m->mothurOut("You must provide a phylip file."); m->mothurOutEndLine();
abort = true;
}
- }
+ }else { m->setPhylipFile(phylipfile); }
//check for required parameters
groupfile = validParameter.validFile(parameters, "group", true);
m->mothurOut("You must provide a group file."); m->mothurOutEndLine();
abort = true;
}
- }
+ }else { m->setGroupFile(groupfile); }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
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);
m->openOutputFile(newGroupFile, outGroups);
for (int i = 0; i < matrix->getNumSeqs(); i++) {
- if (m->control_pressed) { delete groupMap; delete matrix; outGroups.close(); remove(newGroupFile.c_str()); return 0; }
+ if (m->control_pressed) { delete groupMap; delete matrix; outGroups.close(); m->mothurRemove(newGroupFile); return 0; }
Names temp = matrix->getRowInfo(i);
outGroups << temp.seqName << '\t' << temp.groupName << endl;
groupMap = new GroupMap(groupfile);
groupMap->readMap();
- if (m->control_pressed) { delete groupMap; delete matrix; remove(newGroupFile.c_str()); return 0; }
+ if (m->control_pressed) { delete groupMap; delete matrix; m->mothurRemove(newGroupFile); return 0; }
}
setGroups(); //set the groups to be analyzed and sorts them
-
+
+ if (numGroups < 2) { m->mothurOut("[ERROR]: libshuff requires at least 2 groups, you only have " + toString(numGroups) + ", aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ if (m->control_pressed) { delete groupMap; delete matrix; return 0; }
+
/********************************************************************************************/
//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;
- if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
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) {
projects / mothur.git / blobdiff