--- /dev/null
+/*
+ * getlistcountcommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 10/12/09.
+ * Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "getlistcountcommand.h"
+
+//**********************************************************************************************************************
+GetListCountCommand::GetListCountCommand(string option){
+ try {
+ globaldata = GlobalData::getInstance();
+ abort = false;
+ allLines = 1;
+ labels.clear();
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string AlignArray[] = {"list","label"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/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; }
+ }
+
+ string ranRead = globaldata->getListFile();
+
+ //check for required parameters
+ listfile = validParameter.validFile(parameters, "list", true);
+ if ((listfile == "not found") && (globaldata->getListFile() == "")) { mothurOut("You must read a listfile before running the get.listcount command."); mothurOutEndLine(); abort = true; }
+ else if ((listfile == "not found") && (globaldata->getListFile() != "")) { listfile = globaldata->getListFile(); }
+ else if (listfile == "not open") { abort = true; }
+ else { globaldata->setListFile(listfile); }
+
+ //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") { label = ""; }
+ else {
+ if(label != "all") { 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) {
+ errorOut(e, "GetListCountCommand", "GetListCountCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void GetListCountCommand::help(){
+ try {
+ 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");
+ mothurOut("The get.listcount command parameters are list and label. No parameters are required.\n");
+ 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");
+ mothurOut("The get.listcount command should be in the following format: get.listcount(list=yourlistFile, label=yourLabels).\n");
+ mothurOut("Example get.listcount(list=amazon.fn.list, label=0.10).\n");
+ mothurOut("The default value for label is all lines in your inputfile.\n");
+ 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");
+ mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n");
+ }
+ catch(exception& e) {
+ 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);
+
+ input = globaldata->ginput;
+ list = globaldata->gListVector;
+ 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;
+
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if(allLines == 1 || labels.count(list->getLabel()) == 1){
+
+ process(list);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ }
+
+ if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete list;
+ list = input->getListVector(lastLabel);
+
+ process(list);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ }
+
+ lastLabel = list->getLabel();
+
+ delete list;
+ list = input->getListVector();
+ }
+
+
+ //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; }
+ list = input->getListVector(lastLabel);
+
+ process(list);
+ delete list;
+ }
+
+ delete read;
+ globaldata->gListVector = NULL;
+
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "GetListCountCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+//return 1 if error, 0 otherwise
+void GetListCountCommand::process(ListVector* list) {
+ try {
+ string binnames, name, sequence;
+ string outputFileName = getRootName(listfile) + list->getLabel() + ".otu";
+ openOutputFile(outputFileName, out);
+
+ mothurOut(list->getLabel()); mothurOutEndLine();
+
+ //for each bin in the list vector
+ for (int i = 0; i < list->getNumBins(); i++) {
+ binnames = list->get(i);
+ out << i+1 << '\t' << binnames << endl;
+ }
+
+ out.close();
+ }
+ catch(exception& e) {
+ errorOut(e, "GetListCountCommand", "process");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
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