//**********************************************************************************************************************
vector<string> LibShuffCommand::setParameters(){
try {
- CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter piters("iters", "Number", "", "10000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pstep("step", "Number", "", "0.01", "", "", "",false,false); parameters.push_back(pstep);
- CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter pform("form", "Multiple", "discrete-integral", "integral", "", "", "",false,false); parameters.push_back(pform);
- CommandParameter psim("sim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psim);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","coverage-libshuffsummary",false,true,true); parameters.push_back(pphylip);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pgroup);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter piters("iters", "Number", "", "10000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pstep("step", "Number", "", "0.01", "", "", "","",false,false); parameters.push_back(pstep);
+ CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pcutoff);
+ CommandParameter pform("form", "Multiple", "discrete-integral", "integral", "", "", "","",false,false); parameters.push_back(pform);
+ CommandParameter psim("sim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psim);
+ 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); }
}
}
//**********************************************************************************************************************
+string LibShuffCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "coverage") { pattern = "[filename],libshuff.coverage"; }
+ else if (type == "libshuffsummary") { pattern = "[filename],libshuff.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LibShuffCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
LibShuffCommand::LibShuffCommand(){
try {
abort = true; calledHelp = true;
else {
savegroups = groups;
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
string temp;
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "10000"; }
- convert(temp, iters);
+ m->mothurConvert(temp, iters);
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "1.0"; }
- convert(temp, cutOff);
+ m->mothurConvert(temp, cutOff);
temp = validParameter.validFile(parameters, "step", false); if (temp == "not found") { temp = "0.01"; }
- convert(temp, step);
+ m->mothurConvert(temp, step);
temp = validParameter.validFile(parameters, "sim", false); if (temp == "not found") { temp = "F"; }
sim = m->isTrue(temp);
//this is needed because when we read the matrix we sort it into groups in alphabetical order
//the rest of the command and the classes used in this command assume specific order
/********************************************************************************************/
- matrix->setGroups(groupMap->namesOfGroups);
+ matrix->setGroups(groupMap->getNamesOfGroups());
vector<int> sizes;
- for (int i = 0; i < groupMap->namesOfGroups.size(); i++) { sizes.push_back(groupMap->getNumSeqs(groupMap->namesOfGroups[i])); }
+ for (int i = 0; i < (groupMap->getNamesOfGroups()).size(); i++) { sizes.push_back(groupMap->getNumSeqs((groupMap->getNamesOfGroups())[i])); }
matrix->setSizes(sizes);
savedDXYValues = form->evaluateAll();
savedMinValues = form->getSavedMins();
- if (m->control_pressed) { delete form; m->Groups.clear(); delete matrix; delete groupMap; return 0; }
+ if (m->control_pressed) { delete form; m->clearGroups(); delete matrix; delete groupMap; return 0; }
pValueCounts.resize(numGroups);
for(int i=0;i<numGroups;i++){
pValueCounts[i].assign(numGroups, 0);
}
- if (m->control_pressed) { outputTypes.clear(); delete form; m->Groups.clear(); delete matrix; delete groupMap; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; return 0; }
Progress* reading = new Progress();
for(int i=0;i<numGroups-1;i++) {
for(int j=i+1;j<numGroups;j++) {
- if (m->control_pressed) { outputTypes.clear(); delete form; m->Groups.clear(); delete matrix; delete groupMap; delete reading; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
reading->newLine(groupNames[i]+'-'+groupNames[j], iters);
int spoti = groupMap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
for(int p=0;p<iters;p++) {
- if (m->control_pressed) { outputTypes.clear(); delete form; m->Groups.clear(); delete matrix; delete groupMap; delete reading; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
form->randomizeGroups(spoti,spotj);
if(form->evaluatePair(spoti,spotj) >= savedDXYValues[spoti][spotj]) { pValueCounts[i][j]++; }
if(form->evaluatePair(spotj,spoti) >= savedDXYValues[spotj][spoti]) { pValueCounts[j][i]++; }
- if (m->control_pressed) { outputTypes.clear(); delete form; m->Groups.clear(); delete matrix; delete groupMap; delete reading; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
reading->update(p);
}
}
}
- if (m->control_pressed) { outputTypes.clear(); delete form; m->Groups.clear(); delete matrix; delete groupMap; delete reading; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
reading->finish();
delete reading;
printCoverageFile();
//clear out users groups
- m->Groups.clear();
+ m->clearGroups();
delete form;
delete matrix; delete groupMap;
try {
ofstream outCov;
- summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "libshuff.coverage";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipfile));
+ summaryFile = getOutputFileName("coverage", variables);
m->openOutputFile(summaryFile, outCov);
outputNames.push_back(summaryFile); outputTypes["coverage"].push_back(summaryFile);
outCov.setf(ios::fixed, ios::floatfield); outCov.setf(ios::showpoint);
try {
ofstream outSum;
- summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "libshuff.summary";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipfile));
+ summaryFile = getOutputFileName("libshuffsummary",variables);
m->openOutputFile(summaryFile, outSum);
outputNames.push_back(summaryFile); outputTypes["libshuffsummary"].push_back(summaryFile);
void LibShuffCommand::setGroups() {
try {
+ vector<string> myGroups = m->getGroups();
//if the user has not entered specific groups to analyze then do them all
- if (m->Groups.size() == 0) {
+ if (m->getNumGroups() == 0) {
numGroups = groupMap->getNumGroups();
for (int i=0; i < numGroups; i++) {
- m->Groups.push_back(groupMap->namesOfGroups[i]);
+ myGroups.push_back((groupMap->getNamesOfGroups())[i]);
}
} else {
if (savegroups != "all") {
//check that groups are valid
- for (int i = 0; i < m->Groups.size(); i++) {
- if (groupMap->isValidGroup(m->Groups[i]) != true) {
- m->mothurOut(m->Groups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
+ for (int i = 0; i < myGroups.size(); i++) {
+ if (groupMap->isValidGroup(myGroups[i]) != true) {
+ m->mothurOut(myGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
// erase the invalid group from globaldata->Groups
- m->Groups.erase(m->Groups.begin()+i);
+ myGroups.erase(myGroups.begin()+i);
}
}
//if the user only entered invalid groups
- if ((m->Groups.size() == 0) || (m->Groups.size() == 1)) {
+ if ((myGroups.size() == 0) || (myGroups.size() == 1)) {
numGroups = groupMap->getNumGroups();
for (int i=0; i < numGroups; i++) {
- m->Groups.push_back(groupMap->namesOfGroups[i]);
+ myGroups.push_back((groupMap->getNamesOfGroups())[i]);
}
m->mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); m->mothurOutEndLine();
- } else { numGroups = m->Groups.size(); }
+ } else { numGroups = myGroups.size(); }
} else { //users wants all groups
numGroups = groupMap->getNumGroups();
- m->Groups.clear();
+ myGroups.clear();
for (int i=0; i < numGroups; i++) {
- m->Groups.push_back(groupMap->namesOfGroups[i]);
+ myGroups.push_back((groupMap->getNamesOfGroups())[i]);
}
}
}
//sort so labels match
- sort(m->Groups.begin(), m->Groups.end());
+ sort(myGroups.begin(), myGroups.end());
//sort
- sort(groupMap->namesOfGroups.begin(), groupMap->namesOfGroups.end());
+ //sort(groupMap->namesOfGroups.begin(), groupMap->namesOfGroups.end());
- for (int i = 0; i < groupMap->namesOfGroups.size(); i++) { groupMap->groupIndex[groupMap->namesOfGroups[i]] = i; }
+ for (int i = 0; i < (groupMap->getNamesOfGroups()).size(); i++) { groupMap->groupIndex[(groupMap->getNamesOfGroups())[i]] = i; }
- groupNames = m->Groups;
+ groupNames = myGroups;
+ m->setGroups(myGroups);
}
catch(exception& e) {
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