JWS-112 Bumping version of ClustalO (src, binaries and windows) to version 1.2.4.

[jabaws.git] / binaries / src / clustalo / src / hhalign / hhfullalignment-C.h

diff --git a/binaries/src/clustalo/src/hhalign/hhfullalignment-C.h b/binaries/src/clustalo/src/hhalign/hhfullalignment-C.h
index 23d5cc5..8f40fd1 100644 (file)
--- a/binaries/src/clustalo/src/hhalign/hhfullalignment-C.h
+++ b/binaries/src/clustalo/src/hhalign/hhfullalignment-C.h
@@ -15,7 +15,7 @@
  ********************************************************************/
 
 /*
- *  RCS $Id: hhfullalignment-C.h 243 2011-05-31 13:49:19Z fabian $
+ *  RCS $Id: hhfullalignment-C.h 315 2016-12-15 17:18:30Z fabian $
  */
 
 // hhfullalignment.C
@@ -48,6 +48,7 @@ using std::endl;
 #include "hhhit.h"
 #include "hhhalfalignment.h"
 #endif
+//#include "new_new.h" /* memory tracking */
 
 
 
@@ -166,7 +167,7 @@ FullAlignment::AddGaps()
  * @brief Build full alignment -> qa->s[k][h] and ta->s[k][h]
  */
 int
-FullAlignment::Build(HMM& q, Hit& hit)
+FullAlignment::Build(HMM& q, Hit& hit, char zcError[])
 {
   int step;
   char prev_state=MM, state=MM;  
@@ -225,7 +226,7 @@ FullAlignment::Build(HMM& q, Hit& hit)
     }
   }
   else {
-      fprintf(stderr, 
+      sprintf(zcError, 
               "+-------------------------------+\n"
               "| both sequences truncated left |\n"
               "+-------------------------------+\n"
@@ -290,7 +291,7 @@ FullAlignment::Build(HMM& q, Hit& hit)
     }
   }
   else{
-      fprintf(stderr, 
+      sprintf(zcError, 
               "+--------------------------------+\n"
               "| both sequences truncated right |\n"
               "+--------------------------------+\n"
@@ -356,8 +357,8 @@ FullAlignment::PrintHHR(FILE* outf, Hit& hit)
   int iq=hit.i1;  // match state counter for query HMM (displayed in consensus line)
   int jt=hit.j1;  // match state counter for template HMM (displayed in consensus line)
 
-  lq = new(short unsigned int[qa->n+2]);
-  lt = new(short unsigned int[ta->n+2]);
+  lq = new short unsigned int[qa->n+2];
+  lt = new short unsigned int[ta->n+2];
 
   for (k=0; k<qa->n; k++) lq[k]=qa->l[k][hit.i1];
   for (k=0; k<ta->n; k++) lt[k]=ta->l[k][hit.j1];