update gMotifs

gMotifs/README

@@ -18,12 +18,12 @@ To run executables you will need :
 
 3. Run ./counting splicing_change_filename -s species -p protein -t type[redundat/not_redundat] -d date_of_analyses
 
-	i.e ./counting  splicing_change_filename -shg19 -pPTB -tR -d20130929
+	i.e ./counting  splicing_change_filename -sH -pPTB -tR -d20130929
 
 
 4. Run ./tetramer splicing_change_filename -s species -p protein -t type[redundat/not_redundat] -d date_of_analyses
 
-	i.e ./tetramer  splicing_change_filename -shg19 -pPTB -tR -d20130929
+	i.e ./tetramer  splicing_change_filename -sH -pPTB -tR -d20130929
 
 
 

gMotifs/counting.cpp

@@ -16,15 +16,7 @@ int main(int argc, char *argv[]){
 
 	 int ret = 0;
 
-	 if( argc<2 ){
-		 cout << "Missing splicing change filename" << endl;
-		 return -1;
-	 } 
-
-	 string splicing_change(argv[1]),
-  	 percent = string("percent_0.5/");
-
-	ret = counting_per_region(opt,splicing_change,percent);
+	ret = counting_per_region(opt);
 	}catch (exception& e){
 		cerr << "exception caught: " << e.what() << endl;
 	}

gMotifs/geco_array.cpp

@@ -19,7 +19,7 @@
  ***************************************************************************/
 
 #include "geco_array.h"
-#include <string.h>
+//#include <string.h>
 
 using namespace std;
 using namespace geco;

gMotifs/geco_array.h

@@ -35,8 +35,11 @@
 
 #include "geco_base.h"
 #include <math.h>
-#include <string.h>
+#include <string>
 #include <vector>
+#include <memory.h>
+
+using namespace std;
 
 namespace geco {
 

gMotifs/geco_base.cpp

@@ -18,7 +18,8 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 #include "geco_base.h"
-#include <string.h>
+//#include <string.h>
+#include <cstring>
 
 namespace geco {
 //--------------------------------------------------------------------------

gMotifs/geco_base.h

@@ -33,6 +33,7 @@
 #include <math.h>
 #include <exception>
 #include <string>
+#include <memory.h>
 
 namespace geco {