inital test system in place

2 files changed, 131 insertions, 6 deletions

diff --git a/src/c/Makefile b/src/c/Makefile
index 1d3581d..0039230 100644
--- a/src/c/Makefile
+++ b/src/c/Makefile
@@ -1,10 +1,9 @@
 VERSION=\"v1.0.4\"
 UNAME := $(shell uname)
+PWD = $(shell pwd)
 CC = gcc
-QUIKR_TRAIN_CFLAGS = -D$(UNAME) -DVERSION=$(VERSION)
-MULTIFASTA_CFLAGS = -pthread -L../ -I../ -std=gnu99 -fopenmp -D$(UNAME) -DVERSION=$(VERSION)
-QUIKR_CFLAGS = -D$(UNAME) -DVERSION=$(VERSION)
-CFLAGS = -Wall -Wextra -lm -lz 
+MULTIFASTA_CFLAGS = -pthread -L../ -I../ -std=gnu99 -fopenmp
+CFLAGS = -Wall -Wextra -lm -lz  -D$(UNAME) -DVERSION=$(VERSION) 
 
 
 ifndef DEBUG
@@ -13,7 +12,7 @@ else
 CFLAGS += -ggdb3 -O0 
 endif
 
-all: nnls.o kmer_utils.o quikr_train quikr multifasta_to_otu
+all: nnls.o kmer_utils.o quikr_functions.o quikr_train quikr multifasta_to_otu test
 
 nnls.o: nnls.c
 	$(CC) -c nnls.c -o nnls.o  $(CFLAGS)
@@ -26,6 +25,8 @@ multifasta_to_otu: kmer_utils.o nnls.o quikr_functions.o multifasta_to_otu.c
 quikr_train: kmer_utils.o quikr_functions.o quikr_train.c
 	$(CC) quikr_train.c quikr_functions.o kmer_utils.o -o quikr_train $(CFLAGS) $(QUIKR_TRAIN_CFLAGS)
 quikr: kmer_utils.o nnls.o quikr_functions.o quikr.c
-	$(CC) quikr.c quikr_functions.o nnls.o kmer_utils.o -o quikr $(CFLAGS) $(QUIKR_CFLAGS) -I../
+	$(CC) quikr.c quikr_functions.o nnls.o kmer_utils.o -o quikr $(CFLAGS) $(QUIKR_CFLAGS)
 clean:
 	rm -v quikr_train quikr multifasta_to_otu *.o
+test: kmer_utils.o nnls.o quikr_functions.o test.c
+	$(CC) test.c quikr_functions.o nnls.o kmer_utils.o -o test $(CFLAGS) -I$(PWD)
diff --git a/src/c/test.c b/src/c/test.c
new file mode 100644
index 0000000..fa905af
--- /dev/null
+++ b/src/c/test.c
@@ -0,0 +1,124 @@
+#include <ctype.h>
+#include <errno.h>
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include <zlib.h>
+
+#include "quikr.h"
+#include "quikr_functions.h"
+
+
+static int failed = 0;
+
+void status(int test, int pass, char *testname) {
+	fprintf(stdout, "test %d in %s ", test, testname);
+
+	if(pass)
+		fprintf(stdout, "passed.\n");
+	else {
+		fprintf(stdout, "failed. \n");
+		failed = 1;
+	}
+}
+
+#define test_eq(data, value) status(test_number, (data == value), test_name); test_number++; 
+#define test_n_eq(data, value) status(test_number, (data != value), test_name); test_number++; 
+#define test_gt(data, value) status(test_number, (data < value), test_name); test_number++; 
+#define test_lt(data, value) status(test_number, (data > value), test_name); test_number++; 
+
+#define header(test_name) printf("testing %s:\n", test_name);
+#define footer() printf("\n\n");;
+
+void test_count_sequences() {
+
+	int test_number = 1;
+	char *test_name = "test_count_sequences";
+
+	// test 1
+	// Make sure we can count this properly
+	int t_count_sequences_res = count_sequences("tests/data/test.fa");
+	test_eq(t_count_sequences_res, 17414);
+
+	// test 2
+	// Should be zero, since the file is empty
+	t_count_sequences_res = count_sequences("tests/data/empty.fa");
+	test_eq(t_count_sequences_res, 0);
+
+	// test 3
+	// Doesn't exist, count should be zero
+	t_count_sequences_res = count_sequences("non-existant-file");
+	test_eq(t_count_sequences_res, 0);
+
+}
+
+
+void test_normalize_matrix() {
+
+	int test_number = 1;
+	int fail_flag = 0;
+	char *test_name = "test_normailze_matrix";
+	char *type = "%lf";
+
+	double sum = 0;
+	int i = 0;
+	int j = 0;
+
+	double matrix_1[4] = {1,1,1,1};
+	double matrix_2[8] = {2,2,4,4,8,8,16,16};
+
+
+	// test 1
+	// our matrix to sum to 1 properly even with only one row 
+	normalize_matrix(matrix_1, 1, 4);
+	for(i = 0; i < 4; i++) 
+		sum += matrix_1[i];
+
+	test_eq(sum, 1);
+
+	// test 2
+	// each element in the array should be .25
+	for(i = 0; i < 4; i++)
+		if(matrix_1[i] != 0.25)
+			fail_flag = 1;
+
+	test_eq(fail_flag, 0);
+
+	fail_flag = 0;
+	sum = 0;
+	// test 3
+	//  make sure a multidimensional array sums each row properly
+	normalize_matrix(matrix_2, 2, 4);
+	for(j = 0; j < 2; j++) {
+		double row_sum = 0;
+
+		for(i = 0; i < 4; i++) 
+			row_sum += matrix_2[j*2 + i];	
+		
+		// floating point hack
+		if(fabsl(row_sum - 1.0) > .0001)
+			fail_flag = 1;
+	}
+
+	test_eq(fail_flag, (double)0);
+		
+}
+
+int main(int argc, char **argv) {
+	int test_number = 1;
+
+	header("count_sequences");
+	test_count_sequences();
+	footer();
+
+	header("normalize_matrix");
+	test_normalize_matrix();
+	footer();
+
+	if(failed)
+		return EXIT_FAILURE;
+	else
+		return EXIT_SUCCESS;
+};