Bump jaulib 1.0.0, add vscodium IDE, pass .clang-tidy checks

1 files changed, 37 insertions, 37 deletions

diff --git a/src/gentech/gentech.cpp b/src/gentech/gentech.cpp
index 5c2706e..1c3421c 100755
--- a/src/gentech/gentech.cpp
+++ b/src/gentech/gentech.cpp
@@ -70,7 +70,7 @@ Chromosom::Chromosom ( Chromosomen & env, size_type initial_length )
 // Zufaellig erzeugte Chromosomen

 {

     for ( Chromosom::size_type i=initial_length; i > 0; --i) {

-        push_back( Random(env.m_min_nucleotide_value,env.m_max_nucleotide_value) );

+        push_back( Random<size_type>(env.m_min_nucleotide_value,env.m_max_nucleotide_value) );

     }

     assert (size() == initial_length);

 }

@@ -176,7 +176,7 @@ void Chromosom::Load(const std::string& FileName) {
     fclose(file);

 }

 

-int Chromosom::GetNukleotidNumber(size_type nuckleotide_idx) const noexcept

+Chromosom::size_type Chromosom::GetNukleotidNumber(size_type nuckleotide_idx) const noexcept

 {

     nucleotide_t nuckleotide_value=THIS[nuckleotide_idx];

 

@@ -301,10 +301,10 @@ void Chromosom::InsertIntrons (size_type von, size_type length)
 

 void Chromosom::Inversion()

 {

-    const size_type start = Random(0, size()-2);

+    const size_type start = Random<size_type>(0, size()-2);

     assert (start < size()-1);

 

-    const size_type end = Random (start+1, size()-1) ;

+    const size_type end = Random(start+1, size()-1) ;

     assert (end < size());

     assert (end > start);

 

@@ -332,7 +332,7 @@ void Chromosom::Inversion()
 

 void Chromosom::Translocation()

 {

-    const size_type start = Random (0, size()-2);

+    const size_type start = Random<size_type>(0, size()-2);

     assert (start < size()-1);

     const size_type end = Random (start+1, size()-1) ;

     assert (end < size());

@@ -347,7 +347,7 @@ void Chromosom::Translocation()
     erase(start, end+1);

     assert( save.size() == length );

 

-    const size_type dest = Random( 0, size()-1 );

+    const size_type dest = Random<size_type>( 0, size()-1 );

     for(size_type i=0; i<save.size(); ++i) {

         THIS.insert(dest+i, save[i]);

     }

@@ -392,7 +392,7 @@ Chromosomen::Chromosomen (nucleotide_t UserNukleoMinVal,
   m_intro_code_len_sum(0),

   m_spliced_chromosom_count(0),

 

-  m_file_ptk_ptr(0),

+  m_file_ptk_ptr(nullptr),

 

   m_generation_start(0),

   m_generation_end(0),

@@ -448,7 +448,7 @@ Chromosomen::Chromosomen (nucleotide_t UserNukleoMinVal,
 

     // int ChromLen, ChromQuantity, i, j;

     size_type ChromQuantity;

-    if (fread(&ChromQuantity, sizeof(ChromQuantity), 1, file)==0) { // FIXME: Use fixed width type

+    if (fread(&ChromQuantity, sizeof(ChromQuantity), 1, file)==0) {

         ABORT("can't read file %s\n", StartGenFile.c_str());

     }

 

@@ -504,7 +504,7 @@ Chromosomen::Chromosomen ( nucleotide_t UserNukleoMinVal, nucleotide_t UserNukle
   m_intro_code_len_sum(0),

   m_spliced_chromosom_count(0),

 

-  m_file_ptk_ptr(0),

+  m_file_ptk_ptr(nullptr),

 

   m_generation_start(0),

   m_generation_end(0),

@@ -560,16 +560,16 @@ void Chromosomen::Save (const std::string& FileName) const
         }

         // 4-7-94, 2:51 PM

     }

-    int ChromQuantity=size();

-    if (fwrite (&ChromQuantity, sizeof (ChromQuantity), 1, file) != 1 ) { // FIXME: Use fixed width type

+    size_type ChromQuantity = size();

+    if (fwrite (&ChromQuantity, sizeof (ChromQuantity), 1, file) != 1 ) {

         ABORT("can't write to file %s\n", FileName.c_str());

     }

-    for (int j=0; j<ChromQuantity; j++ ) {

-        const int ChromLen = THIS[j].size();

-        if (fwrite (&ChromLen, sizeof (ChromLen), 1, file) != 1) { // FIXME: Use fixed width type

+    for (size_type j=0; j<ChromQuantity; j++ ) {

+        const size_type ChromLen = THIS[j].size();

+        if (fwrite (&ChromLen, sizeof (ChromLen), 1, file) != 1) {

             ABORT("can't write to file %s\n", FileName.c_str());

         }

-        for(int i=0; i<ChromLen; ++i) {

+        for(size_type i=0; i<ChromLen; ++i) {

             nucleotide_t value = THIS[j][i];

             if (fwrite (&value, sizeof (nucleotide_t), 1, file) != 1) {

                 ABORT("can't write to file %s\n", FileName.c_str());

@@ -579,8 +579,8 @@ void Chromosomen::Save (const std::string& FileName) const
     fclose(file);

 }

 

-int Chromosomen::Evolution (double GoalFitness, const std::string& chrptrPtkFile,

-			                double BirthRate, int Bigamie )

+Chromosomen::size_type Chromosomen::Evolution (double GoalFitness, const std::string& chrptrPtkFile,

+			                                   double BirthRate, int Bigamie )

 {

     double BestEverAverageFitness = -1,

            Cut = 0; // Der Cut beim Sterben

@@ -651,7 +651,7 @@ int Chromosomen::Evolution (double GoalFitness, const std::string& chrptrPtkFile
     return m_generation;

 }

 

-void Chromosomen::InitFitness(void)

+void Chromosomen::InitFitness()

 {

     for (size_type i = 0; i < size(); ++i) {

         Chromosom Neu = THIS[i];

@@ -665,7 +665,7 @@ void Chromosomen::NewGeneration(double BirthRate, bool Bigamie)
 {

     indexlist_t ElternPaare;

 

-    size_type l = (size_type) ( size() * BirthRate );

+    size_type l = (size_type) ( (double)size() * BirthRate );

     size_type i;

 

     m_generation_start=time(nullptr);

@@ -695,15 +695,15 @@ void Chromosomen::NewGeneration(double BirthRate, bool Bigamie)
             if (!Bigamie)   {

                 // the hard way ...

                 do {

-                    i = Random(0, size()-1);

+                    i = Random<size_type>(0, size()-1);

                 } while( jau::contains(ElternPaare, i) ) ;

                 ElternPaare.push_back(i);

                 l--;

             } else {

                 // Bigamistische Beziehung JA, aber sexuell !!!

-                int w, m;

-                ElternPaare.push_back((w = Random (0, size()-1))) ;

-                while (w == (m=Random (0, size()-1))) ;

+                size_type w, m;

+                ElternPaare.push_back((w = Random<size_type>(0, size()-1))) ;

+                while (w == (m=Random<size_type>(0, size()-1))) ;

                 ElternPaare.push_back(m) ;

                 l-=2;

             }

@@ -763,14 +763,14 @@ void Chromosomen::NewGeneration(bool Bigamie)
             if( !Bigamie ) {

                 size_type i;

                 do {

-                    i = Random(0, size()-1);

+                    i = Random<size_type>(0, size()-1);

                 } while( jau::contains(ElternPaare, i) ) ;

                 ElternPaare.push_back(i);

                 l--;

             } else { // Bigamistische Beziehung JA, aber sexuell !!!

                 size_type w, m;

-                ElternPaare.push_back( ( w = Random(0, size()-1) ) );

-                while( w == ( m = Random(0, size()-1) ) ) ;

+                ElternPaare.push_back( ( w = Random<size_type>(0, size()-1) ) );

+                while( w == ( m = Random<size_type>(0, size()-1) ) ) ;

                 ElternPaare.push_back(m);

                 l-=2;

             }

@@ -779,9 +779,9 @@ void Chromosomen::NewGeneration(bool Bigamie)
 

     l=ElternPaare.size();

 

-

     // alles ok ?? GERADE ANZAHL DER ELTERN !!!

     assert (l%2==0);

+    (void)l;

 

     // Neue Population...

     l=ElternPaare.size();

@@ -904,7 +904,7 @@ void Chromosomen::CrossingOver (size_type m, size_type w)
 

         // Kreuzungspunkte sortiert eintragen.

         for ( size_type i = 0; i < m_cross_val; ++i ) {

-            CrossPoints.insert( Random(0 , THIS[shortest].size()) );

+            CrossPoints.insert( Random<size_type>(0 , THIS[shortest].size()) );

         }

 

         Chromosom NeuA (*this, 0);

@@ -954,7 +954,7 @@ void Chromosomen::CrossingOver (size_type m, size_type w)
 

 void Chromosomen::Mutation()

 {

-    static size_type next_nukleotide_idx = m_mutation_freq + Random( 0, (size_type)(m_mutation_freq/m_mutation_freq_variance) ) ;

+    static size_type next_nukleotide_idx = m_mutation_freq + Random<size_type>( 0, (size_type)(m_mutation_freq/m_mutation_freq_variance) ) ;

     m_mutations_this_gen=0;

 

     if ( m_mutation_freq > 0 ) {

@@ -964,10 +964,10 @@ void Chromosomen::Mutation()
             const size_type chromosom_len = THIS[chromosom_idx].size();

             while( nukleotide_idx < chromosom_len ) {

                 // Die Mutation.

-                (THIS[chromosom_idx])[nukleotide_idx] = Random ( m_min_nucleotide_value, m_max_nucleotide_value);

+                (THIS[chromosom_idx])[nukleotide_idx] = Random<size_type>( m_min_nucleotide_value, m_max_nucleotide_value);

                 m_mutations_this_gen++;

                 mutated=true;

-                nukleotide_idx += m_mutation_freq + Random( 0, (size_type)(m_mutation_freq/m_mutation_freq_variance) );

+                nukleotide_idx += m_mutation_freq + Random<size_type>( 0, (size_type)(m_mutation_freq/m_mutation_freq_variance) );

             }

             if( nukleotide_idx >= chromosom_len ) {

                 nukleotide_idx -= chromosom_len;

@@ -1050,7 +1050,7 @@ void Chromosomen::CalcWholeFitness()
             BestChrom = i;

         }

     }

-    m_avrg_fitness = Total / size();

+    m_avrg_fitness = Total / (double)size();

     m_fitness_sum = Total;

     m_avrg_chromosom_len = (double)ChromLenSum/(double)size();

     if( m_all_time_best.GetFitness() < m_best_fitness && npos != BestChrom) {

@@ -1080,13 +1080,13 @@ Chromosomen::size_type Chromosomen::GetWorstChromosom() const
 

 double Chromosomen::GetXWorstFitness(size_type count) const

 {

-    doubles_sorted__t Worst;

+    doubles_sorted_t Worst;

 

     if (count == 0) { return -1; } // Falsche Anzahl uebergeben

     for (size_type i=0; i<size(); ++i) {

-        if( Worst.size() < count ) {

-            Worst.insert(THIS[i].GetFitness());

-        } else if( THIS[i].GetFitness() < Worst[count-1] ) {

+        if( Worst.size() < count ||

+            THIS[i].GetFitness() < Worst[count-1] ) 

+        {

             Worst.insert(THIS[i].GetFitness());

         }

     }

@@ -1120,7 +1120,7 @@ const Chromosom &Chromosomen::GetTheBestEverChromosom()
   return (const Chromosom&) m_all_time_best;

 }

 

-void Chromosomen::CalcParameter(void)

+void Chromosomen::CalcParameter()

 {

     if (m_splice_code_ptr==nullptr ||

         m_splice_code_ptr->SpliceCode==nullptr ||