#include "parsimonycommand.h"
/***********************************************************/
-ParsimonyCommand::ParsimonyCommand() {
+ParsimonyCommand::ParsimonyCommand(string option) {
try {
globaldata = GlobalData::getInstance();
+ abort = false;
+ Groups.clear();
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
- //randomtree will tell us if user had their own treefile or if they just want the random distribution
- randomtree = globaldata->getRandomTree();
+ else {
+ //valid paramters for this command
+ string Array[] = {"random","groups","iters","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ 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);
- distFile = globaldata->getTreeFile() + ".pdistrib";
- openOutputFile(distFile, outDist);
+ //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; }
+ }
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() != 0) {
- //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);
- }
- }
+ randomtree = validParameter.validFile(parameters, "random", false); if (randomtree == "not found") { randomtree = ""; }
- //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]);
- }
- }
- }else {
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ //are you trying to use parsimony without reading a tree or saying you want random distribution
+ if (randomtree == "") {
+ if (globaldata->gTree.size() == 0) {
+ m->mothurOut("You must read a treefile and a groupfile or set the randomtree parameter to the output filename you wish, before you may execute the parsimony command."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ //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 = ""; }
+
+ //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 = ""; globaldata->Groups.clear(); }
+ else {
+ splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
+
+ itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
+ convert(itersString, iters);
+
+ if (abort == false) {
+ //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 == "") {
+ T = globaldata->gTree;
+ tmap = globaldata->gTreemap;
+
+ if(outputDir == "") { outputDir += hasPath(globaldata->getTreeFile()); }
+ output = new ColumnFile(outputDir + getSimpleName(globaldata->getTreeFile()) + ".parsimony", itersString);
+ outputNames.push_back(outputDir + getSimpleName(globaldata->getTreeFile()) + ".parsimony");
+
+ sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".psummary";
+ openOutputFile(sumFile, outSum);
+ outputNames.push_back(sumFile);
+ }else { //user wants random distribution
+ savetmap = globaldata->gTreemap;
+ getUserInput();
+
+ if(outputDir == "") { outputDir += hasPath(randomtree); }
+ output = new ColumnFile(outputDir+ getSimpleName(randomtree), itersString);
+ outputNames.push_back(outputDir+ getSimpleName(randomtree));
}
+
+ //set users groups to analyze
+ util = new SharedUtil();
+ util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "parsimony"); //sets the groups the user wants to analyze
+ util->getCombos(groupComb, globaldata->Groups, numComp);
+
+ if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
+
+ pars = new Parsimony(tmap);
+ counter = 0;
+
}
-
- }else { //user wants random distribution
- savetmap = globaldata->gTreemap;
- getUserInput();
- parsFile = randomtree + ".rd_parsimony";
- openOutputFile(parsFile, out);
+
}
-
- 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";
+ m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand");
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";
+}
+
+//**********************************************************************************************************************
+
+void ParsimonyCommand::help(){
+ try {
+ m->mothurOut("The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter.\n");
+ m->mothurOut("The parsimony command parameters are random, groups and iters. No parameters are required.\n");
+ m->mothurOut("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");
+ m->mothurOut("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");
+ m->mothurOut("The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters).\n");
+ m->mothurOut("Example parsimony(random=out, iters=500).\n");
+ m->mothurOut("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");
+ m->mothurOut("and iters is 1000. The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual.\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename).\n\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParsimonyCommand", "help");
exit(1);
}
}
+
+
/***********************************************************/
int ParsimonyCommand::execute() {
try {
+
+ if (abort == true) { return 0; }
+
+ Progress* reading;
+ reading = new Progress("Comparing to random:", iters);
- //get pscore for users tree
- userData.resize(1,0); //data[0] = pscore.
- randomData.resize(1,0); //data[0] = pscore.
-
- //format output
- outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
- outDist << "RandomTree#" << '\t' << "ParsScore" << endl;
+ if (m->control_pressed) {
+ delete reading; delete pars; delete util; delete output;
+ if (randomtree == "") { outSum.close(); }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ globaldata->Groups.clear();
+ 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.
+ rscoreFreq.resize(numComp);
+ uscoreFreq.resize(numComp);
+ rCumul.resize(numComp);
+ uCumul.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]); //userData[0] = pscore
- cout << "Tree " << i+1 << " parsimony score = " << userData[0] << endl;
- //update uscoreFreq
- it = uscoreFreq.find(userData[0]);
- if (it == uscoreFreq.end()) {//new score
- uscoreFreq[userData[0]] = 1;
- }else{ uscoreFreq[userData[0]]++; }
-
- //add users score to valid scores
- validScores[userData[0]] = userData[0];
+ userData = pars->getValues(T[i]); //data = AB, AC, BC, ABC.
- //save score for summary file
- userTreeScores.push_back(userData[0]);
-
+ if (m->control_pressed) {
+ delete reading; delete pars; delete util; delete output;
+ if (randomtree == "") { outSum.close(); }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ globaldata->Groups.clear();
+ return 0;
+ }
+
+
+ //output scores for each combination
+ for(int k = 0; k < numComp; k++) {
+
+ //update uscoreFreq
+ 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[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();
+
//create random relationships between nodes
randT->assembleRandomTree();
+
//get pscore of random tree
randomData = pars->getValues(randT);
-
- //add trees pscore to map of scores
- it2 = rscoreFreq.find(randomData[0]);
- if (it2 != rscoreFreq.end()) {//already have that score
- rscoreFreq[randomData[0]]++;
- }else{//first time we have seen this score
- rscoreFreq[randomData[0]] = 1;
+
+ if (m->control_pressed) {
+ delete reading; delete pars; delete util; delete output; delete randT;
+ if (randomtree == "") { outSum.close(); }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ globaldata->Groups.clear();
+ return 0;
}
+
+ for(int r = 0; r < numComp; r++) {
+ //add trees pscore to map of scores
+ 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[randomData[0]] = randomData[0];
+ //add randoms score to validscores
+ validScores[randomData[r]] = randomData[r];
+ }
+
+ //update progress bar
+ reading->update(j);
- //output info to pdistrib file
- outDist << j+1 << '\t'<< '\t' << randomData[0] << endl;
-
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();
//create random relationships between nodes
+
randT->assembleRandomTree();
+
+ if (m->control_pressed) {
+ delete reading; delete pars; delete util; delete output; delete randT;
+ globaldata->gTreemap = savetmap;
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ globaldata->Groups.clear();
+ return 0;
+ }
+
+
//get pscore of random tree
randomData = pars->getValues(randT);
-
- //add trees pscore to map of scores
- it2 = rscoreFreq.find(randomData[0]);
- if (it2 != rscoreFreq.end()) {//already have that score
- rscoreFreq[randomData[0]]++;
- }else{//first time we have seen this score
- rscoreFreq[randomData[0]] = 1;
+
+ if (m->control_pressed) {
+ delete reading; delete pars; delete util; delete output; delete randT;
+ globaldata->gTreemap = savetmap;
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ globaldata->Groups.clear();
+ return 0;
}
- //add randoms score to validscores
- validScores[randomData[0]] = randomData[0];
-
+ for(int r = 0; r < numComp; r++) {
+ //add trees pscore to map of scores
+ 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[randomData[r]] = randomData[r];
+ }
+
+ //update progress bar
+ reading->update(j);
+
delete randT;
}
}
-
- 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 (it = validScores.begin(); it != validScores.end(); it++) {
- if (randomtree == "") {
- it2 = uscoreFreq.find(it->first);
- //user data has that score
- if (it2 != uscoreFreq.end()) { uscoreFreq[it->first] /= T.size(); ucumul+= it2->second; }
- else { uscoreFreq[it->first] = 0.0000; } //no user trees with that score
- //make uCumul map
- uCumul[it->first] = ucumul;
+
+ for(int a = 0; a < numComp; a++) {
+ 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 == "") {
+ 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;
+ }
+
+ //make rscoreFreq map and rCumul
+ 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;
}
- //make rscoreFreq map and rCumul
- it2 = rscoreFreq.find(it->first);
- //get percentage of random trees with that info
- if (it2 != rscoreFreq.end()) { rscoreFreq[it->first] /= iters; rcumul+= it2->second; }
- else { rscoreFreq[it->first] = 0.0000; } //no random trees with that score
- rCumul[it->first] = rcumul;
+ //find the signifigance of each user trees score when compared to the random trees and save for printing the summary file
+ for (int h = 0; h < userTreeScores[a].size(); h++) {
+ UScoreSig[a].push_back(rCumul[a][userTreeScores[a][h]]);
+ }
}
- //find the signifigance of each user trees score when compared to the random trees and save for printing the summary file
- for (int h = 0; h < userTreeScores.size(); h++) {
- UScoreSig.push_back(rCumul[userTreeScores[h]]);
+ if (m->control_pressed) {
+ delete reading; delete pars; delete util; delete output;
+ if (randomtree == "") { outSum.close(); }
+ else { globaldata->gTreemap = savetmap; }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ globaldata->Groups.clear();
+ return 0;
}
+
+ //finish progress bar
+ reading->finish();
+ delete reading;
+
printParsimonyFile();
- printUSummaryFile();
+ if (randomtree == "") { printUSummaryFile(); }
//reset globaldata's treemap if you just did random distrib
- if (randomtree != "") { globaldata->gTreemap = savetmap; }
+ if (randomtree != "") {
+ //memory leak prevention
+ //if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap; }
+ globaldata->gTreemap = savetmap;
+ }
- //reset randomTree parameter to ""
- globaldata->setRandomTree("");
//reset groups parameter
- globaldata->Groups.clear();
+ globaldata->Groups.clear();
+
+ if (m->control_pressed) {
+ delete pars; delete util; delete output;
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
+ 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 << "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 << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
+ tags.push_back("Score"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
+ }
+
+ for(int a = 0; a < numComp; a++) {
+ output->initFile(groupComb[a], tags);
+ //print each line
+ for (map<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) {
+ if (randomtree == "") {
+ 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{
+ 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();
}
-
- //format output
- out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-
- //print each line
- for (it = validScores.begin(); it != validScores.end(); it++) {
- if (randomtree == "") {
- out << setprecision(6) << it->first << '\t' << '\t' << uscoreFreq[it->first] << '\t' << uCumul[it->first] << '\t' << rscoreFreq[it->first] << '\t' << rCumul[it->first] << endl;
- }else{
- out << setprecision(6) << it->first << '\t' << '\t' << rscoreFreq[it->first] << '\t' << rCumul[it->first] << endl;
- }
- }
-
- 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' << "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++) {
- outSum << setprecision(6) << i+1 << '\t' << '\t' << userTreeScores[i] << '\t' << UScoreSig[i] << endl;
+ for(int a = 0; a < numComp; a++) {
+ 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));
//set tmaps namesOfSeqs
for (int j = 0; j < num; j++) {
getline(cin, s);
//save tmap for later
+ //memory leak prevention
+ //if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap; }
globaldata->gTreemap = tmap;
+ globaldata->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);
}
}
+
/***********************************************************/
+
projects / mothur.git / blobdiff