//**********************************************************************************************************************
-MatrixOutputCommand::MatrixOutputCommand(){
+MatrixOutputCommand::MatrixOutputCommand(string option){
try {
globaldata = GlobalData::getInstance();
- validCalculator = new ValidCalculators();
+ abort = false;
+ allLines = 1;
+ lines.clear();
+ labels.clear();
+ Groups.clear();
+ Estimators.clear();
+
+ //allow user to run help
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"line","label","calc","groups"};
+ 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; }
+ }
+
+ //make sure the user has already run the read.otu command
+ if (globaldata->getSharedFile() == "") {
+ if (globaldata->getListFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the dist.shared command."); mothurOutEndLine(); abort = true; }
+ else if (globaldata->getGroupFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the dist.shared command."); mothurOutEndLine(); abort = true; }
+ }
- int i;
- for (i=0; i<globaldata->Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("matrix", globaldata->Estimators[i]) == true) {
- if (globaldata->Estimators[i] == "jabund") {
- matrixCalculators.push_back(new JAbund());
- }else if (globaldata->Estimators[i] == "sorabund") {
- matrixCalculators.push_back(new SorAbund());
- }else if (globaldata->Estimators[i] == "jclass") {
- matrixCalculators.push_back(new Jclass());
- }else if (globaldata->Estimators[i] == "sorclass") {
- matrixCalculators.push_back(new SorClass());
- }else if (globaldata->Estimators[i] == "jest") {
- matrixCalculators.push_back(new Jest());
- }else if (globaldata->Estimators[i] == "sorest") {
- matrixCalculators.push_back(new SorEst());
- }else if (globaldata->Estimators[i] == "thetayc") {
- matrixCalculators.push_back(new ThetaYC());
- }else if (globaldata->Estimators[i] == "thetan") {
- matrixCalculators.push_back(new ThetaN());
- }else if (globaldata->Estimators[i] == "morisitahorn") {
- matrixCalculators.push_back(new MorHorn());
- }else if (globaldata->Estimators[i] == "braycurtis") {
- matrixCalculators.push_back(new BrayCurtis());
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ line = validParameter.validFile(parameters, "line", false);
+ if (line == "not found") { line = ""; }
+ else {
+ if(line != "all") { splitAtDash(line, lines); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ //make sure user did not use both the line and label parameters
+ if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
+ //if the user has not specified any line or labels use the ones from read.otu
+ else if((line == "") && (label == "")) {
+ allLines = globaldata->allLines;
+ labels = globaldata->labels;
+ lines = globaldata->lines;
+ }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
+
+ calc = validParameter.validFile(parameters, "calc", false);
+ if (calc == "not found") { calc = "jclass-thetayc"; }
+ else {
+ if (calc == "default") { calc = "jclass-thetayc"; }
+ }
+ splitAtDash(calc, Estimators);
+
+ if (abort == false) {
+
+ validCalculator = new ValidCalculators();
+
+ int i;
+ for (i=0; i<Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("matrix", Estimators[i]) == true) {
+ if (Estimators[i] == "jabund") {
+ matrixCalculators.push_back(new JAbund());
+ }else if (Estimators[i] == "sorabund") {
+ matrixCalculators.push_back(new SorAbund());
+ }else if (Estimators[i] == "jclass") {
+ matrixCalculators.push_back(new Jclass());
+ }else if (Estimators[i] == "sorclass") {
+ matrixCalculators.push_back(new SorClass());
+ }else if (Estimators[i] == "jest") {
+ matrixCalculators.push_back(new Jest());
+ }else if (Estimators[i] == "sorest") {
+ matrixCalculators.push_back(new SorEst());
+ }else if (Estimators[i] == "thetayc") {
+ matrixCalculators.push_back(new ThetaYC());
+ }else if (Estimators[i] == "thetan") {
+ matrixCalculators.push_back(new ThetaN());
+ }else if (Estimators[i] == "morisitahorn") {
+ matrixCalculators.push_back(new MorHorn());
+ }else if (Estimators[i] == "braycurtis") {
+ matrixCalculators.push_back(new BrayCurtis());
+ }
+ }
}
+
}
}
- //reset calc for next command
- globaldata->setCalc("");
-
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the MatrixOutputCommand class Function MatrixOutputCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the MatrixOutputCommand class function MatrixOutputCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+//**********************************************************************************************************************
+
+void MatrixOutputCommand::help(){
+ try {
+ mothurOut("The dist.shared command can only be executed after a successful read.otu command.\n");
+ mothurOut("The dist.shared command parameters are groups, calc, line and label. The calc parameter is required, and you may not use line and label at the same time.\n");
+ mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
+ mothurOut("The group names are separated by dashes. The line and label allow you to select what distance levels you would like distance matrices created for, and are also separated by dashes.\n");
+ mothurOut("The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels).\n");
+ mothurOut("Example dist.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund).\n");
+ mothurOut("The default value for groups is all the groups in your groupfile.\n");
+ mothurOut("The default value for calc is jclass and thetayc.\n");
+ validCalculator->printCalc("matrix", cout);
+ mothurOut("The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose.\n");
+ mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
+ }
+ catch(exception& e) {
+ errorOut(e, "MatrixOutputCommand", "help");
exit(1);
- }
+ }
}
+
+
//**********************************************************************************************************************
MatrixOutputCommand::~MatrixOutputCommand(){
- delete input;
- delete read;
+ if (abort == false) {
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete validCalculator;
+ }
}
//**********************************************************************************************************************
int MatrixOutputCommand::execute(){
try {
- int count = 1;
- EstOutput data;
- vector<SharedRAbundVector*> subset;
+ if (abort == true) { return 0; }
+
+ int count = 1;
+
//if the users entered no valid calculators don't execute command
- if (matrixCalculators.size() == 0) { cout << "No valid calculators." << endl; return 0; }
+ if (matrixCalculators.size() == 0) { mothurOut("No valid calculators."); mothurOutEndLine(); return 0; }
//you have groups
read = new ReadOTUFile(globaldata->inputFileName);
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
+ string lastLabel = lookup[0]->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;
+ set<int> userLines = lines;
- if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; return 0;}
+ if (lookup.size() < 2) { mothurOut("You have not provided enough valid groups. I cannot run the command."); mothurOutEndLine(); return 0;}
- numGroups = globaldata->Groups.size();
+ numGroups = lookup.size();
- while(lookup[0] != NULL){
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
+ if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ process(lookup);
- cout << lookup[0]->getLabel() << '\t' << count << endl;
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ userLines.erase(count);
+ }
+
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ process(lookup);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ }
+
+
+ lastLabel = lookup[0]->getLabel();
+
+ //get next line to process
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors();
+ count++;
+ }
+
+ //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 line if you need to
+ if (needToRun == true) {
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ process(lookup);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ }
+
+ //reset groups parameter
+ globaldata->Groups.clear();
+
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "MatrixOutputCommand", "execute");
+ exit(1);
+ }
+}
+/***********************************************************/
+void MatrixOutputCommand::printSims(ostream& out) {
+ try {
+
+ //output column headers
+ out << simMatrix.size() << endl;
+
+ for (int m = 0; m < simMatrix.size(); m++) {
+ out << lookup[m]->getGroup() << '\t';
+ for (int n = 0; n < m; n++) {
+ out << simMatrix[m][n] << '\t';
+ }
+ out << endl;
+ }
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MatrixOutputCommand", "printSims");
+ exit(1);
+ }
+}
+/***********************************************************/
+void MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
+ try {
+
+ EstOutput data;
+ vector<SharedRAbundVector*> subset;
+
//for each calculator
for(int i = 0 ; i < matrixCalculators.size(); i++) {
}
}
- for (int k = 0; k < lookup.size(); k++) {
- for (int l = k; l < lookup.size(); l++) {
+ for (int k = 0; k < thisLookup.size(); k++) {
+ for (int l = k; l < thisLookup.size(); l++) {
if (k != l) { //we dont need to similiarity of a groups to itself
//get estimated similarity between 2 groups
subset.clear(); //clear out old pair of sharedrabunds
//add new pair of sharedrabunds
- subset.push_back(lookup[k]); subset.push_back(lookup[l]);
+ subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
data = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
//save values in similarity matrix
}
}
- exportFileName = getRootName(globaldata->inputFileName) + matrixCalculators[i]->getName() + "." + lookup[0]->getLabel() + ".dist";
+ exportFileName = getRootName(globaldata->inputFileName) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist";
openOutputFile(exportFileName, out);
printSims(out);
out.close();
}
- }
-
- //prevent memory leak
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
-
- //get next line to process
- lookup = input->getSharedRAbundVectors();
- count++;
- }
-
- //reset groups parameter
- globaldata->Groups.clear(); globaldata->setGroups("");
- return 0;
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the MatrixOutputCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the MatrixOutputCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-/***********************************************************/
-void MatrixOutputCommand::printSims(ostream& out) {
- try {
-
- //output column headers
- out << simMatrix.size() << endl;
+
- for (int m = 0; m < simMatrix.size(); m++) {
- out << lookup[m]->getGroup() << '\t';
- for (int n = 0; n < m; n++) {
- out << simMatrix[m][n] << '\t';
- }
- out << endl;
- }
-
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the MatrixOutputCommand class Function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "MatrixOutputCommand", "process");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the MatrixOutputCommand class function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************/
+
projects / mothur.git / blobdiff