Fix failing utility tests

Author: milot-mirdita

src/test/TestAlignment.cpp

@@ -66,7 +66,7 @@ int main (int, const char**) {
     Sequence* dbSeq = new Sequence(10000, 0, &subMat, kmer_size, true, false);
     //dbSeq->mapSequence(1,"lala2",ref_seq);
     dbSeq->mapSequence(1,1,tim2.c_str(), tim2.size());
-    SmithWaterman aligner(15000, subMat.alphabetSize, true, Parameters::DBTYPE_AMINO_ACIDS);
+    SmithWaterman aligner(15000, subMat.alphabetSize, true, 1.0, Parameters::DBTYPE_AMINO_ACIDS);
     int8_t * tinySubMat = new int8_t[subMat.alphabetSize*subMat.alphabetSize];
     for (int i = 0; i < subMat.alphabetSize; i++) {
         for (int j = 0; j < subMat.alphabetSize; j++) {

src/test/TestAlignmentPerformance.cpp

@@ -69,7 +69,7 @@ int main (int, const char**) {
     Sequence* query = new Sequence(10000, 0, &subMat, kmer_size, true, false);
     Sequence* dbSeq = new Sequence(10000, 0, &subMat, kmer_size, true, false);
     //dbSeq->mapSequence(1,"lala2",ref_seq);
-    SmithWaterman aligner(15000, subMat.alphabetSize, false, Parameters::DBTYPE_AMINO_ACIDS);
+    SmithWaterman aligner(15000, subMat.alphabetSize, false, 1.0, Parameters::DBTYPE_AMINO_ACIDS);
     int8_t * tinySubMat = new int8_t[subMat.alphabetSize*subMat.alphabetSize];
     for (int i = 0; i < subMat.alphabetSize; i++) {
         for (int j = 0; j < subMat.alphabetSize; j++) {

src/test/TestAlignmentTraceback.cpp

@@ -164,7 +164,7 @@ int main(int, const char**) {
     Sequence* dbSeq = new Sequence(10000, 0, &subMat, kmer_size, true, false);
     //dbSeq->mapSequence(1,"lala2",ref_seq);
     dbSeq->mapSequence(1,1,tim2.c_str(), tim2.size());
-    SmithWaterman aligner(15000, subMat.alphabetSize, false, Parameters::DBTYPE_AMINO_ACIDS);
+    SmithWaterman aligner(15000, subMat.alphabetSize, false, 1.0, Parameters::DBTYPE_AMINO_ACIDS);
     int8_t * tinySubMat = new int8_t[subMat.alphabetSize*subMat.alphabetSize];
     for (int i = 0; i < subMat.alphabetSize; i++) {
         for (int j = 0; j < subMat.alphabetSize; j++) {

src/test/TestDiagonalScoring.cpp

@@ -94,7 +94,7 @@ int main (int, const char**) {
     CounterResult hits[32];
     UngappedAlignment matcher(10000, &subMat, &lookup);
 
-    SubstitutionMatrix::calcLocalAaBiasCorrection(&subMat, s5.numSequence, s5.L, compositionBias);
+    SubstitutionMatrix::calcLocalAaBiasCorrection(&subMat, s5.numSequence, s5.L, compositionBias, 1.0);
     memset(compositionBias, 0.0, sizeof(float)*s5.L);
 //    std::cout << compositionBias[74] << std::endl;
 //    std::cout << compositionBias[79] << std::endl;
@@ -116,7 +116,7 @@ int main (int, const char**) {
 
 
 
-    SubstitutionMatrix::calcLocalAaBiasCorrection(&subMat, s1.numSequence, s1.L, compositionBias);
+    SubstitutionMatrix::calcLocalAaBiasCorrection(&subMat, s1.numSequence, s1.L, compositionBias, 1.0);
 
     hits[0].id = s1.getId();
     hits[0].diagonal = 0;

src/test/TestDiagonalScoringPerformance.cpp

@@ -88,7 +88,7 @@ int main (int, const char**) {
     }
 
     float * compositionBias = new float[s1.L];
-    SubstitutionMatrix::calcLocalAaBiasCorrection(&subMat, s1.numSequence, s1.L, compositionBias);
+    SubstitutionMatrix::calcLocalAaBiasCorrection(&subMat, s1.numSequence, s1.L, compositionBias, 1.0);
 
 
 

src/test/TestMultipleAlignment.cpp

@@ -32,7 +32,7 @@ int main(int, const char**) {
     //   BaseMatrix::print(subMat.subMatrix, subMat.alphabetSize);
     std::cout << "\n";
     EvalueComputation evaluer(100000, &subMat, par.gapOpen.values.aminoacid(), par.gapExtend.values.aminoacid());
-    Matcher * aligner = new Matcher(Parameters::DBTYPE_AMINO_ACIDS, Parameters::DBTYPE_AMINO_ACIDS, 10000, &subMat, &evaluer, false, par.gapOpen.values.aminoacid(), par.gapExtend.values.aminoacid(), 0.0);
+    Matcher * aligner = new Matcher(Parameters::DBTYPE_AMINO_ACIDS, Parameters::DBTYPE_AMINO_ACIDS, 10000, &subMat, &evaluer, false, 1.0, par.gapOpen.values.aminoacid(), par.gapExtend.values.aminoacid(), 0.0, 40);
     std::vector<Matcher::result_t> alnResults;
     std::vector<std::vector<unsigned char>> seqSet;
     std::cout << "Sequence (id 0):\n";

src/test/TestProfileAlignment.cpp

@@ -788,7 +788,7 @@ int main (int, const char**) {
     const char* sequence2 = "LFILNIISMNKQTKVKGYLLLLLVISSLFISLVGHGYTANKVSAPNPAKEYPQDNLSVIDMKNLPGTQIKSMVKDELQQFLEEQGFRRLKNKSLVDLRRIWLGFMYEDFFYTMHKKTDLPISVIYAFFIIEATNAGIESKLMAKALNPGGIKYRGTGKKMKAMDDCY";
 
     dbSeq->mapSequence(1,1,sequence2, strlen(sequence2));
-    SmithWaterman aligner(15000, subMat.alphabetSize, false, Parameters::DBTYPE_AMINO_ACIDS);
+    SmithWaterman aligner(15000, subMat.alphabetSize, false, 1.0, Parameters::DBTYPE_AMINO_ACIDS);
     int8_t * tinySubMat = new int8_t[subMat.alphabetSize*subMat.alphabetSize];
     aligner.ssw_init(s, s->getAlignmentProfile(), &subMat);
     int32_t maskLen = s->L / 2;