X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=anosimcommand.cpp;h=2a688f59b72c4ba9779ea921149254b3e554b788;hp=79064a4bf6731cfcd1604f2a2c8d28f42e501b13;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=348de0f8b17d84ede77081dcf67bd6ef43496677 diff --git a/anosimcommand.cpp b/anosimcommand.cpp index 79064a4..2a688f5 100644 --- a/anosimcommand.cpp +++ b/anosimcommand.cpp @@ -12,50 +12,68 @@ #include "readphylipvector.h" //********************************************************************************************************************** -vector AnosimCommand::getValidParameters(){ +vector AnosimCommand::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","anosim",false,true,true); parameters.push_back(pdesign); + CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","anosim",false,true,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, "AnosimCommand", "getValidParameters"); + m->errorOut(e, "AnosimCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -AnosimCommand::AnosimCommand(){ +string AnosimCommand::getHelpString(){ try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["anosim"] = tempOutNames; + string helpString = ""; + helpString += "Referenced: Clarke, K. R. (1993). Non-parametric multivariate analysis of changes in community structure. _Australian Journal of Ecology_ 18, 117-143.\n"; + helpString += "The anosim command outputs a .anosim file. \n"; + helpString += "The anosim command parameters are phylip, iters, and alpha. The phylip and design parameters are required, unless you have valid current files.\n"; + helpString += "The design parameter allows you to assign your samples to groups when you are running anosim. It is required. \n"; + 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.\n"; + helpString += "The iters parameter allows you to set number of randomization for the P value. The default is 1000. \n"; + helpString += "The anosim command should be in the following format: anosim(phylip=file.dist, design=file.design).\n"; + helpString += "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e. 1000).\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "AnosimCommand", "AnosimCommand"); + m->errorOut(e, "AnosimCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector AnosimCommand::getRequiredParameters(){ - try { - string Array[] = {"design"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "AnosimCommand", "getRequiredParameters"); - exit(1); - } +string AnosimCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "anosim") { pattern = "[filename],anosim"; } //makes file like: amazon.align + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "AnosimCommand", "getOutputPattern"); + exit(1); + } } //********************************************************************************************************************** -vector AnosimCommand::getRequiredFiles(){ +AnosimCommand::AnosimCommand(){ try { - string Array[] = {}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["anosim"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "AnosimCommand", "getRequiredFiles"); + m->errorOut(e, "AnosimCommand", "AnosimCommand"); exit(1); } } @@ -67,11 +85,10 @@ AnosimCommand::AnosimCommand(string option) { //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string AlignArray[] = {"outputdir","iters","phylip","design", "alpha","inputdir"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -116,23 +133,30 @@ AnosimCommand::AnosimCommand(string option) { phylipFileName = validParameter.validFile(parameters, "phylip", true); if (phylipFileName == "not open") { phylipFileName = ""; abort = true; } else if (phylipFileName == "not found") { - phylipFileName = ""; - } + //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; } + + }else { m->setPhylipFile(phylipFileName); } //check for required parameters designFileName = validParameter.validFile(parameters, "design", true); - if (designFileName == "not open") { abort = true; } + if (designFileName == "not open") { designFileName = ""; abort = true; } else if (designFileName == "not found") { - designFileName = ""; - } + //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; } + }else { m->setDesignFile(designFileName); } string temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } - convert(temp, iters); + m->mothurConvert(temp, iters); temp = validParameter.validFile(parameters, "alpha", false); if (temp == "not found") { temp = "0.05"; } - convert(temp, experimentwiseAlpha); + m->mothurConvert(temp, experimentwiseAlpha); } } @@ -141,33 +165,7 @@ AnosimCommand::AnosimCommand(string option) { exit(1); } } - //********************************************************************************************************************** - -void AnosimCommand::help(){ - try { - m->mothurOut("Referenced: Clarke, K. R. (1993). Non-parametric multivariate analysis of changes in community structure. _Australian Journal of Ecology_ 18, 117-143.\n"); - m->mothurOut("The anosim command outputs a .anosim file. \n"); - m->mothurOut("The anosim 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 anosim. 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 anosim command should be in the following format: anosim(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, "AnosimCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - -AnosimCommand::~AnosimCommand(){} - -//********************************************************************************************************************** - int AnosimCommand::execute(){ try { @@ -192,13 +190,21 @@ int AnosimCommand::execute(){ //link designMap to rows/columns in distance matrix map > origGroupSampleMap; for(int i=0;igetGroup(sampleNames[i])].push_back(i); + string group = designMap->getGroup(sampleNames[i]); + + if (group == "not found") { + m->mothurOut("[ERROR]: " + sampleNames[i] + " is not in your design file, please correct."); m->mothurOutEndLine(); m->control_pressed = true; + }else { origGroupSampleMap[group].push_back(i); } } int numGroups = origGroupSampleMap.size(); + if (m->control_pressed) { delete designMap; return 0; } + //create a new filename ofstream ANOSIMFile; - string ANOSIMFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName)) + "anosim"; + map variables; variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipFileName)); + string ANOSIMFileName = getOutputFileName("anosim", variables); + m->openOutputFile(ANOSIMFileName, ANOSIMFile); outputNames.push_back(ANOSIMFileName); outputTypes["anosim"].push_back(ANOSIMFileName); m->mothurOut("\ncomparison\tR-value\tP-value\n");