version 1.0.32: compilation with libsuma

Makefile

@@ -1,16 +1,13 @@
-EXEC=sumaclust
+EXEC = sumaclust
 
-SUMACLUST_SRC= sumaclust.c \
-               mtcompare_sumaclust.c
+SUMACLUST_SRC = sumaclust.c \
+                mtcompare_sumaclust.c
 
-             
-SUMACLUST_OBJ= $(patsubst %.c,%.o,$(SUMACLUST_SRC))
+SUMACLUST_OBJ = $(patsubst %.c,%.o,$(SUMACLUST_SRC))
 
+SRCS = $(SUMACLUST_SRC)
 
-SRCS= $(SUMACLUST_SRC)
-
-LIB= -lfasta -llcs -lfile -lutils -lm #-ll
-
+LIB = -lsuma -lm #-ll
 
 include ./global.mk
 
@@ -31,8 +28,8 @@ else
         LFLAGS = 
 endif
 
-sumaclust: $(SUMACLUST_OBJ) $(LIBFASTA) $(LIBLCS) $(LIBFILE) $(LIBUTILS)
-	$(CC) $(LDFLAGS) -o $@ $(LFLAGS) $(SUMACLUST_OBJ) $(LIB) $(LIBFASTAPATH) $(LIBLCSPATH) $(LIBFILEPATH) $(LIBUTILSPATH)
+sumaclust: $(SUMACLUST_OBJ) $(LIBSUMA)
+	$(CC) $(LDFLAGS) -o $@ $(LFLAGS) $(SUMACLUST_OBJ) $(LIB) $(LIBSUMAPATH)
 	
 ########
 #
@@ -41,12 +38,7 @@ sumaclust: $(SUMACLUST_OBJ) $(LIBFASTA) $(LIBLCS) $(LIBFILE) $(LIBUTILS)
 ########
 
 clean:
-	rm -f *.o	
-	rm -f *.P
+	rm -f $(SUMACLUST_OBJ)	
 	rm -f $(EXEC)
-	$(MAKE) -C ./sumalibs/libfasta clean
-	$(MAKE) -C ./sumalibs/liblcs clean
-	$(MAKE) -C ./sumalibs/libfile clean
-	$(MAKE) -C ./sumalibs/libutils clean
-
-		
+	$(MAKE) -C ./sumalibs clean
+			

global.mk

@@ -1,13 +1,7 @@
 
-LIBFASTAPATH = -L./sumalibs/libfasta
-LIBLCSPATH   = -L./sumalibs/liblcs
-LIBFILEPATH  = -L./sumalibs/libfile
-LIBUTILSPATH = -L./sumalibs/libutils
+LIBSUMAPATH = -L./sumalibs
 
-LIBFASTA = ./sumalibs/libfasta/libfasta.a
-LIBLCS   = ./sumalibs/liblcs/liblcs.a
-LIBFILE  = ./sumalibs/libfile/libfile.a
-LIBUTILS = ./sumalibs/libutils/libutils.a
+LIBSUMA = ./sumalibs/libsuma.a
 
 CC=gcc
 LDFLAGS=
@@ -32,14 +26,5 @@ default: all
 #
 ########
 
-./sumalibs/libfasta/libfasta.a:
-	$(MAKE) -C ./sumalibs/libfasta
-
-./sumalibs/liblcs/liblcs.a:
-	$(MAKE) -C ./sumalibs/liblcs
-
-./sumalibs/libfile/libfile.a:
-	$(MAKE) -C ./sumalibs/libfile
-
-./sumalibs/libutils/libutils.a:
-	$(MAKE) -C ./sumalibs/libutils
+./sumalibs/libsuma.a:
+	$(MAKE) -C ./sumalibs

sumaclust.c

@@ -23,7 +23,7 @@
 #include "mtcompare_sumaclust.h"
 #include "sumaclust.h"
 
-#define VERSION "1.0.20"
+#define VERSION "1.0.32"
 
 
 /* ----------------------------------------------- */
@@ -585,7 +585,7 @@ void putSeqInCluster(fastaSeqPtr* seq, fastaSeqPtr* center, double score)
 }
 
 
-int compare(fastaSeqPtr* db,  int n, BOOL fastOption, double threshold, BOOL normalize, int reference, BOOL lcsmode,
+int compare(fastaSeqPtr* db, int n, BOOL fastOption, double threshold, BOOL normalize, int reference, BOOL lcsmode,
 		double max_ratio)
 {
 	double       score;
@@ -723,7 +723,7 @@ int compare(fastaSeqPtr* db,  int n, BOOL fastOption, double threshold, BOOL nor
 	free(iseq1-sizeForSeqs+lmax);
 	free(iseq2-sizeForSeqs+lmax);
 
-	if (normalize && reference == ALILEN)
+	if (normalize && (reference == ALILEN))
 		free(address);
 
 	return(k);
@@ -1037,7 +1037,6 @@ int main(int argc, char** argv)
 	// FASTA file
 	if (printFASTA)
 	{
-
 		if (printFASTAtofile)
 		{
 			FASTA_output = fopen(FASTA_file_name, "w");