#include "otuhierarchycommand.h"
//**********************************************************************************************************************
-OtuHierarchyCommand::OtuHierarchyCommand(string option){
+vector<string> OtuHierarchyCommand::setParameters(){
try {
- abort = false;
+ 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<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", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string OtuHierarchyCommand::getHelpString(){
+ try {
+ 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", "getHelpString");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+OtuHierarchyCommand::OtuHierarchyCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["otuheirarchy"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+OtuHierarchyCommand::OtuHierarchyCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = {"list","label"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
+ map<string,string>::iterator it;
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
- listFile = validParameter.validFile(parameters, "list", true);
- if (listFile == "not found") { mothurOut("list is a required parameter for the otu.hierarchy command."); mothurOutEndLine(); abort = true; }
- else if (listFile == "not open") { abort = true; }
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["otuheirarchy"] = 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);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("list");
+ //user has given a template file
+ if(it != parameters.end()){
+ 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; }
+ }
+ }
+ listFile = validParameter.validFile(parameters, "list", 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; }
+
+ //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"){
+ outputDir = "";
+ outputDir += m->hasPath(listFile); //if user entered a file with a path then preserve it
+ }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.validFile(parameters, "label", false);
- if (label == "not found") { mothurOut("label is a required parameter for the otu.hierarchy command."); mothurOutEndLine(); abort = true; }
+ if (label == "not found") { m->mothurOut("label is a required parameter for the otu.hierarchy command."); m->mothurOutEndLine(); abort = true; }
else {
- splitAtDash(label, labels);
- if (labels.size() != 2) { mothurOut("You must provide 2 labels."); mothurOutEndLine(); abort = true; }
- }
+ m->splitAtDash(label, labels);
+ if (labels.size() != 2) { m->mothurOut("You must provide 2 labels."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ output = validParameter.validFile(parameters, "output", false); if (output == "not found") { output = "name"; }
+
+ if ((output != "name") && (output != "number")) { m->mothurOut("output options are name and number. I will use name."); m->mothurOutEndLine(); output = "name"; }
}
}
catch(exception& e) {
- errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand");
+ m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand");
exit(1);
}
}
//**********************************************************************************************************************
-void OtuHierarchyCommand::help(){
- try {
- mothurOut("The otu.hierarchy command is used to see how otus relate at two distances. \n");
- mothurOut("The otu.hierarchy command parameters are list and label. Both parameters are required. \n");
- mothurOut("The otu.hierarchy command should be in the following format: \n");
- mothurOut("otu.hierarchy(list=yourListFile, label=yourLabels).\n");
- mothurOut("Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n");
- mothurOut("The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\n");
- mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n");
- }
- catch(exception& e) {
- 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<ListVector> lists = getListVectors();
+ if (m->control_pressed) { outputTypes.clear(); return 0; }
+
//determine which is little and which is big, putting little first
if (lists.size() == 2) {
//if big is first swap them
reverse(lists.begin(), lists.end());
}
}else{
- mothurOut("error getting listvectors, unable to read 2 different vectors, check your label inputs."); mothurOutEndLine(); return 0;
+ m->mothurOut("error getting listvectors, unable to read 2 different vectors, check your label inputs."); m->mothurOutEndLine(); return 0;
}
//map sequences to bin number in the "little" otu
map<string, int> littleBins;
for (int i = 0; i < lists[0].getNumBins(); i++) {
+
+ if (m->control_pressed) { return 0; }
+
string names = lists[0].get(i);
//parse bin
}
ofstream out;
- string outputFileName = getRootName(listFile) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
- openOutputFile(outputFileName, out);
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
+ 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; }
+
string names = lists[1].get(i);
//output column 1
- out << names << '\t';
+ if (output == "name") { out << names << '\t'; }
+ else { out << i << '\t'; }
map<int, int> bins; //bin numbers in little that are in this bin in big
map<int, int>::iterator it;
string col2 = "";
for (it = bins.begin(); it != bins.end(); it++) {
- col2 += lists[0].get(it->first) + "\t";
+ if (output == "name") { col2 += lists[0].get(it->first) + "\t"; }
+ else { col2 += toString(it->first) + "\t"; }
}
//output column 2
out.close();
+ if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["otuheirarchy"].push_back(outputFileName);
+ m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
- errorOut(e, "OtuHierarchyCommand", "execute");
+ m->errorOut(e, "OtuHierarchyCommand", "execute");
exit(1);
}
}
//open file
ifstream in;
- openInputFile(listFile, in);
+ m->openInputFile(listFile, in);
//get first list vector in file
ListVector* list = NULL;
pos = in.tellg();
lastPos = pos;
list = new ListVector(in);
- gobble(in);
+ m->gobble(in);
lastLabel = list->getLabel();
}
while ((list != NULL) && (userLabels.size() != 0)) {
+
+ if (m->control_pressed) { in.close(); delete list; return lists; }
//is this a listvector that we want?
if(labels.count(list->getLabel()) == 1){
}
//you have a label the user want that is smaller than this label and the last label has not already been processed
- 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();
int savePos = in.tellg();
if (!in.eof()) {
pos = in.tellg();
list = new ListVector(in);
- gobble(in);
+ m->gobble(in);
}else { list = NULL; }
}
-
+ if (m->control_pressed) { in.close(); return lists; }
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- mothurOut("Your file does not include the label " + *it);
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
+ if (m->control_pressed) { in.close(); return lists; }
+
//run last label if you need to
if (needToRun == true) {
if (list != NULL) { delete list; }
}
}
-
+ in.close();
return lists;
}
catch(exception& e) {
- errorOut(e, "OtuHierarchyCommand", "getListVectors");
+ m->errorOut(e, "OtuHierarchyCommand", "getListVectors");
exit(1);
}
}