int TreeGroupCommand::makeSimsShared(InputData& input, SharedRAbundVectors*& lookup, CountTable& ct) {
try {
if (subsample) {
if (subsampleSize == -1) { //user has not set size, set size = smallest samples size
subsampleSize = lookup->getNumSeqsSmallestGroup();
}else {
lookup->removeGroups(subsampleSize);
Groups = lookup->getNamesGroups();
Treenames = Groups;
}
if (lookup->size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command.\n"); m->setControl_pressed(true); return 0; }
}
numGroups = lookup->size();
set<string> processedLabels;
set<string> userLabels = labels;
//as long as you are not at the end of the file or done wih the lines you want
while((lookup != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->getControl_pressed()) { delete lookup; return 1; }
if(allLines == 1 || labels.count(lookup->getLabel()) == 1){
m->mothurOut(lookup->getLabel()+"\n");
createProcesses(lookup, ct);
processedLabels.insert(lookup->getLabel()); userLabels.erase(lookup->getLabel());
}
if ((util.anyLabelsToProcess(lookup->getLabel(), userLabels, "") ) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = lookup->getLabel();
delete lookup;
lookup = input.getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup->getLabel()+"\n");
createProcesses(lookup, ct);
processedLabels.insert(lookup->getLabel()); userLabels.erase(lookup->getLabel());
//restore real lastlabel to save below
lookup->setLabels(saveLabel);
}
lastLabel = lookup->getLabel();
//get next line to process
delete lookup;
lookup = input.getSharedRAbundVectors();
}
if (m->getControl_pressed()) { return 1; }
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
m->mothurOut(". I will use " + lastLabel + ".\n");
needToRun = true;
}else { m->mothurOut(". Please refer to " + lastLabel + ".\n"); }
}
//run last label if you need to
if (needToRun ) {
delete lookup;
lookup = input.getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup->getLabel()+"\n");
createProcesses(lookup, ct);
delete lookup;
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "TreeGroupCommand", "makeSimsShared");
exit(1);
}
}
//**********************************************************************************************************************
int RemoveGroupsCommand::readShared(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
//get group names from sharedfile so we can set Groups to the groupNames we want to keep
//that way we can take advantage of the reads in inputdata and sharedRabundVector
InputData* tempInput = new InputData(sharedfile, "sharedfile");
vector<SharedRAbundVector*> lookup = tempInput->getSharedRAbundVectors();
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
variables["[extension]"] = m->getExtension(sharedfile);
//save m->Groups
vector<string> allGroupsNames = m->getAllGroups();
vector<string> mothurOutGroups = m->getGroups();
vector<string> groupsToKeep;
for (int i = 0; i < allGroupsNames.size(); i++) {
if (!m->inUsersGroups(allGroupsNames[i], m->getGroups())) {
groupsToKeep.push_back(allGroupsNames[i]);
}
}
if (allGroupsNames.size() == groupsToKeep.size()) { m->mothurOut("Your file does not contain any groups you wish to remove."); m->mothurOutEndLine(); m->setGroups(mothurOutGroups); delete tempInput; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
//reset read
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
delete tempInput;
m->setGroups(groupsToKeep);
m->clearAllGroups();
m->saveNextLabel = "";
m->printedSharedHeaders = false;
m->currentSharedBinLabels.clear();
m->sharedBinLabelsInFile.clear();
InputData input(sharedfile, "sharedfile");
lookup = input.getSharedRAbundVectors();
bool wroteSomething = false;
while(lookup[0] != NULL) {
variables["[tag]"] = lookup[0]->getLabel();
string outputFileName = getOutputFileName("shared", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
if (m->control_pressed) { out.close(); m->mothurRemove(outputFileName); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
lookup[0]->printHeaders(out);
for (int i = 0; i < lookup.size(); i++) {
out << lookup[i]->getLabel() << '\t' << lookup[i]->getGroup() << '\t';
lookup[i]->print(out);
wroteSomething = true;
}
//get next line to process
//prevent memory leak
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input.getSharedRAbundVectors();
out.close();
}
m->setGroups(mothurOutGroups);
if (wroteSomething == false) { m->mothurOut("Your file contains only the groups you wish to remove."); m->mothurOutEndLine(); }
string groupsString = "";
for (int i = 0; i < Groups.size()-1; i++) { groupsString += Groups[i] + ", "; }
groupsString += Groups[Groups.size()-1];
m->mothurOut("Removed groups: " + groupsString + " from your shared file."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveGroupsCommand", "readShared");
exit(1);
}
}
int CooccurrenceCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
InputData* input = new InputData(sharedfile, "sharedfile");
vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
string lastLabel = lookup[0]->getLabel();
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
ofstream out;
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
string outputFileName = getOutputFileName("summary", variables);
m->openOutputFile(outputFileName, out);
outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
out << "metric\tlabel\tScore\tzScore\tstandardDeviation\tnp_Pvalue\n";
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
getCooccurrence(lookup, out);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
}
if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = lookup[0]->getLabel();
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
getCooccurrence(lookup, out);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
//restore real lastlabel to save below
lookup[0]->setLabel(saveLabel);
}
lastLabel = lookup[0]->getLabel();
//prevent memory leak
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
if (m->control_pressed) { outputTypes.clear(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
//get next line to process
lookup = input->getSharedRAbundVectors();
}
if (m->control_pressed) { delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
//run last label if you need to
if (needToRun == true) {
for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
lookup = input->getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
getCooccurrence(lookup, out);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
out.close();
//reset groups parameter
delete input;
m->clearGroups();
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(outputFileName); m->mothurOutEndLine();
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "CooccurrenceCommand", "execute");
exit(1);
}
}