*/
#include "matrixoutputcommand.h"
+#include "sharedsobscollectsummary.h"
+#include "sharedchao1.h"
+#include "sharedace.h"
+#include "sharednseqs.h"
#include "sharedjabund.h"
#include "sharedsorabund.h"
#include "sharedjclass.h"
#include "sharedsorest.h"
#include "sharedthetayc.h"
#include "sharedthetan.h"
+#include "sharedkstest.h"
+#include "whittaker.h"
+#include "sharedochiai.h"
+#include "sharedanderbergs.h"
+#include "sharedkulczynski.h"
+#include "sharedkulczynskicody.h"
+#include "sharedlennon.h"
#include "sharedmorisitahorn.h"
#include "sharedbraycurtis.h"
+#include "sharedjackknife.h"
+#include "whittaker.h"
+#include "odum.h"
+#include "canberra.h"
+#include "structeuclidean.h"
+#include "structchord.h"
+#include "hellinger.h"
+#include "manhattan.h"
+#include "structpearson.h"
+#include "soergel.h"
+#include "spearman.h"
+#include "structkulczynski.h"
+#include "structchi2.h"
+#include "speciesprofile.h"
+#include "hamming.h"
+#include "gower.h"
+#include "memchi2.h"
+#include "memchord.h"
+#include "memeuclidean.h"
+#include "mempearson.h"
-
+//**********************************************************************************************************************
+vector<string> MatrixOutputCommand::setParameters(){
+ try {
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
+ CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MatrixOutputCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string MatrixOutputCommand::getHelpString(){
+ try {
+ string helpString = "";
+ ValidCalculators validCalculator;
+ helpString += "The dist.shared command parameters are shared, groups, calc, output and label. shared is a required, unless you have a valid current file.\n";
+ helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
+ helpString += "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";
+ helpString += "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
+ helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n";
+ helpString += "Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n";
+ helpString += "The default value for groups is all the groups in your groupfile.\n";
+ helpString += "The default value for calc is jclass and thetayc.\n";
+ helpString += validCalculator.printCalc("matrix");
+ helpString += "The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MatrixOutputCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+MatrixOutputCommand::MatrixOutputCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
-MatrixOutputCommand::MatrixOutputCommand(){
+MatrixOutputCommand::MatrixOutputCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- validCalculator = new ValidCalculators();
+ abort = false; calledHelp = false;
+ allLines = 1;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
+
+ ValidParameters validParameter;
+
+ //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; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+
+ //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("shared");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["shared"] = inputDir + it->second; }
+ }
+ }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not found") {
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else if (sharedfile == "not open") { sharedfile = ""; 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 += m->hasPath(sharedfile); //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...
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "lt"; }
+ 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"; }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ m->Groups = Groups;
+ }
+
+ calc = validParameter.validFile(parameters, "calc", false);
+ if (calc == "not found") { calc = "jclass-thetayc"; }
+ else {
+ if (calc == "default") { calc = "jclass-thetayc"; }
+ }
+ m->splitAtDash(calc, Estimators);
+
+ if (abort == false) {
- 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());
+ ValidCalculators validCalculator;
+
+ int i;
+ for (i=0; i<Estimators.size(); i++) {
+ if (validCalculator.isValidCalculator("matrix", Estimators[i]) == true) {
+ if (Estimators[i] == "sharedsobs") {
+ matrixCalculators.push_back(new SharedSobsCS());
+ }else if (Estimators[i] == "sharedchao") {
+ matrixCalculators.push_back(new SharedChao1());
+ }else if (Estimators[i] == "sharedace") {
+ matrixCalculators.push_back(new SharedAce());
+ }else 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] == "kstest") {
+ matrixCalculators.push_back(new KSTest());
+ }else if (Estimators[i] == "sharednseqs") {
+ matrixCalculators.push_back(new SharedNSeqs());
+ }else if (Estimators[i] == "ochiai") {
+ matrixCalculators.push_back(new Ochiai());
+ }else if (Estimators[i] == "anderberg") {
+ matrixCalculators.push_back(new Anderberg());
+ }else if (Estimators[i] == "kulczynski") {
+ matrixCalculators.push_back(new Kulczynski());
+ }else if (Estimators[i] == "kulczynskicody") {
+ matrixCalculators.push_back(new KulczynskiCody());
+ }else if (Estimators[i] == "lennon") {
+ matrixCalculators.push_back(new Lennon());
+ }else if (Estimators[i] == "morisitahorn") {
+ matrixCalculators.push_back(new MorHorn());
+ }else if (Estimators[i] == "braycurtis") {
+ matrixCalculators.push_back(new BrayCurtis());
+ }else if (Estimators[i] == "whittaker") {
+ matrixCalculators.push_back(new Whittaker());
+ }else if (Estimators[i] == "odum") {
+ matrixCalculators.push_back(new Odum());
+ }else if (Estimators[i] == "canberra") {
+ matrixCalculators.push_back(new Canberra());
+ }else if (Estimators[i] == "structeuclidean") {
+ matrixCalculators.push_back(new StructEuclidean());
+ }else if (Estimators[i] == "structchord") {
+ matrixCalculators.push_back(new StructChord());
+ }else if (Estimators[i] == "hellinger") {
+ matrixCalculators.push_back(new Hellinger());
+ }else if (Estimators[i] == "manhattan") {
+ matrixCalculators.push_back(new Manhattan());
+ }else if (Estimators[i] == "structpearson") {
+ matrixCalculators.push_back(new StructPearson());
+ }else if (Estimators[i] == "soergel") {
+ matrixCalculators.push_back(new Soergel());
+ }else if (Estimators[i] == "spearman") {
+ matrixCalculators.push_back(new Spearman());
+ }else if (Estimators[i] == "structkulczynski") {
+ matrixCalculators.push_back(new StructKulczynski());
+ }else if (Estimators[i] == "speciesprofile") {
+ matrixCalculators.push_back(new SpeciesProfile());
+ }else if (Estimators[i] == "hamming") {
+ matrixCalculators.push_back(new Hamming());
+ }else if (Estimators[i] == "structchi2") {
+ matrixCalculators.push_back(new StructChi2());
+ }else if (Estimators[i] == "gower") {
+ matrixCalculators.push_back(new Gower());
+ }else if (Estimators[i] == "memchi2") {
+ matrixCalculators.push_back(new MemChi2());
+ }else if (Estimators[i] == "memchord") {
+ matrixCalculators.push_back(new MemChord());
+ }else if (Estimators[i] == "memeuclidean") {
+ matrixCalculators.push_back(new MemEuclidean());
+ }else if (Estimators[i] == "mempearson") {
+ matrixCalculators.push_back(new MemPearson());
+ }
+ }
}
+
}
}
- //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";
+ m->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";
- exit(1);
- }
}
+
//**********************************************************************************************************************
-MatrixOutputCommand::~MatrixOutputCommand(){
- delete input;
- delete read;
-}
+MatrixOutputCommand::~MatrixOutputCommand(){}
//**********************************************************************************************************************
int MatrixOutputCommand::execute(){
try {
- int count = 1;
-
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
//if the users entered no valid calculators don't execute command
- if (matrixCalculators.size() == 0) { cout << "No valid calculators." << endl; return 0; }
-
- //you have groups
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
+ if (matrixCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine(); return 0; }
- input = globaldata->ginput;
+ input = new InputData(sharedfile, "sharedfile");
lookup = input->getSharedRAbundVectors();
- vector<SharedRAbundVector*> lastLookup = lookup;
+ 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 = globaldata->labels;
-
- if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; return 0;}
+ set<string> userLabels = labels;
+
+ if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0;}
+
+ numGroups = lookup.size();
- numGroups = globaldata->Groups.size();
+ if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; }
//as long as you are not at the end of the file or done wih the lines you want
- while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+ while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } m->Groups.clear(); return 0; }
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
- cout << lookup[0]->getLabel() << '\t' << count << endl;
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
process(lookup);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- process(lastLookup);
+ if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookup[0]->getLabel();
- processedLabels.insert(lastLookup[0]->getLabel());
- userLabels.erase(lastLookup[0]->getLabel());
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ process(lookup);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
}
- //prevent memory leak
- if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
- lastLookup = lookup;
+ lastLabel = lookup[0]->getLabel();
//get next line to process
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors();
- count++;
}
+ if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } m->Groups.clear(); return 0; }
+
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
- cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
- //run last line if you need to
+ if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } m->Groups.clear(); return 0; }
+
+ //run last label if you need to
if (needToRun == true) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- process(lastLookup);
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ process(lookup);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
-
+ if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } m->Groups.clear(); return 0; }
//reset groups parameter
- globaldata->Groups.clear(); globaldata->setGroups("");
+ m->Groups.clear();
+
+ //set phylip file as new current phylipfile
+ string current = "";
+ itTypes = outputTypes.find("phylip");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
+ }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
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";
+ m->errorOut(e, "MatrixOutputCommand", "execute");
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.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ //output num seqs
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';
+ if (output == "lt") {
+ 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;
+ }
+ }else{
+ for (int m = 0; m < simMatrix.size(); m++) {
+ out << lookup[m]->getGroup() << '\t';
+ for (int n = 0; n < simMatrix[m].size(); n++) {
+ out << simMatrix[m][n] << '\t';
+ }
+ out << endl;
}
- 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";
+ m->errorOut(e, "MatrixOutputCommand", "printSims");
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);
- }
}
/***********************************************************/
-void MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
+int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
try {
EstOutput data;
//initialize simMatrix
simMatrix.clear();
simMatrix.resize(numGroups);
- for (int m = 0; m < simMatrix.size(); m++) {
+ for (int p = 0; p < simMatrix.size(); p++) {
for (int j = 0; j < simMatrix.size(); j++) {
- simMatrix[m].push_back(0.0);
+ simMatrix[p].push_back(0.0);
}
}
if (k != l) { //we dont need to similiarity of a groups to itself
//get estimated similarity between 2 groups
+ if (m->control_pressed) { return 0; }
+
subset.clear(); //clear out old pair of sharedrabunds
//add new pair of sharedrabunds
subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
+ //if this calc needs all groups to calculate the pair load all groups
+ if (matrixCalculators[i]->getNeedsAll()) {
+ //load subset with rest of lookup for those calcs that need everyone to calc for a pair
+ for (int w = 0; w < thisLookup.size(); w++) {
+ if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
+ }
+ }
+
data = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
//save values in similarity matrix
simMatrix[k][l] = 1.0 - data[0]; //convert similiarity to distance
}
}
- exportFileName = getRootName(globaldata->inputFileName) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist";
- openOutputFile(exportFileName, out);
+ exportFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
+ m->openOutputFile(exportFileName, out);
+ outputNames.push_back(exportFileName); outputTypes["phylip"].push_back(exportFileName);
+
printSims(out);
out.close();
}
-
+ return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the MatrixOutputCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "MatrixOutputCommand", "process");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the MatrixOutputCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************/
projects / mothur.git / blobdiff