#include "otuhierarchycommand.h"
//**********************************************************************************************************************
-vector<string> OtuHierarchyCommand::getValidParameters(){
+vector<string> OtuHierarchyCommand::setParameters(){
try {
- string Array[] = {"list","label","output","outputdir","inputdir"};
- vector<string> 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","otuheirarchy",false,true,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<string> 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 {
- abort = true; calledHelp = true;
- vector<string> 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");
+ m->errorOut(e, "OtuHierarchyCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> OtuHierarchyCommand::getRequiredParameters(){
- try {
- string Array[] = {"list","label"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "OtuHierarchyCommand", "getRequiredParameters");
- exit(1);
- }
+string OtuHierarchyCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "otuheirarchy") { pattern = "[filename],[distance1],[tag],[distance2],otu.hierarchy"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OtuHierarchyCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
-vector<string> OtuHierarchyCommand::getRequiredFiles(){
+OtuHierarchyCommand::OtuHierarchyCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["otuheirarchy"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "OtuHierarchyCommand", "getRequiredFiles");
+ m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand");
exit(1);
}
}
//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 Array[] = {"list","label","output","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
}
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"){
}
//**********************************************************************************************************************
-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 {
}
ofstream out;
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listFile));
+ variables["[distance1]"] = lists[0].getLabel();
+ variables["[tag]"] = "-";
+ variables["[distance2]"] = lists[1].getLabel();
+ string outputFileName = getOutputFileName("otuheirarchy",variables);
m->openOutputFile(outputFileName, out);
//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);
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();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["otuheirarchy"].push_back(outputFileName);
m->mothurOutEndLine();
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