2 * matrixoutputcommand.cpp
5 * Created by Sarah Westcott on 5/20/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "matrixoutputcommand.h"
11 #include "sharedjabund.h"
12 #include "sharedsorabund.h"
13 #include "sharedjclass.h"
14 #include "sharedsorclass.h"
15 #include "sharedjest.h"
16 #include "sharedsorest.h"
17 #include "sharedthetayc.h"
18 #include "sharedthetan.h"
19 #include "sharedmorisitahorn.h"
20 #include "sharedbraycurtis.h"
23 //**********************************************************************************************************************
25 MatrixOutputCommand::MatrixOutputCommand(string option) {
27 globaldata = GlobalData::getInstance();
34 //allow user to run help
35 if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
38 //valid paramters for this command
39 string Array[] = {"label","calc","groups","outputdir","inputdir", "output"};
40 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
42 OptionParser parser(option);
43 map<string,string> parameters = parser.getParameters();
45 ValidParameters validParameter;
47 //check to make sure all parameters are valid for command
48 for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
49 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
52 //if the user changes the output directory command factory will send this info to us in the output parameter
53 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
55 outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
58 //make sure the user has already run the read.otu command
59 if (globaldata->getSharedFile() == "") {
60 if (globaldata->getListFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the dist.shared command."); m->mothurOutEndLine(); abort = true; }
61 else if (globaldata->getGroupFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the dist.shared command."); m->mothurOutEndLine(); abort = true; }
64 //check for optional parameter and set defaults
65 // ...at some point should added some additional type checking...
66 label = validParameter.validFile(parameters, "label", false);
67 if (label == "not found") { label = ""; }
69 if(label != "all") { splitAtDash(label, labels); allLines = 0; }
70 else { allLines = 1; }
73 output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "lt"; }
74 if ((output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are lt and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
76 //if the user has not specified any labels use the ones from read.otu
78 allLines = globaldata->allLines;
79 labels = globaldata->labels;
82 groups = validParameter.validFile(parameters, "groups", false);
83 if (groups == "not found") { groups = ""; }
85 splitAtDash(groups, Groups);
86 globaldata->Groups = Groups;
89 calc = validParameter.validFile(parameters, "calc", false);
90 if (calc == "not found") { calc = "jclass-thetayc"; }
92 if (calc == "default") { calc = "jclass-thetayc"; }
94 splitAtDash(calc, Estimators);
98 validCalculator = new ValidCalculators();
101 for (i=0; i<Estimators.size(); i++) {
102 if (validCalculator->isValidCalculator("matrix", Estimators[i]) == true) {
103 if (Estimators[i] == "jabund") {
104 matrixCalculators.push_back(new JAbund());
105 }else if (Estimators[i] == "sorabund") {
106 matrixCalculators.push_back(new SorAbund());
107 }else if (Estimators[i] == "jclass") {
108 matrixCalculators.push_back(new Jclass());
109 }else if (Estimators[i] == "sorclass") {
110 matrixCalculators.push_back(new SorClass());
111 }else if (Estimators[i] == "jest") {
112 matrixCalculators.push_back(new Jest());
113 }else if (Estimators[i] == "sorest") {
114 matrixCalculators.push_back(new SorEst());
115 }else if (Estimators[i] == "thetayc") {
116 matrixCalculators.push_back(new ThetaYC());
117 }else if (Estimators[i] == "thetan") {
118 matrixCalculators.push_back(new ThetaN());
119 }else if (Estimators[i] == "morisitahorn") {
120 matrixCalculators.push_back(new MorHorn());
121 }else if (Estimators[i] == "braycurtis") {
122 matrixCalculators.push_back(new BrayCurtis());
131 catch(exception& e) {
132 m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
137 //**********************************************************************************************************************
139 void MatrixOutputCommand::help(){
141 m->mothurOut("The dist.shared command can only be executed after a successful read.otu command.\n");
142 m->mothurOut("The dist.shared command parameters are groups, calc, output and label. No parameters are required.\n");
143 m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
144 m->mothurOut("The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n");
145 m->mothurOut("The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
146 m->mothurOut("The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n");
147 m->mothurOut("Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n");
148 m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
149 m->mothurOut("The default value for calc is jclass and thetayc.\n");
150 validCalculator->printCalc("matrix", cout);
151 m->mothurOut("The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose.\n");
152 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
154 catch(exception& e) {
155 m->errorOut(e, "MatrixOutputCommand", "help");
161 //**********************************************************************************************************************
163 MatrixOutputCommand::~MatrixOutputCommand(){
164 if (abort == false) {
165 delete input; globaldata->ginput = NULL;
167 delete validCalculator;
171 //**********************************************************************************************************************
173 int MatrixOutputCommand::execute(){
176 if (abort == true) { return 0; }
178 //if the users entered no valid calculators don't execute command
179 if (matrixCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine(); return 0; }
182 read = new ReadOTUFile(globaldata->inputFileName);
183 read->read(&*globaldata);
185 input = globaldata->ginput;
186 lookup = input->getSharedRAbundVectors();
187 string lastLabel = lookup[0]->getLabel();
189 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
190 set<string> processedLabels;
191 set<string> userLabels = labels;
193 if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); return 0;}
195 numGroups = lookup.size();
197 if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); return 0; }
199 //as long as you are not at the end of the file or done wih the lines you want
200 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
202 if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
204 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
205 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
208 processedLabels.insert(lookup[0]->getLabel());
209 userLabels.erase(lookup[0]->getLabel());
212 if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
213 string saveLabel = lookup[0]->getLabel();
215 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
216 lookup = input->getSharedRAbundVectors(lastLabel);
218 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
221 processedLabels.insert(lookup[0]->getLabel());
222 userLabels.erase(lookup[0]->getLabel());
224 //restore real lastlabel to save below
225 lookup[0]->setLabel(saveLabel);
228 lastLabel = lookup[0]->getLabel();
230 //get next line to process
231 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
232 lookup = input->getSharedRAbundVectors();
235 if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
237 //output error messages about any remaining user labels
238 set<string>::iterator it;
239 bool needToRun = false;
240 for (it = userLabels.begin(); it != userLabels.end(); it++) {
241 m->mothurOut("Your file does not include the label " + *it);
242 if (processedLabels.count(lastLabel) != 1) {
243 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
246 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
250 if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
252 //run last label if you need to
253 if (needToRun == true) {
254 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
255 lookup = input->getSharedRAbundVectors(lastLabel);
257 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
259 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
262 if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
264 //reset groups parameter
265 globaldata->Groups.clear();
267 m->mothurOutEndLine();
268 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
269 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
270 m->mothurOutEndLine();
275 catch(exception& e) {
276 m->errorOut(e, "MatrixOutputCommand", "execute");
280 /***********************************************************/
281 void MatrixOutputCommand::printSims(ostream& out) {
284 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
287 out << simMatrix.size() << endl;
289 if (output == "lt") {
290 for (int m = 0; m < simMatrix.size(); m++) {
291 out << lookup[m]->getGroup() << '\t';
292 for (int n = 0; n < m; n++) {
293 out << simMatrix[m][n] << '\t';
298 for (int m = 0; m < simMatrix.size(); m++) {
299 out << lookup[m]->getGroup() << '\t';
300 for (int n = 0; n < simMatrix[m].size(); n++) {
301 out << simMatrix[m][n] << '\t';
307 catch(exception& e) {
308 m->errorOut(e, "MatrixOutputCommand", "printSims");
312 /***********************************************************/
313 int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
317 vector<SharedRAbundVector*> subset;
319 //for each calculator
320 for(int i = 0 ; i < matrixCalculators.size(); i++) {
322 //initialize simMatrix
324 simMatrix.resize(numGroups);
325 for (int p = 0; p < simMatrix.size(); p++) {
326 for (int j = 0; j < simMatrix.size(); j++) {
327 simMatrix[p].push_back(0.0);
331 for (int k = 0; k < thisLookup.size(); k++) {
332 for (int l = k; l < thisLookup.size(); l++) {
333 if (k != l) { //we dont need to similiarity of a groups to itself
334 //get estimated similarity between 2 groups
336 if (m->control_pressed) { return 0; }
338 subset.clear(); //clear out old pair of sharedrabunds
339 //add new pair of sharedrabunds
340 subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
342 data = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
343 //save values in similarity matrix
344 simMatrix[k][l] = 1.0 - data[0]; //convert similiarity to distance
345 simMatrix[l][k] = 1.0 - data[0]; //convert similiarity to distance
350 exportFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
351 openOutputFile(exportFileName, out);
352 outputNames.push_back(exportFileName);
362 catch(exception& e) {
363 m->errorOut(e, "MatrixOutputCommand", "process");
367 /***********************************************************/