First version of alignment functions (imported from suma* programs)

src/obi_align.c

@@ -0,0 +1,109 @@
+/****************************************************************************
+ * Sequence alignment functions				                                *
+ ****************************************************************************/
+
+/**
+ * @file obi_align.c
+ * @author Celine Mercier
+ * @date May 4th 2016
+ * @brief Functions handling sequence alignments.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdbool.h>
+
+#include "obidebug.h"
+#include "obierrno.h"
+#include "obitypes.h"
+#include "obiview.h"
+#include "sse_banded_LCS_alignment.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+// TODO
+// use openMP pragmas : garder scores en memoire et ecrire a la fin?
+// tout ecrire en stdint?
+// check NUC_SEQS and score type (int or float if normalize)
+// what's with multiple sequence/line columns?
+// make function that put blobs in int16
+
+
+int obi_align_one_column(Obiview_p seq_view, OBIDMS_column_p seq_column, Obiview_p score_view, OBIDMS_column_p score_column, double threshold, bool normalize, int reference, bool similarity_mode)
+{
+	index_t i, j, k;
+	index_t seq_count;
+	char* seq1;
+	char* seq2;
+	double score;
+
+	k = 0;
+
+	if ((seq_column->header)->returned_data_type != OBI_SEQ)
+	{
+		obi_set_errno(OBI_ALIGN_ERROR);
+		obidebug(1, "\nTrying to align a column of a different type than OBI_SEQ");
+		return -1;
+	}
+
+	if ((normalize && ((score_column->header)->returned_data_type != OBI_FLOAT)) ||
+			(!normalize && ((score_column->header)->returned_data_type != OBI_INT)))
+	{
+		obi_set_errno(OBI_ALIGN_ERROR);
+		obidebug(1, "\nTrying to store alignment scores in a column of an inappropriate type");
+		return -1;
+	}
+
+	seq_count = (seq_column->header)->lines_used;
+
+	for (i=0; i < (seq_count - 1); i++)
+	{
+		for (j=i+1; j < seq_count; j++)
+		{
+			//fprintf(stderr, "\ni=%lld, j=%lld, k=%lld", i, j, k);
+
+			seq1 = obi_column_get_obiseq_with_elt_idx_in_view(seq_view, seq_column, i, 0);
+			seq2 = obi_column_get_obiseq_with_elt_idx_in_view(seq_view, seq_column, j, 0);
+
+			if ((seq1 == NULL) || (seq2 == NULL))
+			{
+				obidebug(1, "\nError retrieving sequences to align");
+				return -1;
+			}
+
+			// TODO filter
+			score = generic_sse_banded_lcs_align(seq1, seq2, threshold, normalize, reference, similarity_mode);
+
+			if (normalize)
+			{
+				if (obi_column_set_obifloat_with_elt_idx_in_view(score_view, score_column, k, 0, (obifloat_t) score) < 0)
+				{
+					obidebug(1, "\nError writing alignment score in a column");
+					return -1;
+				}
+			}
+			else
+			{
+				if (obi_column_set_obiint_with_elt_idx_in_view(score_view, score_column, k, 0, (obiint_t) score) < 0)
+				{
+					obidebug(1, "\nError writing alignment score in a column");
+					return -1;
+				}
+			}
+
+			k++;
+		}
+	}
+
+	return 0;
+}
+
+
+int obi_align_two_columns(OBIDMS_column_p seq_column_1, OBIDMS_column_p seq_column_2, OBIDMS_column_p score_column, double threshold, bool normalize, int reference, bool similarity_mode)
+{
+	// TODO
+	return 0;
+}