//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
}
m->runParse = true;
- m->Groups.clear();
- m->namesOfGroups.clear();
+ m->clearGroups();
+ m->clearAllGroups();
m->Treenames.clear();
m->names.clear();
//check for required parameters
treefile = validParameter.validFile(parameters, "tree", true);
- if (treefile == "not open") { abort = 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") { abort = true; }
+ if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
- convert(itersString, iters);
+ m->mothurConvert(itersString, iters);
string temp = validParameter.validFile(parameters, "distance", false);
if (temp == "not found") { phylip = false; outputForm = ""; }
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
if (!random) { iters = 0; } //turn off random calcs
+
+ if (namefile == "") {
+ vector<string> files; files.push_back(treefile);
+ parser.getNameFile(files);
+ }
}
if (m->control_pressed) {
delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
- m->Groups.clear();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ m->clearGroups();
return 0;
}
util = new SharedUtil();
string s; //to make work with setgroups
- util->setGroups(m->Groups, tmap->namesOfGroups, s, numGroups, "weighted"); //sets the groups the user wants to analyze
- util->getCombos(groupComb, m->Groups, numComp);
+ Groups = m->getGroups();
+ vector<string> nameGroups = tmap->getNamesOfGroups();
+ util->setGroups(Groups, nameGroups, s, numGroups, "weighted"); //sets the groups the user wants to analyze
+ util->getCombos(groupComb, Groups, numComp);
+ m->setGroups(Groups);
delete util;
weighted = new Weighted(tmap, includeRoot);
for (int i = 0; i < T.size(); i++) {
if (m->control_pressed) { delete tmap; delete weighted;
- for (int i = 0; i < T.size(); i++) { delete T[i]; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ for (int i = 0; i < T.size(); i++) { delete T[i]; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
counter = 0;
rScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC...
userData = weighted->getValues(T[i], processors, outputDir); //userData[0] = weightedscore
if (m->control_pressed) { delete tmap; delete weighted;
- for (int i = 0; i < T.size(); i++) { delete T[i]; } if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ for (int i = 0; i < T.size(); i++) { delete T[i]; } if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//save users score
for (int s=0; s<numComp; s++) {
vector< vector<string> > namesOfGroupCombos;
for (int a=0; a<numGroups; a++) {
for (int l = 0; l < a; l++) {
- vector<string> groups; groups.push_back(m->Groups[a]); groups.push_back(m->Groups[l]);
+ vector<string> groups; groups.push_back((m->getGroups())[a]); groups.push_back((m->getGroups())[l]);
namesOfGroupCombos.push_back(groups);
}
}
#endif
if (m->control_pressed) { delete tmap; delete weighted;
- for (int i = 0; i < T.size(); i++) { delete T[i]; } delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ for (int i = 0; i < T.size(); i++) { delete T[i]; } delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//report progress
// m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();
if (m->control_pressed) { delete tmap; delete weighted;
- for (int i = 0; i < T.size(); i++) { delete T[i]; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ for (int i = 0; i < T.size(); i++) { delete T[i]; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
printWSummaryFile();
if (phylip) { createPhylipFile(); }
//clear out users groups
- m->Groups.clear();
+ m->clearGroups();
delete tmap; delete weighted;
for (int i = 0; i < T.size(); i++) { delete T[i]; }
if (m->control_pressed) {
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
return 0;
}
double tempScore;
for (int j = lines[(i+1)].start; j < (lines[(i+1)].start + lines[(i+1)].num); j++) { in >> tempScore; scores[j].push_back(tempScore); }
in.close();
- remove(s.c_str());
+ m->mothurRemove(s);
}
return 0;
void UnifracWeightedCommand::printWSummaryFile() {
try {
//column headers
- outSum << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t' << "WSig" << endl;
- m->mothurOut("Tree#\tGroups\tWScore\tWSig"); m->mothurOutEndLine();
+ outSum << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t';
+ m->mothurOut("Tree#\tGroups\tWScore\t");
+ if (random) { outSum << "WSig"; m->mothurOut("WSig"); }
+ outSum << endl; m->mothurOutEndLine();
//format output
outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" + toString((1/float(iters))) + "\n");
}
}else{
- outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl;
- cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl;
- m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t0.00\n");
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << endl;
+ m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\n");
}
count++;
}
if ((outputForm == "lt") || (outputForm == "square")) {
//output numSeqs
- out << m->Groups.size() << endl;
+ out << m->getNumGroups() << endl;
}
//make matrix with scores in it
- vector< vector<float> > dists; dists.resize(m->Groups.size());
- for (int i = 0; i < m->Groups.size(); i++) {
- dists[i].resize(m->Groups.size(), 0.0);
+ vector< vector<float> > dists; dists.resize(m->getNumGroups());
+ for (int i = 0; i < m->getNumGroups(); i++) {
+ dists[i].resize(m->getNumGroups(), 0.0);
}
//flip it so you can print it
- for (int r=0; r<m->Groups.size(); r++) {
+ for (int r=0; r<m->getNumGroups(); r++) {
for (int l = 0; l < r; l++) {
dists[r][l] = utreeScores[count];
dists[l][r] = utreeScores[count];
}
//output to file
- for (int r=0; r<m->Groups.size(); r++) {
+ for (int r=0; r<m->getNumGroups(); r++) {
//output name
- string name = m->Groups[r];
+ string name = (m->getGroups())[r];
if (name.length() < 10) { //pad with spaces to make compatible
while (name.length() < 10) { name += " "; }
}
out << name << '\t';
//output distances
- for (int l = 0; l < m->Groups.size(); l++) { out << dists[r][l] << '\t'; }
+ for (int l = 0; l < m->getNumGroups(); l++) { out << dists[r][l] << '\t'; }
out << endl;
}else{
//output distances
for (int l = 0; l < r; l++) {
- string otherName = m->Groups[l];
+ string otherName = (m->getGroups())[l];
if (otherName.length() < 10) { //pad with spaces to make compatible
while (otherName.length() < 10) { otherName += " "; }
}
projects / mothur.git / blobdiff