+ added some docu
[qpalma.git] / dyn_prog / qpalma_dp.h
index 9940b86..0253cd0 100644 (file)
@@ -1,6 +1,8 @@
 #ifndef _QPALMA_DP_H_
 #define _QPALMA_DP_H_
 
+#include "Python.h"
+
 #include "penalty_info.h"
 #include "debug_tools.h"
 
@@ -72,12 +74,12 @@ class Alignment {
       double* alignmentscores;
       struct penalty_struct** qualityFeaturesAllPaths;
 
-      int dna_len;
-      int est_len;
-      int mlen;
-      int nr_paths;
+      size_t dna_len;
+      size_t est_len;
+      size_t mlen;
+      size_t nr_paths;
 
-      int result_len;
+      size_t result_len;
       int* DNA_ARRAY;
       int* EST_ARRAY;
 
@@ -128,11 +130,17 @@ class Alignment {
       bool print_matrix);
 
       void getDNAEST();
-      void getAlignmentResults(int* s_align, int* e_align,
-      int* mmatrix_p, double* alignscores, double* qScores);
 
       int getResultLength() { return result_len; }
-      void getAlignmentArrays(int* dna_align, int* est_align);
+
+      void getAlignmentResultsOld(int* s_align, int* e_align,
+      int* mmatrix_p, double* alignscores, double* qScores);
+    
+      void getAlignmentArraysOld(int* dna_align, int* est_align);
+
+
+      PyObject* getAlignmentResults();
+      PyObject* getAlignmentArrays();
 };
 
 #endif  // _QPALMA_DP_H_