From 5e8c9db58fc4f23d02b5a34c406a9a6fbda6267e Mon Sep 17 00:00:00 2001 From: Cameron Gilchrist Date: Tue, 5 Mar 2024 16:45:26 +0900 Subject: [PATCH] Remove guide tree from easy-msa msa2lddt arguments --- src/workflow/EasyMSA.cpp | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/src/workflow/EasyMSA.cpp b/src/workflow/EasyMSA.cpp index 087f00d..78199dc 100644 --- a/src/workflow/EasyMSA.cpp +++ b/src/workflow/EasyMSA.cpp @@ -96,19 +96,18 @@ int easymsa(int argc, const char **argv, const Command &command) { cmd.addVariable("CREATEDB_PAR", par.createParameterString(par.structurecreatedb).c_str()); // needs to be last - std::vector msa2lddtWithoutHtml; + std::vector msa2lddtWithoutTree; par.PARAM_GAP_OPEN.wasSet = true; par.PARAM_GAP_EXTEND.wasSet = true; par.PARAM_MATCH_RATIO.wasSet = true; par.PARAM_FILTER_MSA.wasSet = true; par.reportCommand = par.createParameterString(par.easymsaworkflow, true); - // for (size_t i = 0; i < par.msa2lddt.size(); i++) { - // if (par.msa2lddt[i]->uniqid != par.PARAM_LDDT_HTML.uniqid && - // par.msa2lddt[i]->uniqid != par.PARAM_GUIDE_TREE.uniqid) { - // msa2lddtWithoutHtml.push_back(par.msa2lddt[i]); - // } - // } - // cmd.addVariable("MSA2LDDT_PAR", par.createParameterString(msa2lddtWithoutHtml).c_str()); + for (size_t i = 0; i < par.msa2lddt.size(); i++) { + if (par.msa2lddt[i]->uniqid != par.PARAM_GUIDE_TREE.uniqid) { + msa2lddtWithoutTree.push_back(par.msa2lddt[i]); + } + } + cmd.addVariable("MSA2LDDT_PAR", par.createParameterString(msa2lddtWithoutTree).c_str()); std::string program = tmpDir + "/easymsa.sh"; FileUtil::writeFile(program, easymsa_sh, easymsa_sh_len);