view_add_column(view, ID_COLUMN, -1, ID_COLUMN, OBI_STR, 0, 1, ID_COLUMN, "", NULL, -1, "Ids", true) < 0)
 		{
 			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
 			return NULL;
 		}
 		// Adding definition column
-		if (obi_view_add_column(view, DEFINITION_COLUMN, -1, OBI_STR, 0, 1, DEFINITION_COLUMN, "", NULL, -1, "Definitions", true) < 0)
+		if (obi_view_add_column(view, DEFINITION_COLUMN, -1, DEFINITION_COLUMN, OBI_STR, 0, 1, DEFINITION_COLUMN, "", NULL, -1, "Definitions", true) < 0)
 		{
 			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
 			return NULL;
 		}
 		// Adding quality column
 		associated_nuc_column = obi_view_get_column(view, NUC_SEQUENCE_COLUMN);
-		if (obi_view_add_column(view, QUALITY_COLUMN, -1, OBI_QUAL, 0, 1, QUALITY_COLUMN, "", (associated_nuc_column->header)->name, (associated_nuc_column->header)->version, "Sequence qualities", true) < 0)		// TODO discuss automatic association
+		if (obi_view_add_column(view, QUALITY_COLUMN, -1, QUALITY_COLUMN, OBI_QUAL, 0, 1, QUALITY_COLUMN, "", (associated_nuc_column->header)->name, (associated_nuc_column->header)->version, "Sequence qualities", true) < 0)		// TODO discuss automatic association
 		{
 			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
 			return NULL;
@@ -1131,8 +1297,11 @@ int obi_view_unmap_file(OBIDMS_p dms, Obiview_infos_p view_infos)
 
 Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name)
 {
-	Obiview_p			view;
-	int					i;
+	Obiview_p					view;
+	const char* 				column_name;
+	obiversion_t				column_version;
+	OBIDMS_column_p				column_pointer;
+	int							i;
 
 	// Alllocate the memory for the view structure
 	view = (Obiview_p) malloc(sizeof(Obiview_t));
@@ -1164,13 +1333,18 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name)
 	// Open the columns to read
 	for (i=0; i < ((view->infos)->column_count); i++)
 	{
-		(view->columns)[i] = obi_open_column(dms, (((view->infos)->column_references)+i)->column_name, (((view->infos)->column_references)+i)->version);
-		if ((view->columns)[i] == NULL)
+		column_name = ((((view->infos)->column_references)[i]).column_refs).column_name;
+		column_version = ((((view->infos)->column_references)[i]).column_refs).version;
+
+		column_pointer = obi_open_column(dms, column_name, column_version);
+		if (column_pointer == NULL)
 		{
-			obidebug(1, "\nError opening a column for a view: column %d: %s, version %d", i, (((view->infos)->column_references)+i)->column_name, (((view->infos)->column_references)+i)->version);
+			obidebug(1, "\nError opening a column for a view: column %d: %s, version %d", i, column_name, column_version);
 			obi_close_view(view);
 			return NULL;
 		}
+		(view->columns)[i] = column_pointer;
+
 	}
 
 	view->dms = dms;
@@ -1179,6 +1353,14 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name)
 	view->nb_predicates = 0;
 	view->predicate_functions = NULL;
 
+	// Create the column dictionary associating each column alias with its pointer
+	if (create_column_dict(view) < 0)
+	{
+		obidebug(1, "\nError creating the column dictionary when opening a view");
+		obi_close_view(view);
+		return NULL;
+	}
+
 	return view;
 }
 
@@ -1186,6 +1368,7 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name)
 int obi_view_add_column(Obiview_p view,
 						const char* column_name,
 						obiversion_t version_number,
+						const char* alias,
 						OBIType_t data_type,
 						index_t nb_lines,
 						index_t nb_elements_per_line,
@@ -1196,10 +1379,10 @@ int obi_view_add_column(Obiview_p view,
 						const char* comments,
 						bool create)	// all infos for creation or open
 {
-	int             i;
-	OBIDMS_column_p column;
-	OBIDMS_column_p column_buffer;
-	OBIDMS_column_p current_line_selection;
+	int             			i;
+	OBIDMS_column_p 			column;
+	OBIDMS_column_p 			column_buffer;
+	OBIDMS_column_p 			current_line_selection;
 
 	// Check that the view is not read-only
 	if (view->read_only)
@@ -1275,14 +1458,29 @@ int obi_view_add_column(Obiview_p view,
 		return -1;
 	}
 
-	// Store column in the view
+	// Store column pointer in the view structure
 	(view->columns)[(view->infos)->column_count] = column;
+
+	// If an alias is not defined, it's the original name of the column. 	// TODO discuss
+	if (alias == NULL)
+		alias = column_name;
+
+	// Save column alias
+	strcpy((((view->infos)->column_references)[(view->infos)->column_count]).alias, alias);
+
 	(view->infos)->column_count++;
 	if ((view->infos)->column_count == 1)	// first column in the view
-		(view->infos)->line_count = (column->header)->lines_used;
+		(view->infos)->line_count = nb_lines;
 
-	// Update reference in view infos
-	update_column_refs(view);
+	// Update column references and dictionary
+	update_column_refs_and_dict(view);
+
+//	// Print dict
+//	for (i=0; i<((view->infos)->column_count); i++)
+//	{
+//		fprintf(stderr, "\n\nalias: %s", (((view->infos)->column_references)[i]).alias);
+//		fprintf(stderr, "\npointer: %x\n", obi_view_get_column(view, (((view->infos)->column_references)[i]).alias));
+//	}
 
 	return 0;
 }
@@ -1303,59 +1501,107 @@ int obi_view_delete_column(Obiview_p view, const char* column_name)
 		return -1;
 	}
 
-	found = 0;
-
+	found = false;
 	for (i=0; i<((view->infos)->column_count); i++)
 	{
-		if (!strcmp((((view->columns)[i])->header)->name, column_name))
+		if ((!found) && (!strcmp((((view->infos)->column_references)[i]).alias, column_name)))
 		{
 			obi_close_column((view->columns)[i]);
-			found = 1;
+			found = true;
 		}
 		if (found)
 		{
 			if (i != (((view->infos)->column_count) - 1))	// not the last one
+			{	// Shift the pointer and the references
 				(view->columns)[i] = (view->columns)[i+1];
+				strcpy((((view->infos)->column_references)[i]).alias, (((view->infos)->column_references)[i+1]).alias);
+				strcpy(((((view->infos)->column_references)[i]).column_refs).column_name, ((((view->infos)->column_references)[i+1]).column_refs).column_name);
+				((((view->infos)->column_references)[i]).column_refs).version = ((((view->infos)->column_references)[i+1]).column_refs).version;
+			}
 			else  	// Last column
 				(view->columns)[i] = NULL;
 		}
 	}
 
 	if (!found)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to delete a column: column not found");
 		return -1;
+	}
 
 	((view->infos)->column_count)--;
 
-	// Update reference in view infos
-	update_column_refs(view);
+	// Update column dictionary
+	update_column_dict(view);
 
 	return 0;
 }
 
 
 OBIDMS_column_p obi_view_get_column(Obiview_p view, const char* column_name)
+{
+	return (OBIDMS_column_p)(ht_get(view->column_dict, column_name));
+}
+
+
+OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const char* column_name)
 {
 	int i;
 
-	for (i=0; i<((view->infos)->column_count); i++)
+	for (i=0; i < (view->infos)->column_count; i++)
 	{
-		if (!(strcmp((((view->columns)[i])->header)->name, column_name)))
-			return (view->columns)[i];
+		if (strcmp((((view->infos)->column_references)[i]).alias, column_name) == 0)
+			return ((view->columns)+i);
 	}
+	obidebug(1, "\nError: column not found");
 	return NULL;
 }
 
 
-OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const char* column_name)	// TODO delete?
+int obi_view_create_column_alias(Obiview_p view, const char* current_name, const char* alias)
 {
 	int i;
+	bool found;
 
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to change a column alias in a read-only view");
+		return -1;
+	}
+
+	// Check that the new alias is unique
+	if (ht_get(view->column_dict, alias) != NULL)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError: the new name/alias identifying a column in a view is not unique");
+		return -1;
+	}
+
+	// Set the new alias in the column references
+	found = false;
 	for (i=0; i<((view->infos)->column_count); i++)
 	{
-		if (!(strcmp((((view->columns)[i])->header)->name, column_name)))
-			return ((view->columns)+i);
+		if (!strcmp((((view->infos)->column_references)[i]).alias, current_name))
+		{
+			strcpy((((view->infos)->column_references)[i]).alias, alias);
+			found = true;
+		}
 	}
-	return NULL;
+
+	if (found == false)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError: can't find the column '%s' to change its alias", current_name);
+		return -1;
+	}
+
+	// Update the column dictionary
+	update_column_dict(view);
+
+	return 0;
 }
 
 
@@ -1503,6 +1749,9 @@ int obi_close_view(Obiview_p view)
 		}
 	}
 
+	// Free the column dictionary
+	ht_free(view->column_dict);
+
 	// Unmap view file
 	if (obi_view_unmap_file(view->dms, view->infos) < 0)
 	{

src/obiview.h

@@ -25,6 +25,7 @@
 #include "obidms.h"
 #include "obidmscolumn.h"
 #include "obierrno.h"
+#include "hashtable.h"
 
 
 #define OBIVIEW_NAME_MAX_LENGTH (1000)   		/**< The maximum length of an OBIDMS view name.
@@ -54,6 +55,18 @@
                                 	 	  	  	 */
 
 
+/**
+ * @brief Structure for column aliases.
+ * 		  Column aliases are alternative names used to identify a column in the context of a view.
+ */
+typedef struct Alias_column_pair {
+	Column_reference_t	column_refs;   						/**< References (name and version) of the column.
+		 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	char 				alias[OBIDMS_COLUMN_MAX_NAME+1];	/**< Alias of the column in the context of a view.
+	 	 	 								 	 	 	 	 */
+} Alias_column_pair_t, *Alias_column_pair_p;
+
+
 /**
  * @brief Structure for a closed view stored in the view file.
  * 		  Views are identified by their name.
@@ -77,8 +90,8 @@ typedef struct Obiview_infos {
 																	 */
 	int 				column_count;    							/**< The number of columns in the view.
 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	Column_reference_t	column_references[MAX_NB_OPENED_COLUMNS];   /**< References (name and version) for all the columns in the view.
- 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	Alias_column_pair_t column_references[MAX_NB_OPENED_COLUMNS];   /**< References (name, version and alias) for all the columns in the view.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 	char 				comments[OBIVIEW_COMMENTS_MAX_LENGTH+1];	/**< Comments, additional informations on the view.
  	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 } Obiview_infos_t, *Obiview_infos_p;
@@ -88,27 +101,30 @@ typedef struct Obiview_infos {
  * @brief Structure for an opened view.
  */
 typedef struct Obiview {
-	Obiview_infos_p     infos;											/**< A pointer on the mapped view informations.
-		 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	OBIDMS_p         	dms;    										/**< A pointer on the DMS to which the view belongs.
-	 	 	    													 	 */
-	bool             	read_only;    									/**< Whether the view is read-only or can be modified.
+	Obiview_infos_p  infos;												/**< A pointer on the mapped view informations.
+		 	 	 	  	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	OBIDMS_p         dms;    											/**< A pointer on the DMS to which the view belongs.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	bool             read_only;    										/**< Whether the view is read-only or can be modified.
 																	 	 */
-	OBIDMS_column_p  	line_selection;    								/**< A pointer on the column containing the line selection
+	OBIDMS_column_p  line_selection;    								/**< A pointer on the column containing the line selection
 																	 	 *   associated with the view if there is one.
 																	 	 *   This line selection is read-only, and when a line from the view is read,
 																	 	 *   it is this line selection that is used.
 																	 	 */
-	OBIDMS_column_p  	new_line_selection;    							/**< A pointer on the column containing the new line selection being built
+	OBIDMS_column_p  new_line_selection;    							/**< A pointer on the column containing the new line selection being built
 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   to associate with the view, if there is one.
 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   When a line is selected with obi_select_line() or obi_select_lines(),
 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   it is recorded in this line selection.
 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	OBIDMS_column_p  	columns[MAX_NB_OPENED_COLUMNS];    				/**< Array of pointers on all the columns of the view.
+	OBIDMS_column_p  columns[MAX_NB_OPENED_COLUMNS];    				/**< Array of pointers on all the columns of the view.
 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	int					nb_predicates;    								/**< Number of predicates to test when closing the view.
+	hashtable_p		 column_dict;										/**< Hash table storing the pairs of column names or aliases with the associated
+																		 *   column pointers.
+																		 */
+	int				 nb_predicates;    									/**< Number of predicates to test when closing the view.
  	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	char* 				(**predicate_functions)(struct Obiview* view);  /**< Array of pointers on all predicate functions to test when closing the view.
+	char* 			 (**predicate_functions)(struct Obiview* view);     /**< Array of pointers on all predicate functions to test when closing the view.
 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 } Obiview_t, *Obiview_p;
 
@@ -275,6 +291,7 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name);
  * @param view A pointer on the view.
  * @param column_name The name of the column.
  * @param version_number The version of the column if it should be opened and not created (if -1, the latest version is retrieved).
+ * @param alias The unique name used to identify the column in the context of this view.
  * @param data_type The OBIType code of the data.
  * @param nb_lines The number of lines to be stored.
  * @param nb_elements_per_line The number of elements per line.
@@ -293,6 +310,7 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name);
 int obi_view_add_column(Obiview_p view,
 						const char* column_name,
 						obiversion_t version_number,
+						const char* alias,
 						OBIType_t data_type,
 						index_t nb_lines,
 						index_t nb_elements_per_line,
@@ -354,6 +372,27 @@ OBIDMS_column_p obi_view_get_column(Obiview_p view, const char* column_name);
 OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const char* column_name);
 
 
+/**
+ * @brief Changes the name that identifies a column in the context of a view.
+ *
+ * In the context of a view, each column is identified by a name that is unique in this view.
+ *
+ * @warning The view must be writable.
+ *
+ * @param view A pointer on the view.
+ * @param current_name The current name that identifies the column in this view.
+ * @param alias The new name that should be used to identify the column in this view.
+ *
+ * @returns A value indicating the success of the operation.
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since July 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_view_create_column_alias(Obiview_p view, const char* current_name, const char* alias);
+
+
 /**
  * @brief Selects a line in the context of a view.
  *
@@ -450,22 +489,7 @@ int obi_close_view(Obiview_p view);
 int obi_save_and_close_view(Obiview_p view);
 
 
-/**
- * @brief Closes the structure containing all the informations written in the view file.
- *
- * @param views A pointer on the view informations structure.
- *
- * @returns A value indicating the success of the operation.
- * @retval 0 if the operation was successfully completed.
- * @retval -1 if an error occurred.
- *
- * @since February 2016
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-int obi_close_view_infos(Obiviews_infos_all_p views);
-
-
-// TODO in following functions would it be better to use column names instead of column pointers?
+//  in following functions would it be better to use column names instead of column pointers?
 //		check if it would be a gain or loss of time
 
 /**