X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=otuhierarchycommand.cpp;h=2f99aa6091452933f6796f21aa043449bfce1dd4;hb=a6cf29fa4dac0909c7582cb1094151d34093ee76;hp=022ff3af04dcc23933b05f4b7a76d3131db20ac2;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp index 022ff3a..2f99aa6 100644 --- a/otuhierarchycommand.cpp +++ b/otuhierarchycommand.cpp @@ -10,64 +10,67 @@ #include "otuhierarchycommand.h" //********************************************************************************************************************** -vector OtuHierarchyCommand::getValidParameters(){ +vector OtuHierarchyCommand::setParameters(){ try { - string Array[] = {"list","label","output","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + CommandParameter poutput("output", "Multiple", "name-number", "name", "", "", "",false,false); parameters.push_back(poutput); + CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist); + CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); + 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, "OtuHierarchyCommand", "getValidParameters"); + m->errorOut(e, "OtuHierarchyCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -OtuHierarchyCommand::OtuHierarchyCommand(){ +string OtuHierarchyCommand::getHelpString(){ try { - //initialize outputTypes - vector tempOutNames; - outputTypes["otuheirarchy"] = tempOutNames; + string helpString = ""; + helpString += "The otu.hierarchy command is used to see how otus relate at two distances. \n"; + helpString += "The otu.hierarchy command parameters are list, label and output. list and label parameters are required. \n"; + helpString += "The output parameter allows you to output the names of the sequence in the OTUs or the OTU numbers. Options are name and number, default is name. \n"; + helpString += "The otu.hierarchy command should be in the following format: \n"; + helpString += "otu.hierarchy(list=yourListFile, label=yourLabels).\n"; + helpString += "Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n"; + helpString += "The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\n"; + helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand"); - exit(1); - } -} -//********************************************************************************************************************** -vector OtuHierarchyCommand::getRequiredParameters(){ - try { - string Array[] = {"list","label"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "OtuHierarchyCommand", "getRequiredParameters"); + m->errorOut(e, "OtuHierarchyCommand", "getHelpString"); exit(1); } } + //********************************************************************************************************************** -vector OtuHierarchyCommand::getRequiredFiles(){ +OtuHierarchyCommand::OtuHierarchyCommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["otuheirarchy"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "OtuHierarchyCommand", "getRequiredFiles"); + m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand"); exit(1); } } //********************************************************************************************************************** OtuHierarchyCommand::OtuHierarchyCommand(string option) { try { - abort = false; + abort = false; calledHelp = false; //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string Array[] = {"list","label","output","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -99,8 +102,15 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) { } listFile = validParameter.validFile(parameters, "list", true); - if (listFile == "not found") { m->mothurOut("list is a required parameter for the otu.hierarchy command."); m->mothurOutEndLine(); abort = true; } - else if (listFile == "not open") { abort = true; } + if (listFile == "not found") { + listFile = m->getListFile(); + if (listFile != "") { m->mothurOut("Using " + listFile + " as input file for the list parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine(); + abort = true; + } + }else if (listFile == "not open") { abort = true; } + else { m->setListFile(listFile); } //if the user changes the output directory command factory will send this info to us in the output parameter outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ @@ -130,33 +140,10 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) { } //********************************************************************************************************************** -void OtuHierarchyCommand::help(){ - try { - m->mothurOut("The otu.hierarchy command is used to see how otus relate at two distances. \n"); - m->mothurOut("The otu.hierarchy command parameters are list, label and output. list and label parameters are required. \n"); - m->mothurOut("The output parameter allows you to output the names of the sequence in the OTUs or the OTU numbers. Options are name and number, default is name. \n"); - m->mothurOut("The otu.hierarchy command should be in the following format: \n"); - m->mothurOut("otu.hierarchy(list=yourListFile, label=yourLabels).\n"); - m->mothurOut("Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n"); - m->mothurOut("The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "OtuHierarchyCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - -OtuHierarchyCommand::~OtuHierarchyCommand(){} - -//********************************************************************************************************************** - int OtuHierarchyCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } //get listvectors that correspond to labels requested, (or use smart distancing to get closest listvector) vector lists = getListVectors(); @@ -199,7 +186,7 @@ int OtuHierarchyCommand::execute(){ //go through each bin in "big" otu and output the bins in "little" otu which created it for (int i = 0; i < lists[1].getNumBins(); i++) { - if (m->control_pressed) { outputTypes.clear(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; } string names = lists[1].get(i); @@ -232,7 +219,7 @@ int OtuHierarchyCommand::execute(){ out.close(); - if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0; } m->mothurOutEndLine(); m->mothurOut("Output File Name: "); m->mothurOutEndLine();