+/*
+ * otuhierarchycommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 1/19/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "otuhierarchycommand.h"
+
+//**********************************************************************************************************************
+OtuHierarchyCommand::OtuHierarchyCommand(string option){
+ try {
+ abort = false;
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"list","label"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator 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; }
+
+
+ //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; }
+ else {
+ splitAtDash(label, labels);
+ if (labels.size() != 2) { mothurOut("You must provide 2 labels."); mothurOutEndLine(); abort = true; }
+ }
+ }
+
+ }
+ catch(exception& e) {
+ 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; }
+
+ //get listvectors that correspond to labels requested, (or use smart distancing to get closest listvector)
+ vector<ListVector> lists = getListVectors();
+
+ //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{
+ mothurOut("error getting listvectors, unable to read 2 different vectors, check your label inputs."); 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++) {
+ 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 = getRootName(listFile) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
+ 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++) {
+
+ string names = lists[1].get(i);
+
+ //output column 1
+ out << names << '\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++) {
+ col2 += lists[0].get(it->first) + "\t";
+ }
+
+ //output column 2
+ out << col2 << endl;
+ }
+
+ out.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ 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;
+ 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);
+ gobble(in);
+ lastLabel = list->getLabel();
+ }
+
+ while ((list != NULL) && (userLabels.size() != 0)) {
+
+ //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 ((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);
+ gobble(in);
+ }else { list = NULL; }
+ }
+
+
+
+ //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);
+ if (processedLabels.count(lastLabel) != 1) {
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ needToRun = true;
+ }else {
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ }
+ }
+
+ //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;
+ }
+ }
+
+
+ return lists;
+ }
+ catch(exception& e) {
+ errorOut(e, "OtuHierarchyCommand", "getListVectors");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+
+
+
+