Remove translatenucs from more parameter lists

Author: milot-mirdita

src/commons/Parameters.cpp

@@ -1292,7 +1292,6 @@ Parameters::Parameters():
     linsearchworkflow = combineList(align, kmersearch);
     linsearchworkflow = combineList(linsearchworkflow, swapresult);
     linsearchworkflow = combineList(linsearchworkflow, extractorfs);
-    linsearchworkflow = combineList(linsearchworkflow, translatenucs);
     linsearchworkflow = combineList(linsearchworkflow, offsetalignment);
     linsearchworkflow.push_back(&PARAM_RUNNER);
     linsearchworkflow.push_back(&PARAM_REUSELATEST);
@@ -1392,7 +1391,6 @@ Parameters::Parameters():
 
     mapworkflow = combineList(prefilter, rescorediagonal);
     mapworkflow = combineList(mapworkflow, extractorfs);
-    mapworkflow = combineList(mapworkflow, translatenucs);
     mapworkflow.push_back(&PARAM_START_SENS);
     mapworkflow.push_back(&PARAM_SENS_STEPS);
     mapworkflow.push_back(&PARAM_RUNNER);

src/multihit/MultiHitSearch.cpp

@@ -35,9 +35,6 @@ int multihitsearch(int argc, const char **argv, const Command &command) {
     for (size_t i = 0; i < par.extractorfs.size(); i++){
         par.extractorfs[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
     }
-    for (size_t i = 0; i < par.translatenucs.size(); i++){
-        par.translatenucs[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
-    }
     for (size_t i = 0; i < par.splitsequence.size(); i++) {
         par.splitsequence[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
     }

src/workflow/ClusterUpdate.cpp

@@ -35,9 +35,6 @@ int clusterupdate(int argc, const char **argv, const Command& command) {
     for (size_t i = 0; i < par.extractorfs.size(); i++) {
         par.extractorfs[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
     }
-    for (size_t i = 0; i < par.translatenucs.size(); i++) {
-        par.translatenucs[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
-    }
     for (size_t i = 0; i < par.splitsequence.size(); i++) {
         par.splitsequence[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
     }

src/workflow/CreateIndex.cpp

@@ -82,9 +82,6 @@ int createlinindex(int argc, const char **argv, const Command& command) {
     for (size_t i = 0; i < par.extractorfs.size(); i++) {
         par.extractorfs[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
     }
-    for (size_t i = 0; i < par.translatenucs.size(); i++) {
-        par.translatenucs[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
-    }
     par.PARAM_COMPRESSED.addCategory(MMseqsParameter::COMMAND_EXPERT);
     par.PARAM_THREADS.removeCategory(MMseqsParameter::COMMAND_EXPERT);
     par.PARAM_V.removeCategory(MMseqsParameter::COMMAND_EXPERT);
@@ -131,9 +128,6 @@ int createindex(int argc, const char **argv, const Command& command) {
     for (size_t i = 0; i < par.splitsequence.size(); i++) {
         par.splitsequence[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
     }
-    for (size_t i = 0; i < par.translatenucs.size(); i++) {
-        par.translatenucs[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
-    }
     par.PARAM_COMPRESSED.addCategory(MMseqsParameter::COMMAND_EXPERT);
     par.PARAM_THREADS.removeCategory(MMseqsParameter::COMMAND_EXPERT);
     par.PARAM_V.removeCategory(MMseqsParameter::COMMAND_EXPERT);

src/workflow/EasyRbh.cpp

@@ -23,9 +23,6 @@ int easyrbh(int argc, const char **argv, const Command &command) {
     for (size_t i = 0; i < par.extractorfs.size(); i++){
         par.extractorfs[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
     }
-    for (size_t i = 0; i < par.translatenucs.size(); i++){
-        par.translatenucs[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
-    }
     for (size_t i = 0; i < par.result2profile.size(); i++){
         par.result2profile[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
     }

src/workflow/EasySearch.cpp

@@ -42,9 +42,6 @@ int doeasysearch(int argc, const char **argv, const Command &command, bool linse
     for (size_t i = 0; i < par.extractorfs.size(); i++){
         par.extractorfs[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
     }
-    for (size_t i = 0; i < par.translatenucs.size(); i++){
-        par.translatenucs[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
-    }
     for (size_t i = 0; i < par.splitsequence.size(); i++) {
         par.splitsequence[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
     }

src/workflow/Linsearch.cpp

@@ -40,9 +40,6 @@ int linsearch(int argc, const char **argv, const Command &command) {
     for (size_t i = 0; i < par.extractorfs.size(); i++) {
         par.extractorfs[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
     }
-    for (size_t i = 0; i < par.translatenucs.size(); i++) {
-        par.translatenucs[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
-    }
     par.PARAM_COMPRESSED.removeCategory(MMseqsParameter::COMMAND_EXPERT);
     par.PARAM_THREADS.removeCategory(MMseqsParameter::COMMAND_EXPERT);
     par.PARAM_V.removeCategory(MMseqsParameter::COMMAND_EXPERT);
@@ -143,7 +140,6 @@ int linsearch(int argc, const char **argv, const Command &command) {
         par.translate = 1;
         cmd.addVariable("ORF_PAR", par.createParameterString(par.extractorfs).c_str());
         cmd.addVariable("OFFSETALIGNMENT_PAR", par.createParameterString(par.offsetalignment).c_str());
-        cmd.addVariable("TRANSLATE_PAR", par.createParameterString(par.translatenucs).c_str());
         cmd.addVariable("SEARCH", program.c_str());
         program = std::string(tmpDir + "/translated_search.sh");
         FileUtil::writeFile(program, Linsearch::translated_search_sh, Linsearch::translated_search_sh_len);

src/workflow/Map.cpp

@@ -32,9 +32,6 @@ int map(int argc, const char **argv, const Command &command) {
     for (size_t i = 0; i < par.extractorfs.size(); i++){
         par.extractorfs[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
     }
-    for (size_t i = 0; i < par.translatenucs.size(); i++){
-        par.translatenucs[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
-    }
     par.PARAM_COMPRESSED.removeCategory(MMseqsParameter::COMMAND_EXPERT);
     par.PARAM_V.removeCategory(MMseqsParameter::COMMAND_EXPERT);
     par.PARAM_THREADS.removeCategory(MMseqsParameter::COMMAND_EXPERT);

src/workflow/Rbh.cpp

@@ -27,9 +27,6 @@ int rbh(int argc, const char **argv, const Command &command) {
     for (size_t i = 0; i < par.extractorfs.size(); i++){
         par.extractorfs[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
     }
-    for (size_t i = 0; i < par.translatenucs.size(); i++){
-        par.translatenucs[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
-    }
     for (size_t i = 0; i < par.splitsequence.size(); i++) {
         par.splitsequence[i]->addCategory(MMseqsParameter::COMMAND_EXPERT);
     }