--- /dev/null
+/*
+ * otuhierarchycommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 1/19/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "otuhierarchycommand.h"
+
+//**********************************************************************************************************************
+vector<string> OtuHierarchyCommand::setParameters(){
+ try {
+ 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; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ 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 (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { 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; }
+ 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"){
+ 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") { m->mothurOut("label is a required parameter for the otu.hierarchy command."); m->mothurOutEndLine(); abort = true; }
+ else {
+ 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) {
+ m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int OtuHierarchyCommand::execute(){
+ try {
+
+ 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
+ if (lists[0].getNumBins() < lists[1].getNumBins()) {
+ reverse(lists.begin(), lists.end());
+ }
+ }else{
+ 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
+ while (names.find_first_of(',') != -1) {
+ string name = names.substr(0,names.find_first_of(','));
+ names = names.substr(names.find_first_of(',')+1, names.length());
+ littleBins[name] = i;
+ }
+
+ //get last name
+ littleBins[names] = i;
+ }
+
+ ofstream 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(); m->mothurRemove(outputFileName); return 0; }
+
+ string names = lists[1].get(i);
+
+ //output column 1
+ 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;
+
+ //parse bin
+ while (names.find_first_of(',') != -1) {
+ string name = names.substr(0,names.find_first_of(','));
+ names = names.substr(names.find_first_of(',')+1, names.length());
+ bins[littleBins[name]] = littleBins[name];
+ }
+
+ //get last name
+ bins[littleBins[names]] = littleBins[names];
+
+ string col2 = "";
+ for (it = bins.begin(); it != bins.end(); it++) {
+ if (output == "name") { col2 += lists[0].get(it->first) + "\t"; }
+ else { col2 += toString(it->first) + "\t"; }
+ }
+
+ //output column 2
+ out << col2 << endl;
+ }
+
+ out.close();
+
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); 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) {
+ m->errorOut(e, "OtuHierarchyCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+//returns a vector of listVectors where "little" vector is first
+vector<ListVector> OtuHierarchyCommand::getListVectors() {
+ try {
+
+ int pos; //to use in smart distancing, position of last read in file
+ int lastPos;
+ vector<ListVector> lists;
+
+ //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;
+
+ //open file
+ ifstream in;
+ m->openInputFile(listFile, in);
+
+ //get first list vector in file
+ ListVector* list = NULL;
+ string lastLabel = "";
+ if (!in.eof()) {
+ pos = in.tellg();
+ lastPos = pos;
+ list = new ListVector(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){
+
+ //make copy of listvector
+ ListVector temp(*list);
+ lists.push_back(temp);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ }
+
+ //you have a label the user want that is smaller than this label and the last label has not already been processed
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+ int savePos = in.tellg();
+
+ //get smart distance line
+ delete list;
+ in.seekg(lastPos);
+ if (!in.eof()) {
+ list = new ListVector(in);
+ }else { list = NULL; }
+
+ //make copy of listvector
+ ListVector temp(*list);
+ lists.push_back(temp);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
+ in.seekg(savePos);
+ }
+
+ lastLabel = list->getLabel();
+ lastPos = pos;
+
+ //get next line
+ delete list;
+ if (!in.eof()) {
+ pos = in.tellg();
+ list = new ListVector(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++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ 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.seekg(lastPos);
+ if (!in.eof()) {
+ list = new ListVector(in);
+
+ //make copy of listvector
+ ListVector temp(*list);
+ lists.push_back(temp);
+
+ delete list;
+ }
+ }
+
+ in.close();
+ return lists;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OtuHierarchyCommand", "getListVectors");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+
+
+
+
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