#include "getlistcountcommand.h"
+//**********************************************************************************************************************
+vector<string> GetListCountCommand::setParameters(){
+ try {
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","otu",false,true, true); parameters.push_back(plist);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter parasort("sort", "Multiple", "name-otu", "otu", "", "", "","",false,false); parameters.push_back(parasort);
+ 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, "GetListCountCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string GetListCountCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The get.otulist command parameters are list, sort and label. list is required, unless you have a valid current list file.\n";
+ helpString += "The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n";
+ helpString += "The sort parameter allows you to select how you want the output displayed. Options are otu and name.\n";
+ helpString += "If otu is selected the output will be otu number followed by the list of names in that otu.\n";
+ helpString += "If name is selected the output will be a sequence name followed by its otu number.\n";
+ helpString += "The get.otulist command should be in the following format: get.otulist(list=yourlistFile, label=yourLabels).\n";
+ helpString += "Example get.otulist(list=amazon.fn.list, label=0.10).\n";
+ helpString += "The default value for label is all lines in your inputfile.\n";
+ helpString += "The get.otulist command outputs a .otu file for each distance you specify listing the bin number and the names of the sequences in that bin.\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, "GetListCountCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string GetListCountCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "otu") { pattern = "[filename],[tag],otu"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetListCountCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetListCountCommand::GetListCountCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["otu"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetListCountCommand", "GetListCountCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
GetListCountCommand::GetListCountCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
- labels.clear();
//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 AlignArray[] = {"list","label","outputdir","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
- string ranRead = globaldata->getListFile();
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["otu"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
it = parameters.find("list");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["list"] = inputDir + it->second; }
}
//check for required parameters
listfile = validParameter.validFile(parameters, "list", true);
- if ((listfile == "not found") && (globaldata->getListFile() == "")) { m->mothurOut("You must read a listfile before running the get.listcount command."); m->mothurOutEndLine(); abort = true; }
- else if ((listfile == "not found") && (globaldata->getListFile() != "")) { listfile = globaldata->getListFile(); }
+ 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("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
else if (listfile == "not open") { abort = true; }
- else { globaldata->setListFile(listfile); }
+ else { m->setListFile(listfile); }
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
+ sort = validParameter.validFile(parameters, "sort", false); if (sort == "not found") { sort = "otu"; }
+ if ((sort != "otu") && (sort != "name")) { m->mothurOut( sort + " is not a valid sort option. Options are otu and name. I will use otu."); m->mothurOutEndLine(); sort = "otu"; }
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
-
- //if the user has not specified any labels use the ones from read.otu
- if ((label == "") && (ranRead != "")) {
- allLines = globaldata->allLines;
- labels = globaldata->labels;
- }
}
}
catch(exception& e) {
}
//**********************************************************************************************************************
-void GetListCountCommand::help(){
- try {
- m->mothurOut("The get.listcount command can only be executed after a successful read.otu command of a listfile or providing a list file using the list parameter.\n");
- m->mothurOut("The get.listcount command parameters are list and label. No parameters are required.\n");
- m->mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n");
- m->mothurOut("The get.listcount command should be in the following format: get.listcount(list=yourlistFile, label=yourLabels).\n");
- m->mothurOut("Example get.listcount(list=amazon.fn.list, label=0.10).\n");
- m->mothurOut("The default value for label is all lines in your inputfile.\n");
- m->mothurOut("The get.listcount command outputs a .otu file for each distance you specify listing the bin number and the names of the sequences in that bin.\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, "GetListCountCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-GetListCountCommand::~GetListCountCommand(){}
-
-//**********************************************************************************************************************
-
int GetListCountCommand::execute(){
try {
- if (abort == true) { return 0; }
-
- globaldata->setFormat("list");
-
- //read list file
- read = new ReadOTUFile(listfile);
- read->read(&*globaldata);
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
- input = globaldata->ginput;
- list = globaldata->gListVector;
+ input = new InputData(listfile, "list");
+ list = input->getListVector();
string lastLabel = list->getLabel();
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
-
+
+ if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if(allLines == 1 || labels.count(list->getLabel()) == 1){
process(list);
+
+ if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
}
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
delete list;
list = input->getListVector(lastLabel);
process(list);
+
+ if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
if (list != NULL) { delete list; }
list = input->getListVector(lastLabel);
- process(list);
+ process(list);
+
+ if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
delete list;
}
- delete read;
- globaldata->gListVector = NULL;
+ delete input;
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
//return 1 if error, 0 otherwise
void GetListCountCommand::process(ListVector* list) {
try {
- string binnames, name, sequence;
- if (outputDir == "") { outputDir += hasPath(listfile); }
- string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + list->getLabel() + ".otu";
- openOutputFile(outputFileName, out);
- outputNames.push_back(outputFileName);
+ string binnames;
+ if (outputDir == "") { outputDir += m->hasPath(listfile); }
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[tag]"] = list->getLabel();
+ string outputFileName = getOutputFileName("otu", variables);
+
+ m->openOutputFile(outputFileName, out);
+ outputNames.push_back(outputFileName); outputTypes["otu"].push_back(outputFileName);
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
//for each bin in the list vector
for (int i = 0; i < list->getNumBins(); i++) {
+ if (m->control_pressed) { break; }
+
binnames = list->get(i);
- out << i+1 << '\t' << binnames << endl;
+
+ if (sort == "otu") {
+ out << i+1 << '\t' << binnames << endl;
+ }else{ //sort = name
+ vector<string> names;
+ m->splitAtComma(binnames, names);
+
+ for (int j = 0; j < names.size(); j++) {
+ out << names[j] << '\t' << i+1 << endl;
+ }
+ }
}
out.close();
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