fix errors

src/commons/StructureSmithWaterman.cpp

@@ -645,7 +645,7 @@ StructureSmithWaterman::s_align StructureSmithWaterman::alignStartPosBacktrace<S
 template
 StructureSmithWaterman::s_align StructureSmithWaterman::alignStartPosBacktrace<StructureSmithWaterman::PROFILE_HMM>(const unsigned char*, const unsigned char*, int32_t, const uint8_t, const uint8_t, const uint8_t, std::string& , StructureSmithWaterman::s_align, const int, const float, const int32_t);
 
-void trimCIGAR(std::string &cigar, int &qStart, int &qEnd, int &tStart, int &tEnd) {
+void trimCIGAR(std::string &cigar, int &qEnd, int &tEnd) {
     int i = 0;
     while (cigar[i] != 'M') {
         if (cigar[i] == 'D') {
@@ -714,12 +714,13 @@ Matcher::result_t StructureSmithWaterman::simpleGotoh(
         short **target_profile_word_3di,
         int32_t query_start, int32_t query_end,
         int32_t target_start, int32_t target_end,
-        const short gap_open, const short gap_extend, bool targetIsProfile,
-        size_t queryId,
-        size_t targetId
+        const short gap_open, const short gap_extend
+        // bool targetIsProfile,
+        // size_t queryId,
+        // size_t targetId
 ) {
     // defining constants for backtracing
-    const uint8_t B        = 0b00000001;
+    // const uint8_t B        = 0b00000001;
     const uint8_t H        = 0b00000010;
     const uint8_t F        = 0b00000100;
     const uint8_t E        = 0b00001000;
@@ -876,7 +877,7 @@ Matcher::result_t StructureSmithWaterman::simpleGotoh(
     // Adjust CIGAR string to start/end on M
     // q/dbStart and q/dbEnd are already correct, no need to adjust here
     // q/dbStart set to last M j/i, q/dbEnd last M .ref/.read
-    trimCIGAR(cigar, qStart, qEnd, dbStart, dbEnd);
+    trimCIGAR(cigar, qEnd, dbEnd);
 
     delete[] workspace;
     delete[] btMatrix;

src/commons/StructureSmithWaterman.h

@@ -160,9 +160,10 @@ class StructureSmithWaterman{
         short **target_profile_word_3di,
         int32_t query_start, int32_t query_end,
         int32_t target_start, int32_t target_end,
-        const short gap_open, const short gap_extend, bool targetIsProfile,
-        size_t queryId,
-        size_t targetId
+        const short gap_open, const short gap_extend
+        // bool targetIsProfile,
+        // size_t queryId,
+        // size_t targetId
     );
 
     /*!	@function	Create the query profile using the query sequence.

src/strucclustutils/refinemsa.cpp

@@ -86,7 +86,6 @@ void refineOne(
     MsaFilter &filter_3di,
     SubstitutionMatrix &subMat_3di,
     StructureSmithWaterman &structureSmithWaterman,
-    float matchRatio,
     std::vector<int> &seqLens,
     bool filterMsa,
     bool compBiasCorrection,
@@ -99,7 +98,6 @@ void refineOne(
     bool wg,
     int gapExtend,
     int gapOpen,
-    size_t maxSeqLength,
     std::vector<Sequence*> &sequences_aa,
     std::vector<Sequence*> &sequences_ss
 ) {
@@ -125,31 +123,31 @@ void refineOne(
     deleteGapCols(group2, cigars_aa, cigars_ss);
 
     // generate masks for each sub MSA
-    std::string mask1 = computeProfileMask(group1, cigars_aa, seqLens, subMat_aa, 1);
-    std::string mask2 = computeProfileMask(group2, cigars_aa, seqLens, subMat_aa, 1);
+    std::string mask1 = computeProfileMask(group1, cigars_aa, seqLens, subMat_aa, 1.0);
+    std::string mask2 = computeProfileMask(group2, cigars_aa, seqLens, subMat_aa, 1.0);
     std::vector<int> map1 = maskToMapping(mask1);
     std::vector<int> map2 = maskToMapping(mask2);
 
     // msa2profile
     std::string profile1_aa = msa2profile(
         group1, cigars_aa, mask1, calculator_aa, filter_aa,
         subMat_aa, filterMsa, compBiasCorrection, qid, filterMaxSeqId,
-        Ndiff, covMSAThr, qsc, filterMinEnable, wg, maxSeqLength
+        Ndiff, covMSAThr, qsc, filterMinEnable, wg
     );
     std::string profile1_ss = msa2profile(
         group1, cigars_ss, mask1, calculator_3di, filter_3di,
         subMat_3di, filterMsa, compBiasCorrection, qid, filterMaxSeqId,
-        Ndiff, covMSAThr, qsc, filterMinEnable, wg, maxSeqLength
+        Ndiff, covMSAThr, qsc, filterMinEnable, wg
     );
     std::string profile2_aa = msa2profile(
         group2, cigars_aa, mask2, calculator_aa, filter_aa,
         subMat_aa, filterMsa, compBiasCorrection, qid, filterMaxSeqId,
-        Ndiff, covMSAThr, qsc, filterMinEnable, wg, maxSeqLength
+        Ndiff, covMSAThr, qsc, filterMinEnable, wg
     );
     std::string profile2_ss = msa2profile(
         group2, cigars_ss, mask2, calculator_3di, filter_3di,
         subMat_3di, filterMsa, compBiasCorrection, qid, filterMaxSeqId,
-        Ndiff, covMSAThr, qsc, filterMinEnable, wg, maxSeqLength
+        Ndiff, covMSAThr, qsc, filterMinEnable, wg
     );
     assert(profile1_aa.length() == profile1_ss.length());
     assert(profile2_aa.length() == profile2_ss.length());
@@ -213,7 +211,6 @@ void refineMany(
     bool compBiasCorrection,
     bool wg,
     float filterMaxSeqId,
-    float matchRatio,
     float qsc,
     int Ndiff,
     float covMSAThr,
@@ -256,9 +253,9 @@ void refineMany(
             cigars_new_aa, cigars_new_ss,
             calculator_aa, filter_aa, subMat_aa,
             calculator_3di, filter_3di, subMat_3di,
-            structureSmithWaterman, matchRatio, lengths, filterMsa, compBiasCorrection,
+            structureSmithWaterman, lengths, filterMsa, compBiasCorrection,
             qid, filterMaxSeqId, Ndiff, covMSAThr, qsc, filterMinEnable,
-            wg, gapExtend, gapOpen, maxSeqLen,
+            wg, gapExtend, gapOpen,
             sequences_aa, sequences_ss
         );
         float lddtScore = std::get<2>(calculate_lddt(cigars_new_aa, subset, indices, lengths, seqDbrCA, pairThreshold));
@@ -277,7 +274,7 @@ void refineMany(
     if (delta > 0.0) {
         std::cout << std::fixed << std::setprecision(4) << "Final LDDT: " << prevLDDT << " (+" << delta << ")\n";
     } else {
-        std::cout << "Could not improve MSA\n";
+        std::cout << "Did not improve MSA\n";
     }
     for (size_t i = 0; i < sequences_aa.size(); i++) {
         delete sequences_aa[i];
@@ -361,7 +358,7 @@ int refinemsa(int argc, const char **argv, const Command& command) {
         tinySubMatAA, tinySubMat3Di, &seqDbrCA, cigars_aa, cigars_ss,
         calculator_aa, filter_aa, subMat_aa, calculator_3di, filter_3di, subMat_3di,
         structureSmithWaterman, par.refineIters, par.compBiasCorrection, par.wg, par.filterMaxSeqId,
-        par.matchRatio, par.qsc, par.Ndiff, par.covMSAThr,
+        par.qsc, par.Ndiff, par.covMSAThr,
         par.filterMinEnable, par.filterMsa, par.gapExtend.values.aminoacid(), par.gapOpen.values.aminoacid(),
         par.maxSeqLen, par.qid, par.pairThreshold, indices, lengths
     );

src/strucclustutils/refinemsa.h

@@ -18,7 +18,7 @@ void refineMany(
     bool compBiasCorrection,
     bool wg,
     float filterMaxSeqId,
-    float matchRatio,
+    // float matchRatio,
     float qsc,
     int Ndiff,
     float covMSAThr,

src/strucclustutils/structuremsa.cpp

@@ -9,7 +9,6 @@
 #include "MathUtil.h"
 #include "MsaFilter.h"
 #include "MultipleAlignment.h"
-#include "Newick.h"
 #include "PSSMCalculator.h"
 #include "Parameters.h"
 #include "Sequence.h"
@@ -303,10 +302,7 @@ Matcher::result_t pairwiseAlignment(
         0,
         target_aa->L,
         gapOpen,
-        gapExtend,
-        targetIsProfile,
-        query_aa->getId(),
-        target_aa->getId()
+        gapExtend
     );
 
     for (int32_t i = 0; i < aligner.get_profile()->alphabetSize; i++) {
@@ -671,7 +667,7 @@ std::string computeProfileMask(
     for (int i = 0; i < lengthWithGaps; i++) {
         float matches = colValues[i];
         float gaps = colValues[lengthWithGaps + i];
-        bool state = (gaps / (gaps + matches)) > matchRatio;
+        bool state = (gaps / (gaps + matches)) >= matchRatio;
         mask.push_back(state ? '1' : '0');
     }
 
@@ -705,8 +701,7 @@ std::string msa2profile(
     float covMSAThr,
     float qsc,
     int filterMinEnable,
-    bool wg,
-    size_t maxSeqLength
+    bool wg
 ) {
     // length of sequences after masking
     int lengthWithMask = 0;
@@ -1240,11 +1235,10 @@ void updateCIGARS(
         updateTargetCIGAR(cigars_aa[index], cigars_ss[index], tBt, tPreGaps, tPreSequence, tEndGaps, tEndSequence);
 }
 
-void testSeqLens(std::vector<size_t> &indices, std::vector<std::vector<Instruction2> > &cigars, std::vector<int> &lengths) {
-    for (int index : indices) {
-        int length = cigarLength(cigars[index], false);
+void testSeqLens(std::vector<size_t> &MAYBE_UNUSED(indices), std::vector<std::vector<Instruction2> > &MAYBE_UNUSED(cigars), std::vector<int> &MAYBE_UNUSED(lengths)) {
+    for (int MAYBE_UNUSED(index) : indices) {
+        assert(lengths[index] == cigarLength(cigars[index], false));
         // std::cout << headers[index] << '\t' << lengths[index] << '\t' << length << '\n';
-        assert(lengths[index] == length);
     }
 }
 
@@ -1706,7 +1700,7 @@ int structuremsa(int argc, const char **argv, const Command& command, bool preCl
 if (true) {
             // calculate LDDT of merged alignment
             float lddtScore = std::get<2>(calculate_lddt(cigars_aa, groups[mergedId], dbKeys, seqLens, &seqDbrCA, par.pairThreshold));
-            std::cout << std::fixed << std::setprecision(3)
+            std::cout << std::fixed << std::setprecision(4)
                 << queryIsProfile << "\t" << targetIsProfile << '\t' << headers[mergedId] << "\t" << headers[targetId]
                 << "\tLDDT: " << lddtScore << '\t' << res.score;
             if (tmaligned){
@@ -1737,8 +1731,7 @@ if (true) {
                 par.covMSAThr,
                 par.qsc,
                 par.filterMinEnable,
-                par.wg,
-                1
+                par.wg
             );
             std::string profile_3di = msa2profile(
                 groups[mergedId],
@@ -1755,8 +1748,7 @@ if (true) {
                 par.covMSAThr,
                 par.qsc,
                 par.filterMinEnable,
-                par.wg,
-                par.maxSeqLen
+                par.wg
             );
             assert(profile_aa.length() == profile_3di.length());
 
@@ -1790,7 +1782,7 @@ if (true) {
         refineMany(
             tinySubMatAA, tinySubMat3Di, &seqDbrCA, cigars_aa, cigars_ss, calculator_aa,
             filter_aa, subMat_aa, calculator_3di, filter_3di, subMat_3di, structureSmithWaterman,
-            par.refineIters, par.compBiasCorrection, par.wg, par.filterMaxSeqId, par.matchRatio, par.qsc,
+            par.refineIters, par.compBiasCorrection, par.wg, par.filterMaxSeqId, par.qsc,
             par.Ndiff, par.covMSAThr, par.filterMinEnable, par.filterMsa, par.gapExtend.values.aminoacid(),
             par.gapOpen.values.aminoacid(), par.maxSeqLen, par.qid, par.pairThreshold, dbKeys, seqLens
         );

src/strucclustutils/structuremsa.h

@@ -63,27 +63,6 @@ union Instruction2 {
     }
 };
 
-std::string fastamsa2profile(
-    std::string & msa,
-    PSSMCalculator &pssmCalculator,
-    MsaFilter &filter,
-    SubstitutionMatrix &subMat,
-    size_t maxSeqLength,
-    size_t maxSetSize,
-    float matchRatio,
-    bool filterMsa,
-    bool compBiasCorrection,
-    std::string & qid,
-    float filterMaxSeqId,
-    float Ndiff,
-    float covMSAThr,
-    float qsc,
-    int filterMinEnable,
-    bool wg,
-    bool *externalMaskedColumns,
-    float scoreBias
-);
-
 void getMergeInstructions(
     Matcher::result_t &res,
     std::vector<int> &map1,
@@ -131,8 +110,7 @@ std::string msa2profile(
     float covMSAThr,
     float qsc,
     int filterMinEnable,
-    bool wg,
-    size_t maxSeqLength
+    bool wg
 );
 
 void updateCIGARS(