Maximum memory usage reduced, sequence is deleted when profile is cre…

…ated.
citiususc · May 25, 2022 · e9e4632 · e9e4632
1 parent f7d117a
commit e9e4632
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Showing 3 changed files with 6 additions and 3 deletions.
diff --git a/src/Alignment.cpp b/src/Alignment.cpp
@@ -304,7 +304,7 @@ void Alignment::readAlignment() {
 }
 
 void Alignment::clearAlignmentSeqs() {
- seqs.clear();
+ seqs.resize(0);
 }
 
 void Alignment::clearAlignment() {

diff --git a/src/Constants.h b/src/Constants.h
@@ -54,7 +54,7 @@ namespace veryfasttree {
  const std::string codesStringNT = "ACGT";
 
  const std::string name = "VeryFastTree";
- const std::string version = "3.1.0";
+ const std::string version = "3.1.1";
  const std::string compileFlags =
  "(OpenMP"
  #ifdef __AVX__

diff --git a/src/NeighbourJoining.tcc b/src/NeighbourJoining.tcc
@@ -233,7 +233,8 @@ AbsNeighbourJoining(void)::printNJInternal(std::ostream &out, bool useLen) {
 }
 
 AbsNeighbourJoining(void)::seqsToProfiles() {
- profiles.resize(maxnodes, Profile(nPos, constraintSeqs.size()));
+ profiles.reserve(maxnodes);
+ profiles.resize(seqs.size(), Profile(nPos, constraintSeqs.size()));
  uint8_t charToCode[256];
  int64_t counts[256] = {}; /*Array of zeros*/
 
@@ -266,6 +267,7 @@ AbsNeighbourJoining(void)::seqsToProfiles() {
  profile.weights[j] = 1.0;
  }
  }
+ seqs[i] = std::string();
  if (!constraintSeqs.empty()) {
  auto &constraintSeq = constraintSeqs[i];
  for (int64_t j = 0; j < (int64_t) constraintSeq.size(); j++) {
@@ -288,6 +290,7 @@ AbsNeighbourJoining(void)::seqsToProfiles() {
  }
  }
  }
+ profiles.resize(maxnodes, Profile(nPos, constraintSeqs.size()));
 
  int64_t totCount = 0;
  for (int i = 0; i < 256; i++) {