*/
#include "parsimonycommand.h"
+#include "treereader.h"
+//**********************************************************************************************************************
+vector<string> ParsimonyCommand::setParameters(){
+ try {
+ CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter prandom("random", "String", "", "", "", "", "",false,false); parameters.push_back(prandom);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ 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, "ParsimonyCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ParsimonyCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The parsimony command parameters are tree, group, name, random, groups, processors and iters. tree parameter is required unless you have valid current tree file or are using random.\n";
+ helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 1 valid group.\n";
+ helpString += "The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree.\n";
+ helpString += "The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters).\n";
+ helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
+ helpString += "Example parsimony(random=out, iters=500).\n";
+ helpString += "The default value for random is "" (meaning you want to use the trees in your inputfile, randomtree=out means you just want the random distribution of trees outputted to out.rd_parsimony),\n";
+ helpString += "and iters is 1000. The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParsimonyCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ParsimonyCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "parsimony") { outputFileName = "parsimony"; }
+ else if (type == "psummary") { outputFileName = "psummary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParsimonyCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+ParsimonyCommand::ParsimonyCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["parsimony"] = tempOutNames;
+ outputTypes["psummary"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand");
+ exit(1);
+ }
+}
/***********************************************************/
-ParsimonyCommand::ParsimonyCommand() {
+ParsimonyCommand::ParsimonyCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
+ abort = false; calledHelp = false;
+ Groups.clear();
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
- //randomtree will tell us if user had their own treefile or if they just want the random distribution
- randomtree = globaldata->getRandomTree();
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
+
+ ValidParameters validParameter;
- //user has entered their own tree
- if (randomtree == "") {
- T = globaldata->gTree;
- tmap = globaldata->gTreemap;
- parsFile = globaldata->getTreeFile() + ".parsimony";
- openOutputFile(parsFile, out);
- sumFile = globaldata->getTreeFile() + ".psummary";
- openOutputFile(sumFile, outSum);
- }else { //user wants random distribution
- savetmap = globaldata->gTreemap;
- getUserInput();
- parsFile = randomtree + ".rd_parsimony";
- openOutputFile(parsFile, out);
+ //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["parsimony"] = tempOutNames;
+ outputTypes["psummary"] = 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("tree");
+ //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["tree"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //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["group"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //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["name"] = inputDir + it->second; }
+ }
+ }
+
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+
+ randomtree = validParameter.validFile(parameters, "random", false); if (randomtree == "not found") { randomtree = ""; }
+
+ //are you trying to use parsimony without reading a tree or saying you want random distribution
+ if (randomtree == "") {
+ //check for required parameters
+ treefile = validParameter.validFile(parameters, "tree", true);
+ if (treefile == "not open") { treefile = ""; abort = true; }
+ else if (treefile == "not found") { //if there is a current design file, use it
+ treefile = m->getTreeFile();
+ if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setTreeFile(treefile); }
+
+ //check for required parameters
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { namefile = ""; abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
+ }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; if (randomtree == "") { outputDir += m->hasPath(treefile); } }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; m->clearGroups(); }
+ else {
+ m->splitAtDash(groups, Groups);
+ m->setGroups(Groups);
+ }
+
+ itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
+ m->mothurConvert(itersString, iters);
+
+ string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
+
+ if (namefile == "") {
+ vector<string> files; files.push_back(treefile);
+ parser.getNameFile(files);
+ }
+
}
-
- //set users groups to analyze
- setGroups();
- convert(globaldata->getIters(), iters); //how many random trees to generate
- pars = new Parsimony(tmap);
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function ParsimonyCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ParsimonyCommand class function ParsimonyCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand");
exit(1);
}
}
int ParsimonyCommand::execute() {
try {
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+
+ //randomtree will tell us if user had their own treefile or if they just want the random distribution
+ //user has entered their own tree
+ if (randomtree == "") {
+
+ m->setTreeFile(treefile);
+
+ TreeReader* reader = new TreeReader(treefile, groupfile, namefile);
+ T = reader->getTrees();
+ tmap = T[0]->getTreeMap();
+ delete reader;
+
+ if(outputDir == "") { outputDir += m->hasPath(treefile); }
+ output = new ColumnFile(outputDir + m->getSimpleName(treefile) + "." + getOutputFileNameTag("parsimony"), itersString);
+ outputNames.push_back(outputDir + m->getSimpleName(treefile) + "." + getOutputFileNameTag("parsimony"));
+ outputTypes["parsimony"].push_back(outputDir + m->getSimpleName(treefile) + "." + getOutputFileNameTag("parsimony"));
+
+ sumFile = outputDir + m->getSimpleName(treefile) + "." + getOutputFileNameTag("psummary");
+ m->openOutputFile(sumFile, outSum);
+ outputNames.push_back(sumFile);
+ outputTypes["psummary"].push_back(sumFile);
+ }else { //user wants random distribution
+ getUserInput();
+
+ if(outputDir == "") { outputDir += m->hasPath(randomtree); }
+ output = new ColumnFile(outputDir+ m->getSimpleName(randomtree), itersString);
+ outputNames.push_back(outputDir+ m->getSimpleName(randomtree));
+ outputTypes["parsimony"].push_back(outputDir+ m->getSimpleName(randomtree));
+ }
+
+ //set users groups to analyze
+ SharedUtil util;
+ vector<string> mGroups = m->getGroups();
+ vector<string> tGroups = tmap->getNamesOfGroups();
+ util.setGroups(mGroups, tGroups, allGroups, numGroups, "parsimony"); //sets the groups the user wants to analyze
+ util.getCombos(groupComb, mGroups, numComp);
+ m->setGroups(mGroups);
+
+ if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
+
+ Parsimony pars;
+ counter = 0;
+
+ Progress* reading;
+ reading = new Progress("Comparing to random:", iters);
+
+ if (m->control_pressed) {
+ delete reading; delete output;
+ delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ if (randomtree == "") { outSum.close(); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ m->clearGroups();
+ return 0;
+ }
+
+
//get pscore for users tree
userData.resize(numComp,0); //data = AB, AC, BC, ABC.
randomData.resize(numComp,0); //data = AB, AC, BC, ABC.
uscoreFreq.resize(numComp);
rCumul.resize(numComp);
uCumul.resize(numComp);
- validScores.resize(numComp);
userTreeScores.resize(numComp);
UScoreSig.resize(numComp);
if (randomtree == "") {
//get pscores for users trees
for (int i = 0; i < T.size(); i++) {
- cout << "Processing tree " << i+1 << endl;
- userData = pars->getValues(T[i]); //data = AB, AC, BC, ABC.
+ userData = pars.getValues(T[i], processors, outputDir); //data = AB, AC, BC, ABC.
+ if (m->control_pressed) {
+ delete reading; delete output;
+ delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ if (randomtree == "") { outSum.close(); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ m->clearGroups();
+ return 0;
+ }
+
+
//output scores for each combination
for(int k = 0; k < numComp; k++) {
+
//update uscoreFreq
- it = uscoreFreq[k].find(userData[k]);
+ map<int,double>::iterator it = uscoreFreq[k].find(userData[k]);
if (it == uscoreFreq[k].end()) {//new score
uscoreFreq[k][userData[k]] = 1;
}else{ uscoreFreq[k][userData[k]]++; }
//add users score to valid scores
- validScores[k][userData[k]] = userData[k];
+ validScores[userData[k]] = userData[k];
//save score for summary file
userTreeScores[k].push_back(userData[k]);
//get pscores for random trees
for (int j = 0; j < iters; j++) {
+
//create new tree with same num nodes and leaves as users
- randT = new Tree();
+ randT = new Tree(tmap);
+
//create random relationships between nodes
randT->assembleRandomTree();
+
//get pscore of random tree
- randomData = pars->getValues(randT);
+ randomData = pars.getValues(randT, processors, outputDir);
+ if (m->control_pressed) {
+ delete reading; delete output; delete randT;
+ if (randomtree == "") { outSum.close(); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ m->clearGroups();
+ return 0;
+ }
+
for(int r = 0; r < numComp; r++) {
//add trees pscore to map of scores
- it2 = rscoreFreq[r].find(randomData[r]);
- if (it2 != rscoreFreq[r].end()) {//already have that score
+ map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
+ if (it != rscoreFreq[r].end()) {//already have that score
rscoreFreq[r][randomData[r]]++;
}else{//first time we have seen this score
rscoreFreq[r][randomData[r]] = 1;
}
//add randoms score to validscores
- validScores[r][randomData[r]] = randomData[r];
+ validScores[randomData[r]] = randomData[r];
}
+ //update progress bar
+ reading->update(j);
+
delete randT;
}
+
}else {
//get pscores for random trees
for (int j = 0; j < iters; j++) {
+
//create new tree with same num nodes and leaves as users
- randT = new Tree();
+ randT = new Tree(tmap);
//create random relationships between nodes
+
randT->assembleRandomTree();
+
+ if (m->control_pressed) {
+ delete reading; delete output; delete randT; delete tmap;
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;
+ }
+
+
//get pscore of random tree
- randomData = pars->getValues(randT);
+ randomData = pars.getValues(randT, processors, outputDir);
+ if (m->control_pressed) {
+ delete reading; delete output; delete randT; delete tmap;
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;
+ }
+
for(int r = 0; r < numComp; r++) {
//add trees pscore to map of scores
- it2 = rscoreFreq[r].find(randomData[r]);
- if (it2 != rscoreFreq[r].end()) {//already have that score
+ map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
+ if (it != rscoreFreq[r].end()) {//already have that score
rscoreFreq[r][randomData[r]]++;
}else{//first time we have seen this score
rscoreFreq[r][randomData[r]] = 1;
}
//add randoms score to validscores
- validScores[r][randomData[r]] = randomData[r];
+ validScores[randomData[r]] = randomData[r];
}
+ //update progress bar
+ reading->update(j);
+
delete randT;
}
}
-
- float rcumul = 0.0000;
- float ucumul = 0.0000;
-
+
for(int a = 0; a < numComp; a++) {
- //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
- for (it = validScores[a].begin(); it != validScores[a].end(); it++) {
+ float rcumul = 0.0000;
+ float ucumul = 0.0000;
+ //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
+ for (map<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) {
if (randomtree == "") {
- it2 = uscoreFreq[a].find(it->first);
+ map<int,double>::iterator it2 = uscoreFreq[a].find(it->first);
//user data has that score
if (it2 != uscoreFreq[a].end()) { uscoreFreq[a][it->first] /= T.size(); ucumul+= it2->second; }
else { uscoreFreq[a][it->first] = 0.0000; } //no user trees with that score
//make uCumul map
- uCumul[a][it->first] = ucumul-a;
+ uCumul[a][it->first] = ucumul;
}
//make rscoreFreq map and rCumul
- it2 = rscoreFreq[a].find(it->first);
+ map<int,double>::iterator it2 = rscoreFreq[a].find(it->first);
//get percentage of random trees with that info
if (it2 != rscoreFreq[a].end()) { rscoreFreq[a][it->first] /= iters; rcumul+= it2->second; }
else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
- rCumul[a][it->first] = rcumul-a;
+ rCumul[a][it->first] = rcumul;
}
//find the signifigance of each user trees score when compared to the random trees and save for printing the summary file
}
}
+ if (m->control_pressed) {
+ delete reading; delete output;
+ delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ if (randomtree == "") { outSum.close(); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ return 0;
+ }
+
+ //finish progress bar
+ reading->finish();
+ delete reading;
+
printParsimonyFile();
if (randomtree == "") { printUSummaryFile(); }
+
+ delete output; delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
- //reset globaldata's treemap if you just did random distrib
- if (randomtree != "") { globaldata->gTreemap = savetmap; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;}
- //reset randomTree parameter to ""
- globaldata->setRandomTree("");
- //reset groups parameter
- globaldata->Groups.clear(); globaldata->setGroups("");
+ 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 ParsimonyCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ParsimonyCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ParsimonyCommand", "execute");
exit(1);
}
}
/***********************************************************/
void ParsimonyCommand::printParsimonyFile() {
try {
- //column headers
+ vector<double> data;
+ vector<string> tags;
+
if (randomtree == "") {
- out << "Comb" << '\t' << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
+ tags.push_back("Score"); tags.push_back("UserFreq"); tags.push_back("UserCumul"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
}else {
- out << "Comb" << '\t' << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
+ tags.push_back("Score"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
}
-
- //format output
- out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-
+
for(int a = 0; a < numComp; a++) {
+ output->initFile(groupComb[a], tags);
//print each line
- for (it = validScores[a].begin(); it != validScores[a].end(); it++) {
+ for (map<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) {
if (randomtree == "") {
- out << setprecision(6) << groupComb[a] << '\t' << it->first << '\t' << '\t'<< uscoreFreq[a][it->first] << '\t' << uCumul[a][it->first] << '\t' << rscoreFreq[a][it->first] << '\t' << rCumul[a][it->first] << endl;
+ data.push_back(it->first); data.push_back(uscoreFreq[a][it->first]); data.push_back(uCumul[a][it->first]); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
}else{
- out << setprecision(6) << groupComb[a] << '\t' << it->first << '\t' << '\t' << rscoreFreq[a][it->first] << '\t' << rCumul[a][it->first] << endl;
+ data.push_back(it->first); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
}
+ output->output(data);
+ data.clear();
}
+ output->resetFile();
}
- out.close();
-
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function printParsimonyFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ParsimonyCommand class function printParsimonyFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ParsimonyCommand", "printParsimonyFile");
exit(1);
}
}
/***********************************************************/
-void ParsimonyCommand::printUSummaryFile() {
+int ParsimonyCommand::printUSummaryFile() {
try {
//column headers
- outSum << "Tree#" << '\t' << "Comb" << '\t' << "ParsScore" << '\t' << '\t' << "ParsSig" << endl;
+ outSum << "Tree#" << '\t' << "Groups" << '\t' << "ParsScore" << '\t' << "ParsSig" << endl;
+ m->mothurOut("Tree#\tGroups\tParsScore\tParsSig"); m->mothurOutEndLine();
//format output
outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
//print each line
for (int i = 0; i< T.size(); i++) {
for(int a = 0; a < numComp; a++) {
- outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << userTreeScores[a][i] << '\t' << UScoreSig[a][i] << endl;
- cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << userTreeScores[a][i] << '\t' << UScoreSig[a][i] << endl;
+ if (m->control_pressed) { outSum.close(); return 0; }
+ if (UScoreSig[a][i] > (1/(float)iters)) {
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
+ m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString(UScoreSig[a][i])); m->mothurOutEndLine();
+ }else {
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << "<" << (1/float(iters)) << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << "<" << (1/float(iters)) << endl;
+ m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString((1/float(iters)))); m->mothurOutEndLine();
+ }
}
}
outSum.close();
+ return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function printUSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ParsimonyCommand class function printUSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ParsimonyCommand", "printUSummaryFile");
exit(1);
}
}
//create treemap
tmap = new TreeMap();
- cout << "Please enter the number of groups you would like to analyze: ";
+ m->mothurOut("Please enter the number of groups you would like to analyze: ");
cin >> numGroups;
-
+ m->mothurOutJustToLog(toString(numGroups)); m->mothurOutEndLine();
+
int num, count;
count = 1;
numEachGroup.resize(numGroups, 0);
+
for (int i = 1; i <= numGroups; i++) {
- cout << "Please enter the number of sequences in group " << i << ": ";
+ m->mothurOut("Please enter the number of sequences in group " + toString(i) + ": ");
cin >> num;
+ m->mothurOutJustToLog(toString(num)); m->mothurOutEndLine();
//set tmaps seqsPerGroup
tmap->seqsPerGroup[toString(i)] = num;
- tmap->namesOfGroups.push_back(toString(i));
+ tmap->addGroup(toString(i));
//set tmaps namesOfSeqs
for (int j = 0; j < num; j++) {
string s;
getline(cin, s);
- //save tmap for later
- globaldata->gTreemap = tmap;
+ m->Treenames = tmap->namesOfSeqs;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function getUserInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ParsimonyCommand class function getUserInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ParsimonyCommand", "getUserInput");
exit(1);
}
}
/***********************************************************/
-void ParsimonyCommand::setGroups() {
- try {
- string allGroups = "";
- numGroups = 0;
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() != 0) {
- if (globaldata->Groups[0] != "all") {
- //check that groups are valid
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
- cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
- // erase the invalid group from globaldata->Groups
- globaldata->Groups.erase(globaldata->Groups.begin()+i);
- }
- }
-
- //if the user only entered invalid groups
- if (globaldata->Groups.size() == 0) {
- cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- numGroups++;
- allGroups += tmap->namesOfGroups[i];
- }
- }else {
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- allGroups += tmap->namesOfGroups[i];
- numGroups++;
- }
- }
- }else{//user has enter "all" and wants the default groups
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- numGroups++;
- allGroups += tmap->namesOfGroups[i];
- }
- globaldata->setGroups("");
- }
- }else {
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- allGroups += tmap->namesOfGroups[i];
- }
- numGroups = 1;
- }
-
- //calculate number of comparsions
- numComp = 0;
- for (int r=0; r<numGroups; r++) {
- for (int l = r+1; l < numGroups; l++) {
- groupComb.push_back(globaldata->Groups[r]+globaldata->Groups[l]);
- numComp++;
- }
- }
-
- //ABC
- if (numComp != 1) {
- groupComb.push_back(allGroups);
- numComp++;
- }
-
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ParsimonyCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
-}
-/*****************************************************************/
-