string Array[] = {"groups","iters"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- parser = new OptionParser();
- parser->parse(option, parameters); delete parser;
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
- ValidParameters* validParameter = new ValidParameters();
+ ValidParameters validParameter;
//check to make sure all parameters are valid for command
- for (it4 = parameters.begin(); it4 != parameters.end(); it4++) {
- if (validParameter->isValidParameter(it4->first, myArray, it4->second) != true) { abort = true; }
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
if (globaldata->gTree.size() == 0) {//no trees were read
- cout << "You must execute the read.tree command, before you may execute the unifrac.unweighted command." << endl; abort = true; }
+ mothurOut("You must execute the read.tree command, before you may execute the unifrac.unweighted command."); mothurOutEndLine(); abort = true; }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
- groups = validParameter->validFile(parameters, "groups", false);
+ groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
splitAtDash(groups, Groups);
globaldata->Groups = Groups;
}
- itersString = validParameter->validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
+ itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
convert(itersString, iters);
- delete validParameter;
if (abort == false) {
T = globaldata->gTree;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function UnifracUnweightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function UnifracUnweightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracUnweightedCommand", "UnifracUnweightedCommand");
exit(1);
}
}
void UnifracUnweightedCommand::help(){
try {
- cout << "The unifrac.unweighted command can only be executed after a successful read.tree command." << "\n";
- cout << "The unifrac.unweighted command parameters are groups and iters. No parameters are required." << "\n";
- cout << "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";
- cout << "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";
- cout << "The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters)." << "\n";
- cout << "Example unifrac.unweighted(groups=A-B-C, iters=500)." << "\n";
- cout << "The default value for groups is all the groups in your groupfile, and iters is 1000." << "\n";
- cout << "The unifrac.unweighted command output two files: .unweighted and .uwsummary their descriptions are in the manual." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
+ mothurOut("The unifrac.unweighted command can only be executed after a successful read.tree command.\n");
+ mothurOut("The unifrac.unweighted command parameters are groups and iters. No parameters are required.\n");
+ 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");
+ 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");
+ mothurOut("The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters).\n");
+ mothurOut("Example unifrac.unweighted(groups=A-B-C, iters=500).\n");
+ mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n");
+ mothurOut("The unifrac.unweighted command output two files: .unweighted and .uwsummary their descriptions are in the manual.\n");
+ mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracUnweightedCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//create new tree with same num nodes and leaves as users
outSum << "Tree#" << '\t' << "Groups" << '\t' << "UWScore" <<'\t' << "UWSig" << endl;
- cout << "Tree#" << '\t' << "Groups" << '\t' << "UWScore" << '\t' << "UWSig" << endl;
+ mothurOut("Tree#\tGroups\tUWScore\tUWSig"); mothurOutEndLine();
//get pscores for users trees
for (int i = 0; i < T.size(); i++) {
for (int j = 0; j < iters; j++) {
//we need a different getValues because when we swap the labels we only want to swap those in each parwise comparison
randomData = unweighted->getValues(T[i], "", "");
-
+
for(int k = 0; k < numComp; k++) {
//add trees unweighted score to map of scores
- it2 = rscoreFreq[k].find(randomData[k]);
- if (it2 != rscoreFreq[k].end()) {//already have that score
+ map<float,float>::iterator it = rscoreFreq[k].find(randomData[k]);
+ if (it != rscoreFreq[k].end()) {//already have that score
rscoreFreq[k][randomData[k]]++;
}else{//first time we have seen this score
rscoreFreq[k][randomData[k]] = 1;
for(int a = 0; a < numComp; a++) {
float rcumul = 1.0000;
//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++) {
+ for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
//make rscoreFreq map and rCumul
- it2 = rscoreFreq[a].find(it->first);
+ map<float,float>::iterator it2 = rscoreFreq[a].find(it->first);
rCumul[a][it->first] = rcumul;
//get percentage of random trees with that info
if (it2 != rscoreFreq[a].end()) { rscoreFreq[a][it->first] /= iters; rcumul-= it2->second; }
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracUnweightedCommand", "execute");
exit(1);
}
}
for(int a = 0; a < numComp; a++) {
output->initFile(groupComb[a], tags);
//print each line
- for (it = validScores.begin(); it != validScores.end(); it++) {
+ for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
data.push_back(it->first); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
output->output(data);
data.clear();
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUnweightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function printUnweightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracUnweightedCommand", "printUnweightedFile");
exit(1);
}
}
for(int a = 0; a < numComp; a++) {
outSum << i+1 << '\t';
- cout << i+1 << '\t';
+ mothurOut(toString(i+1) + "\t");
if (UWScoreSig[a][0] > (1/(float)iters)) {
outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
+ mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t" + toString(UWScoreSig[a][0])); mothurOutEndLine();
}else {
outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
+ mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t<" + toString((1/float(iters)))); mothurOutEndLine();
}
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracUnweightedCommand", "printUWSummaryFile");
exit(1);
}
}
projects / mothur.git / blobdiff