--- /dev/null
+/*
+ * sensspeccommand.cpp
+ * Mothur
+ *
+ * Created by Pat Schloss on 7/6/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "sensspeccommand.h"
+
+//***************************************************************************************************************
+
+SensSpecCommand::SensSpecCommand(string option) {
+ try {
+
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ string temp;
+
+ //valid paramters for this command
+ string AlignArray[] = {"list", "phylip", "column", "name", "hard", "label", "cutoff", "outputdir", "inputdir"};
+
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+
+ 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; }
+ }
+
+ //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 = 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; }
+ }
+
+ it = parameters.find("phylip");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["phylip"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("column");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["column"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+
+ }
+ //check for required parameters
+ listFile = validParameter.validFile(parameters, "list", true);
+ if (listFile == "not found") { m->mothurOut("list is a required parameter for the sens.spec command."); m->mothurOutEndLine(); abort = true; }
+ else if (listFile == "not open") { abort = true; }
+
+ distFile = validParameter.validFile(parameters, "column", true);
+ format = "column";
+ if(distFile == "not found") {
+ distFile = validParameter.validFile(parameters, "phylip", true);
+ format = "phylip";
+ }
+ if(distFile == "not found") { m->mothurOut("either column or phylip are required for the sens.spec command."); m->mothurOutEndLine(); abort = true; }
+ else if (distFile == "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 += 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...
+ temp = validParameter.validFile(parameters, "hard", false);
+ if (temp == "not found"){ hard = 0; }
+ else if(!isTrue(temp)) { hard = 0; }
+ else if(isTrue(temp)) { hard = 1; }
+
+// temp = validParameter.validFile(parameters, "name", true);
+// if (temp == "not found") { nameFile = ""; }
+// else if(temp == "not open") { abort = true; }
+// else { nameFile = temp; }
+// cout << "name:\t" << nameFile << endl;
+
+ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = ""; }
+ convert(temp, cutoff);
+ cout << "cutoff:\t" << cutoff << endl;
+
+// cutoff = 0.0349;
+
+ lineLabel = validParameter.validFile(parameters, "label", false); if (lineLabel == "not found") { lineLabel = ""; }
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SensSpecCommand", "SensSpecCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void SensSpecCommand::help(){
+ try {
+ m->mothurOut("The sens.spec command reads a fastaFile and creates .....\n");
+
+
+
+ m->mothurOut("Example sens.spec(...).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
+ m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SensSpecCommand", "help");
+ exit(1);
+ }
+}
+
+
+//***************************************************************************************************************
+
+SensSpecCommand::~SensSpecCommand(){ /* do nothing */ }
+
+//***************************************************************************************************************
+
+int SensSpecCommand::execute(){
+ try{
+ if (abort == true) { return 0; }
+
+ if(format == "phylip") { processPhylip(); }
+// else if(format == "column") { processColumn(seqMap); }
+
+
+// string seqList;
+// map<string, int> seqMap;
+
+
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SensSpecCommand", "execute");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+
+void SensSpecCommand::processPhylip(){
+ try{
+ ifstream inputListFile;
+ openInputFile(listFile, inputListFile);
+
+ string label;
+ int numOTUs;
+
+ map<string, int> seqMap;
+ string seqList;
+
+ while(inputListFile){
+ inputListFile >> label >> numOTUs;
+ for(int i=0;i<numOTUs;i++){
+ inputListFile >> seqList;
+ int seqListLength = seqList.length();
+ string seqName = "";
+ for(int j=0;j<seqListLength;j++){
+
+ if(seqList[j] == ','){
+ seqMap[seqName] = i;
+ seqName = "";
+ }
+ else{
+ seqName += seqList[j];
+ }
+
+ }
+ seqMap[seqName] = i;
+ }
+ }
+ inputListFile.close();
+
+ int lNumSeqs = seqMap.size();
+ int pNumSeqs = 0;
+
+ ifstream phylipFile;
+ openInputFile(distFile, phylipFile);
+ phylipFile >> pNumSeqs;
+ if(pNumSeqs != lNumSeqs){ cout << "numSeq mismatch!" << endl; }
+
+ string seqName;
+ double distance;
+ vector<int> otuIndices(lNumSeqs, -1);
+
+ truePositives = 0;
+ falsePositives = 0;
+ trueNegatives = 0;
+ falseNegatives = 0;
+
+
+ for(int i=0;i<lNumSeqs;i++){
+ phylipFile >> seqName;
+ otuIndices[i] = seqMap[seqName];
+
+ for(int j=0;j<i;j++){
+ phylipFile >> distance;
+ if(distance <= cutoff){
+ if(otuIndices[i] == otuIndices[j]){
+ truePositives++;
+ }
+ else{
+ falseNegatives++;
+ }
+ }
+ else{
+ if(otuIndices[i] == otuIndices[j]){
+ falsePositives++;
+ }
+ else{
+ trueNegatives++;
+ }
+ }
+ }
+ }
+ phylipFile.close();
+
+ cout << "truePositives:\t" << truePositives << endl;
+ cout << "trueNegatives:\t" << trueNegatives << endl;
+ cout << "falsePositives:\t" << falsePositives << endl;
+ cout << "falseNegatives:\t" << falseNegatives << endl;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SensSpecCommand", "processPhylip");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+
+//void SensSpecCommand::processColumn(map<string, int> seqMap){
+//
+// truePositives = 0;
+// falsePositives = 0;
+// trueNegatives = numDists;
+// falseNegatives = 0;
+//
+// ifstream columnFile;
+// openInputFile(distFile, columnFile);
+//
+// string seqNameA, seqNameB, oldSeqNameA;
+// int otuA, otuB, oldOTUA;
+// double distance;
+//
+// while(columnFile){
+// columnFile >> seqNameA >> seqNameB >> distance;
+//
+// if(seqNameA == oldSeqNameA) { otuA = oldOTUA; }
+// else { otuA = seqMap[seqNameA]; oldOTUA = otuA; }
+//
+// otuB = seqMap[seqNameB];
+//
+// if(distance <= cutoff){
+// if(otuA == otuB){
+// truePositives++;
+// }
+// else{
+// falseNegatives++;
+// }
+// trueNegatives--;
+// }
+// else{
+// if(otuA == otuB){
+// falsePositives++;
+// trueNegatives--;
+// }
+// }
+//
+// gobble(columnFile);
+// }
+// columnFile.close();
+//
+// cout << "truePositives:\t" << truePositives << endl;
+// cout << "trueNegatives:\t" << trueNegatives << endl;
+// cout << "falsePositives:\t" << falsePositives << endl;
+// cout << "falseNegatives:\t" << falseNegatives << endl;
+//}
+
+//***************************************************************************************************************
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