added the new homoplasy merging

cbcrg · Mar 5, 2023 · 472cf43 · 472cf43
1 parent 488dd86
commit 472cf43
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Showing 4 changed files with 296 additions and 227 deletions.
diff --git a/lib/dp_lib/util_dp_drivers.c b/lib/dp_lib/util_dp_drivers.c
@@ -2841,6 +2841,17 @@ Alignment * align_two_structures ( Sequence *S, int s1, int s2, char *mode)
 }
 
 
+Alignment * align_two_sequences_with_external_method ( char *seq1, char *seq2, char *method)
+{
+  static char *in=vtmpnam  (NULL);
+  static char *out=vtmpnam (NULL);
+
+  if (!seq1 || !seq2 || !method)return NULL;
+  string2file (in, "w",">A\n%s\n>B\n%s\n", seq1, seq2);
+  safe_remove (out);
+  printf_system ("dynamic.pl -method %s -seq %s -outfile %s", method, in, out);
+  return quick_read_aln(out);
+}
 
 Alignment * align_two_sequences ( char *seq1, char *seq2, char *in_matrix, int gop, int gep, char *in_align_mode)
 {

diff --git a/lib/dp_lib/util_dp_drivers.h b/lib/dp_lib/util_dp_drivers.h
@@ -79,6 +79,7 @@ Constraint_list *hash_pair (TC_method *M , char *in_seq, Constraint_list *CL);
 
 void toggle_case_in_align_two_sequences(int value);
 Alignment * align_two_structures ( Sequence *S, int s1, int s2, char *mode);
+Alignment * align_two_sequences_with_external_method ( char *seq1, char *seq2, char *method);
 Alignment * align_two_sequences ( char *seq1, char *seq2, char *matrix, int gop, int gep, char *align_mode);
 Alignment *align_two_streches4dpa ( char *s0, char *s1, char *in_matrix, int gop, int gep, char *in_align_mode, Alignment *A);
 Alignment * align_two_sequences4dpa ( char *padded1, char *seq1, char *padded2, char *seq2,char *matrix, int gop, int gep, char *align_mode, Alignment *R);