Adapt metaeuk to recent changes to allow sub-sub-projects in mmseqs

Author: milot-mirdita

src/commons/LocalParameters.h

@@ -70,7 +70,6 @@ class LocalParameters : public Parameters {
     PARAMETER(PARAM_LEN_SCAN_FOR_START)
     int lenScanForStart;
 
-private:
     LocalParameters() : 
         Parameters(),
         PARAM_REVERSE_FRAGMENTS(PARAM_REVERSE_FRAGMENTS_ID,"--reverse-fragments", "Reverse AA Fragments", "reverse AA fragments to compute under null [0,1]", typeid(int), (void *) &reverseFragments, "^[0-1]{1}$"),
@@ -160,6 +159,7 @@ class LocalParameters : public Parameters {
 
         citations.emplace(CITATION_METAEUK, "Levy Karin E, Mirdita M, Soeding J: MetaEuk – sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics. biorxiv, 851964 (2019).");
     }
+private:
     LocalParameters(LocalParameters const&);
     ~LocalParameters() {};
     void operator=(LocalParameters const&);

src/metaeuk.cpp

@@ -18,7 +18,7 @@ void (*validatorUpdate)(void) = 0;
 std::vector<KmerThreshold> externalThreshold = {};
 
 LocalParameters& localPar = LocalParameters::getLocalInstance();
-std::vector<struct Command> commands = {
+std::vector<struct Command> metaeukCommands = {
         // Main tools (workflows for non-experts)
         {"predictexons",             predictexons,            &localPar.predictexonsworkflow,    COMMAND_MAIN,
                 "Call optimal exon sets based on protein similarity",
@@ -96,3 +96,12 @@ std::vector<struct Command> commands = {
 };
 
 std::vector<DatabaseDownload> externalDownloads = {};
+
+extern std::vector<Command> baseCommands;
+void init() {
+    registerCommands(&baseCommands);
+    registerCommands(&metaeukCommands);
+}
+
+void (*initCommands)(void) = init;
+void initParameterSingleton() { new LocalParameters; }