From a9eedba0769723f2d3be53a0253e6436486ec0d7 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Sun, 14 Aug 2022 11:24:50 +0200
Subject: [PATCH] add `setMaxNumThreads` and `setMinOffsetsPerThread` methods
 to the `WFAligner` class

---
 bindings/cpp/WFAligner.cpp      |  9 +++++++++
 bindings/cpp/WFAligner.hpp      |  5 +++++
 wavefront/wavefront_aligner.c   | 18 ++++++++++++++++++
 wavefront/wavefront_aligner.h   |  7 ++++++-
 wavefront/wavefront_bialigner.c | 14 ++++++++++++++
 wavefront/wavefront_bialigner.h |  7 ++++++-
 6 files changed, 58 insertions(+), 2 deletions(-)

diff --git a/bindings/cpp/WFAligner.cpp b/bindings/cpp/WFAligner.cpp
index ce571de..d2f4c82 100644
--- a/bindings/cpp/WFAligner.cpp
+++ b/bindings/cpp/WFAligner.cpp
@@ -210,6 +210,15 @@ void WFAligner::setMaxMemory(
     const uint64_t maxMemoryAbort) {
   wavefront_aligner_set_max_memory(wfAligner,maxMemoryResident,maxMemoryAbort);
 }
+// Parallelization
+void WFAligner::setMaxNumThreads(
+        const int maxNumThreads) {
+    wavefront_aligner_set_max_num_threads(wfAligner, maxNumThreads);
+}
+void WFAligner::setMinOffsetsPerThread(
+        const int minOffsetsPerThread) {
+    wavefront_aligner_set_min_offsets_per_thread(wfAligner, minOffsetsPerThread);
+}
 /*
  * Accessors
  */
diff --git a/bindings/cpp/WFAligner.hpp b/bindings/cpp/WFAligner.hpp
index 5d6a31d..fbdec2a 100644
--- a/bindings/cpp/WFAligner.hpp
+++ b/bindings/cpp/WFAligner.hpp
@@ -136,6 +136,11 @@ class WFAligner {
   void setMaxMemory(
       const uint64_t maxMemoryResident,
       const uint64_t maxMemoryAbort);
+  // Parallelization
+  void setMaxNumThreads(
+      const int maxNumThreads);
+  void setMinOffsetsPerThread(
+      const int minOffsetsPerThread);
   // Accessors
   int getAlignmentScore();
   int getAlignmentStatus();
diff --git a/wavefront/wavefront_aligner.c b/wavefront/wavefront_aligner.c
index 27b16b6..020ce36 100644
--- a/wavefront/wavefront_aligner.c
+++ b/wavefront/wavefront_aligner.c
@@ -394,6 +394,24 @@ void wavefront_aligner_set_max_memory(
         wf_aligner->bialigner,max_memory_resident,max_memory_abort);
   }
 }
+void wavefront_aligner_set_max_num_threads(
+        wavefront_aligner_t* const wf_aligner,
+        const int max_num_threads) {
+    wf_aligner->system.max_num_threads = max_num_threads;
+    if (wf_aligner->bialigner != NULL) {
+        wavefront_bialigner_set_max_num_threads(
+          wf_aligner->bialigner,max_num_threads);
+    }
+}
+void wavefront_aligner_set_min_offsets_per_thread(
+        wavefront_aligner_t* const wf_aligner,
+        const int min_offsets_per_thread) {
+    wf_aligner->system.min_offsets_per_thread = min_offsets_per_thread;
+    if (wf_aligner->bialigner != NULL) {
+        wavefront_bialigner_set_min_offsets_per_thread(
+                wf_aligner->bialigner,min_offsets_per_thread);
+    }
+}
 /*
  * Utils
  */
diff --git a/wavefront/wavefront_aligner.h b/wavefront/wavefront_aligner.h
index 977f596..77cca4b 100644
--- a/wavefront/wavefront_aligner.h
+++ b/wavefront/wavefront_aligner.h
@@ -202,7 +202,12 @@ void wavefront_aligner_set_max_memory(
     wavefront_aligner_t* const wf_aligner,
     const uint64_t max_memory_resident,
     const uint64_t max_memory_abort);
-
+void wavefront_aligner_set_max_num_threads(
+        wavefront_aligner_t* const wf_aligner,
+        const int max_num_threads);
+void wavefront_aligner_set_min_offsets_per_thread(
+        wavefront_aligner_t* const wf_aligner,
+        const int min_offsets_per_thread);
 /*
  * Utils
  */
diff --git a/wavefront/wavefront_bialigner.c b/wavefront/wavefront_bialigner.c
index c250f74..f77dd46 100644
--- a/wavefront/wavefront_bialigner.c
+++ b/wavefront/wavefront_bialigner.c
@@ -129,3 +129,17 @@ void wavefront_bialigner_set_max_memory(
   wf_bialigner->alg_subsidiary->system.max_memory_resident = max_memory_resident;
   wf_bialigner->alg_subsidiary->system.max_memory_abort = max_memory_abort;
 }
+void wavefront_bialigner_set_max_num_threads(
+        wavefront_bialigner_t* const wf_bialigner,
+        const int max_num_threads) {
+    wf_bialigner->alg_forward->system.max_num_threads = max_num_threads;
+    wf_bialigner->alg_reverse->system.max_num_threads = max_num_threads;
+    wf_bialigner->alg_subsidiary->system.max_num_threads = max_num_threads;
+}
+void wavefront_bialigner_set_min_offsets_per_thread(
+        wavefront_bialigner_t* const wf_bialigner,
+        const int min_offsets_per_thread) {
+    wf_bialigner->alg_forward->system.min_offsets_per_thread = min_offsets_per_thread;
+    wf_bialigner->alg_reverse->system.min_offsets_per_thread = min_offsets_per_thread;
+    wf_bialigner->alg_subsidiary->system.min_offsets_per_thread = min_offsets_per_thread;
+}
diff --git a/wavefront/wavefront_bialigner.h b/wavefront/wavefront_bialigner.h
index c12ea07..f787a04 100644
--- a/wavefront/wavefront_bialigner.h
+++ b/wavefront/wavefront_bialigner.h
@@ -89,5 +89,10 @@ void wavefront_bialigner_set_max_memory(
     wavefront_bialigner_t* const wf_bialigner,
     const uint64_t max_memory_resident,
     const uint64_t max_memory_abort);
-
+void wavefront_bialigner_set_max_num_threads(
+    wavefront_bialigner_t* const wf_bialigner,
+    const int max_num_threads);
+void wavefront_bialigner_set_min_offsets_per_thread(
+        wavefront_bialigner_t* const wf_bialigner,
+        const int min_offsets_per_thread);
 #endif /* WAVEFRONT_BIALIGNER_H_ */