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.weighted command." << endl; abort = true; }
+ mothurOut("You must execute the read.tree command, before you may execute the unifrac.weighted 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 UnifracWeightedCommand class Function UnifracWeightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function UnifracWeightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand");
exit(1);
}
}
void UnifracWeightedCommand::help(){
try {
- cout << "The unifrac.weighted command can only be executed after a successful read.tree command." << "\n";
- cout << "The unifrac.weighted 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 2 valid groups." << "\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.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters)." << "\n";
- cout << "Example unifrac.weighted(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.weighted command output two files: .weighted and .wsummary 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.weighted command can only be executed after a successful read.tree command.\n");
+ mothurOut("The unifrac.weighted 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 2 valid groups.\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.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters).\n");
+ mothurOut("Example unifrac.weighted(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.weighted command output two files: .weighted and .wsummary 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 UnifracWeightedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracWeightedCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************/
//so if you have 1000 random trees the index returned is 100
//then there are 900 trees with a score greater then you.
//giving you a signifigance of 0.900
- int index = findIndex(userData[f], f); if (index == -1) { cout << "error in UnifracWeightedCommand" << endl; exit(1); } //error code
+ int index = findIndex(userData[f], f); if (index == -1) { mothurOut("error in UnifracWeightedCommand"); mothurOutEndLine(); exit(1); } //error code
//the signifigance is the number of trees with the users score or higher
WScoreSig.push_back((iters-index)/(float)iters);
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracWeightedCommand", "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 UnifracWeightedCommand class Function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracWeightedCommand", "printWeightedFile");
exit(1);
}
}
try {
//column headers
outSum << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t' << "WSig" << endl;
- cout << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t' << "WSig" << endl;
+ mothurOut("Tree#\tGroups\tWScore\tWSig"); mothurOutEndLine();
//format output
outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
if (WScoreSig[count] > (1/(float)iters)) {
outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
+ mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t" + toString(WScoreSig[count])); mothurOutEndLine();
}else{
outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
+ mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" + toString((1/float(iters)))); mothurOutEndLine();
}
count++;
}
outSum.close();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracWeightedCommand", "printWSummaryFile");
exit(1);
}
}
return rScores[index].size();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracWeightedCommand", "findIndex");
exit(1);
}
}
for (int f = 0; f < numComp; f++) {
for (int i = 0; i < rScores[f].size(); i++) { //looks like 0,0,1,1,1,2,4,7... you want to make a map that say rScoreFreq[0] = 2, rScoreFreq[1] = 3...
validScores[rScores[f][i]] = rScores[f][i];
- it = rScoreFreq[f].find(rScores[f][i]);
+ map<float,float>::iterator it = rScoreFreq[f].find(rScores[f][i]);
if (it != rScoreFreq[f].end()) {
rScoreFreq[f][rScores[f][i]]++;
}else{
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 UnifracWeightedCommand class Function calculateFreqsCums. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function calculateFreqsCums. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracWeightedCommand", "calculateFreqsCums");
exit(1);
}
-
}
/***********************************************************/
projects / mothur.git / blobdiff