X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlistcountcommand.cpp;fp=getlistcountcommand.cpp;h=f14e17a951eec96494dd36a87d259f6117cc758c;hb=c4fb347858dd8cfea4d2933f429fff4130dca65b;hp=0000000000000000000000000000000000000000;hpb=58cc09a375d1e1afceef3b036574ff21394ccc4d;p=mothur.git

diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp
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+++ b/getlistcountcommand.cpp
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+/*
+ *  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);
+	}
+}
+//**********************************************************************************************************************
+
+