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--- a/src/mlagan.c
+++ b/src/mlagan.c
@@ -46,6 +46,7 @@
return 1;
}
+int printXMFAAlign(FILE* outfile, align* myalign);
void usage(void) {
printf("mlagan seqfile_1 seqfile_2 [... seqfile_%d] [-parameters]\n\n",
--- a/src/order.c
+++ b/src/order.c
@@ -28,6 +28,8 @@
align* makeAlign(dmat* mydm, char* seq1, char* seq2);
+int printMFAAlign(char* seq1, char* seq2, align* myalign, char* n1, char* n2);
+int printXMFAAlign(char* seq1, char* seq2, align* myalign, char* n1, char* n2);
char* alpha = "ATCGN.";
--- a/src/prolagan.c
+++ b/src/prolagan.c
@@ -49,6 +49,7 @@
return 1;
}
+int printXMFAAlign(FILE* outfile, align* myalign);
void usage(void) {
printf("mlagan seqfile_1 seqfile_2 [... seqfile_%d] [-parameters]\n\n",
--- a/src/utils/cstat.c
+++ b/src/utils/cstat.c
@@ -3,6 +3,7 @@
#include <string.h>
#include <math.h>
#include <assert.h>
+#include <ctype.h>
#define MAX_SEQ 31
#define MAX(a,b) ((a)>(b)?(a):(b))
--- a/src/utils/overlay.c
+++ b/src/utils/overlay.c
@@ -2,6 +2,7 @@
#include <stdio.h>
#include <assert.h>
#include <string.h>
+#include <ctype.h>
#define MAX_SEQS 63
#define MIN2(y,z) ((y)<(z))?(y):(z)
--- a/src/utils/scorecontigs.c
+++ b/src/utils/scorecontigs.c
@@ -3,6 +3,7 @@
#include <string.h>
#include <math.h>
#include <assert.h>
+#include <ctype.h>
#define MAX_SEQ 1024
#define MAX(a,b) ((a)>(b)?(a):(b))
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