X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=amovacommand.cpp;h=f1e5f61197475b43d52d7dac46dab04cc7f657c2;hb=0571957d68cbbc0e425af1db8e808f826010b9e2;hp=b9b5deeb5e670ef2f119eb09bded37ab870efe4d;hpb=7b287636ea67fb2254b119c21b4057a177d3ce19;p=mothur.git diff --git a/amovacommand.cpp b/amovacommand.cpp index b9b5dee..f1e5f61 100644 --- a/amovacommand.cpp +++ b/amovacommand.cpp @@ -11,56 +11,60 @@ #include "readphylipvector.h" #include "groupmap.h" + //********************************************************************************************************************** -vector AmovaCommand::getValidParameters(){ +vector AmovaCommand::setParameters(){ try { - string Array[] = {"outputdir","iters","phylip","design","alpha", "inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign); + CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip); + CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters); + CommandParameter palpha("alpha", "Number", "", "0.05", "", "", "",false,false); parameters.push_back(palpha); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } return myArray; } catch(exception& e) { - m->errorOut(e, "AmovaCommand", "getValidParameters"); - exit(1); - } -} -//********************************************************************************************************************** -AmovaCommand::AmovaCommand(){ - try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["amova"] = tempOutNames; - } - catch(exception& e) { - m->errorOut(e, "AmovaCommand", "AmovaCommand"); + m->errorOut(e, "AmovaCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -vector AmovaCommand::getRequiredParameters(){ +string AmovaCommand::getHelpString(){ try { - string Array[] = {"design"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; + string helpString = ""; + helpString += "Referenced: Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46."; + helpString += "The amova command outputs a .amova file."; + helpString += "The amova command parameters are phylip, iters, and alpha. The phylip and design parameters are required, unless you have valid current files."; + helpString += "The design parameter allows you to assign your samples to groups when you are running amova. It is required."; + helpString += "The design file looks like the group file. It is a 2 column tab delimited file, where the first column is the sample name and the second column is the group the sample belongs to."; + helpString += "The iters parameter allows you to set number of randomization for the P value. The default is 1000."; + helpString += "The amova command should be in the following format: amova(phylip=file.dist, design=file.design)."; + helpString += "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e. 1000)."; + return helpString; } catch(exception& e) { - m->errorOut(e, "AmovaCommand", "getRequiredParameters"); + m->errorOut(e, "AmovaCommand", "getHelpString"); exit(1); } } + //********************************************************************************************************************** -vector AmovaCommand::getRequiredFiles(){ +AmovaCommand::AmovaCommand(){ try { - string Array[] = {}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["amova"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "AmovaCommand", "getRequiredFiles"); + m->errorOut(e, "AmovaCommand", "AmovaCommand"); exit(1); } } //********************************************************************************************************************** - AmovaCommand::AmovaCommand(string option) { try { abort = false; calledHelp = false; @@ -69,9 +73,7 @@ AmovaCommand::AmovaCommand(string option) { if(option == "help") { help(); abort = true; calledHelp = true; } else { - //valid paramters for this command - string AlignArray[] = {"design","outputdir","iters","phylip","alpha", "inputdir"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -115,22 +117,21 @@ AmovaCommand::AmovaCommand(string option) { phylipFileName = validParameter.validFile(parameters, "phylip", true); if (phylipFileName == "not open") { phylipFileName = ""; abort = true; } - else if (phylipFileName == "not found") { phylipFileName = ""; } - else if (designFileName == "not found") { - designFileName = ""; - m->mothurOut("You must provide an phylip file."); - m->mothurOutEndLine(); - abort = true; + else if (phylipFileName == "not found") { + //if there is a current phylip file, use it + phylipFileName = m->getPhylipFile(); + if (phylipFileName != "") { m->mothurOut("Using " + phylipFileName + " as input file for the phylip parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; } } //check for required parameters designFileName = validParameter.validFile(parameters, "design", true); if (designFileName == "not open") { abort = true; } else if (designFileName == "not found") { - designFileName = ""; - m->mothurOut("You must provide an design file."); - m->mothurOutEndLine(); - abort = true; + //if there is a current design file, use it + designFileName = m->getDesignFile(); + if (designFileName != "") { m->mothurOut("Using " + designFileName + " as input file for the design parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current design file and the design parameter is required."); m->mothurOutEndLine(); abort = true; } } string temp = validParameter.validFile(parameters, "iters", false); @@ -147,30 +148,6 @@ AmovaCommand::AmovaCommand(string option) { exit(1); } } - -//********************************************************************************************************************** - -void AmovaCommand::help(){ - try { - m->mothurOut("Referenced: Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.\n"); - m->mothurOut("The amova command outputs a .amova file. \n"); - m->mothurOut("The amova command parameters are phylip, iters, and alpha. The phylip and design parameters are required.\n"); - m->mothurOut("The design parameter allows you to assign your samples to groups when you are running amova. It is required. \n"); - m->mothurOut("The design file looks like the group file. It is a 2 column tab delimited file, where the first column is the sample name and the second column is the group the sample belongs to.\n"); - m->mothurOut("The iters parameter allows you to set number of randomization for the P value. The default is 1000. \n"); - m->mothurOut("The amova command should be in the following format: amova(phylip=file.dist, design=file.design).\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e. 1000).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "AmovaCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - -AmovaCommand::~AmovaCommand(){} - //********************************************************************************************************************** int AmovaCommand::execute(){