From bba0d801c0959d70de6735f0d6b8fff6dd4cab0a Mon Sep 17 00:00:00 2001
From: Milot Mirdita <milot@mirdita.de>
Date: Thu, 30 May 2024 17:16:11 +0900
Subject: [PATCH] Adapt metaeuk to recent changes to allow sub-sub-projects in
 mmseqs

---
 src/commons/LocalParameters.h |  2 +-
 src/metaeuk.cpp               | 11 ++++++++++-
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/src/commons/LocalParameters.h b/src/commons/LocalParameters.h
index b980ccb..7f79978 100644
--- a/src/commons/LocalParameters.h
+++ b/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&);
diff --git a/src/metaeuk.cpp b/src/metaeuk.cpp
index 2753775..e89426c 100644
--- a/src/metaeuk.cpp
+++ b/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; }
\ No newline at end of file