breaking: fix parameter singleton in subprojects

With subprojects who have their own Parameter class it can happen that
the MMseqs2 Parameters object is constructed first (in MMseqsBase.cpp)
and then the subproject singleton is accessed and but is already wrongly initialized 
as the parent.

Here we introduce a function initParameterSingleton that decides who to initialize.
Subprojects need to provide this function that calls the correct Parameters constructor now.

src/commons/Parameters.h

@@ -59,6 +59,8 @@ struct MMseqsParameter {
     }
 };
 
+void initParameterSingleton(void);
+#define DEFAULT_PARAMETER_SINGLETON_INIT void initParameterSingleton() { new Parameters; }
 
 class Parameters {
 public:
@@ -712,13 +714,11 @@ class Parameters {
     static Parameters& getInstance()
     {
         if (instance == NULL) {
-            initInstance();
+            initParameterSingleton();
         }
         return *instance;
     }
-    static void initInstance() {
-        new Parameters;
-    }
+    friend void initParameterSingleton(void);
 
     void setDefaults();
     void initMatrices();

src/mmseqs.cpp

@@ -1,6 +1,7 @@
 #include "Command.h"
 #include "DownloadDatabase.h"
 #include "Prefiltering.h"
+#include "Parameters.h"
 
 const char* binary_name = "mmseqs";
 const char* tool_name = "MMseqs2";
@@ -19,6 +20,8 @@ void init() {
 }
 void (*initCommands)(void) = init;
 
+DEFAULT_PARAMETER_SINGLETON_INIT;
+
 std::vector<DatabaseDownload> externalDownloads = {};
 std::vector<KmerThreshold> externalThreshold = {};
 

src/test/TestAlignment.cpp

@@ -20,6 +20,7 @@
 #include "Matcher.h"
 
 const char* binary_name = "test_alignment";
+DEFAULT_PARAMETER_SINGLETON_INIT;
 
 int main (int, const char**) {
     const size_t kmer_size=6;

src/test/TestAlignmentPerformance.cpp

@@ -24,6 +24,7 @@
 #include "StripedSmithWaterman.h"
 
 const char* binary_name = "test_alignmentperformance";
+DEFAULT_PARAMETER_SINGLETON_INIT;
 
 #define MAX_FILENAME_LIST_FILES 4096
 

src/test/TestAlignmentTraceback.cpp

@@ -18,6 +18,7 @@
 #include "Parameters.h"
 
 const char* binary_name = "test_alignmenttraceback";
+DEFAULT_PARAMETER_SINGLETON_INIT;
 
 struct scores{
     short H;

src/test/TestAlp.cpp

@@ -43,6 +43,7 @@ Contents: pairwise alignment algorithms
 #include "sls_alignment_evaluer.hpp"
 
 const char* binary_name = "test_alp";
+DEFAULT_PARAMETER_SINGLETON_INIT;
 
 using namespace Sls;
 using namespace std;

src/test/TestBacktraceTranslator.cpp

@@ -1,5 +1,4 @@
 #include "BacktraceTranslator.h"
-#include "Parameters.h"
 
 const char* binary_name = "test_backtracetranslator";
 

src/test/TestBestAlphabet.cpp

@@ -14,7 +14,6 @@
 #include "DBReader.h"
 #include "Sequence.h"
 #include "Indexer.h"
-#include "Parameters.h"
 
 const char* binary_name = "test_bestalphabet";
 

src/test/TestCompositionBias.cpp

@@ -9,6 +9,7 @@
 #include "Parameters.h"
 
 const char* binary_name = "test_compositionbias";
+DEFAULT_PARAMETER_SINGLETON_INIT;
 
 void calcLocalAaBiasCorrection(Sequence* seq, SubstitutionMatrix * m){
     const int windowSize = 40;

src/test/TestDiagonalScoring.cpp

@@ -14,6 +14,7 @@
 #include "Parameters.h"
 
 const char* binary_name = "test_diagonalscoring";
+DEFAULT_PARAMETER_SINGLETON_INIT;
 
 int main (int, const char**) {
     size_t kmer_size = 6;

src/test/TestDiagonalScoringPerformance.cpp

@@ -20,6 +20,7 @@ KSEQ_INIT(int, read)
 #include "Parameters.h"
 
 const char* binary_name = "test_diagonalscoringperformance";
+DEFAULT_PARAMETER_SINGLETON_INIT;
 
 int main (int, const char**) {
     size_t kmer_size = 6;

src/test/TestKmerGenerator.cpp

@@ -15,6 +15,7 @@
 #include "Parameters.h"
 
 const char* binary_name = "test_kmergenerator";
+DEFAULT_PARAMETER_SINGLETON_INIT;
 
 int main (int, const char**) {
     const size_t kmer_size=6;

src/test/TestKmerNucl.cpp

@@ -6,6 +6,7 @@
 #include "Orf.h"
 
 const char* binary_name = "test_kmernucl";
+DEFAULT_PARAMETER_SINGLETON_INIT;
 
 std::string kmerToSting(size_t idx, int size) {
     char output[32];

src/test/TestKmerScore.cpp

@@ -8,6 +8,7 @@
 #include "Parameters.h"
 
 const char* binary_name = "test_kmerscore";
+DEFAULT_PARAMETER_SINGLETON_INIT;
 
 int main (int, const char**) {
     const size_t kmer_size = 6;

src/test/TestKwayMerge.cpp

@@ -8,7 +8,6 @@
 
 #include "SubstitutionMatrix.h"
 #include "Sequence.h"
-#include "Parameters.h"
 
 const char* binary_name = "test_kwaymerge";
 struct KmerEntry{

src/test/TestMultipleAlignment.cpp

@@ -14,6 +14,7 @@
 #include "Parameters.h"
 
 const char* binary_name = "test_multiplealignment";
+DEFAULT_PARAMETER_SINGLETON_INIT;
 
 int main(int, const char**) {
     Parameters& par = Parameters::getInstance();

src/test/TestPSSM.cpp

@@ -15,6 +15,7 @@
 #include "MultipleAlignment.h"
 
 const char* binary_name = "test_pssm";
+DEFAULT_PARAMETER_SINGLETON_INIT;
 
 int main (int, const char**) {
     Parameters& par = Parameters::getInstance();

src/test/TestPSSMPrune.cpp

@@ -16,6 +16,7 @@
 #include <string.h>
 
 const char* binary_name = "test_pssmprune";
+DEFAULT_PARAMETER_SINGLETON_INIT;
 
 int main (int, const char**) {
     Parameters& par = Parameters::getInstance();

src/test/TestProfileAlignment.cpp

@@ -19,6 +19,7 @@
 #include "Parameters.h"
 
 const char* binary_name = "test_profilealignment";
+DEFAULT_PARAMETER_SINGLETON_INIT;
 
 int main (int, const char**) {
     const size_t kmer_size=6;

src/test/TestReduceMatrix.cpp

@@ -12,6 +12,7 @@
 #include "Parameters.h"
 
 const char* binary_name = "test_reducematrix";
+DEFAULT_PARAMETER_SINGLETON_INIT;
 
 int main (int, const char**) {
     const int reductionAlphabetSize = 17;

src/test/TestScoreMatrixSerialization.cpp

@@ -5,6 +5,7 @@
 #include "Debug.h"
 
 const char* binary_name = "test_scorematrixserialization";
+DEFAULT_PARAMETER_SINGLETON_INIT;
 
 int main (int, const char**) {
     Parameters& par = Parameters::getInstance();

src/test/TestSequenceIndex.cpp

@@ -11,6 +11,7 @@
 #include "Parameters.h"
 
 const char* binary_name = "test_sequenceindex";
+DEFAULT_PARAMETER_SINGLETON_INIT;
 
 int main (int, const char**) {
     size_t kmer_size = 6;

src/test/TestTanTan.cpp

@@ -11,6 +11,7 @@
 #include "Parameters.h"
 
 const char* binary_name = "test_tantan";
+DEFAULT_PARAMETER_SINGLETON_INIT;
 
 int main (int, const char**) {
     const size_t kmer_size = 6;