//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->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") {
- //if there is a current design file, use it
- groupfile = m->getGroupFile();
- if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
- else { m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ if (groupfile == "not open") { groupfile = ""; 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 = m->hasPath(treefile); }
string temp;
temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
- convert(temp, freq);
+ m->mothurConvert(temp, freq);
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
- convert(temp, iters);
+ m->mothurConvert(temp, iters);
temp = validParameter.validFile(parameters, "rarefy", false); if (temp == "not found") { temp = "F"; }
rarefy = m->isTrue(temp);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
if ((!collect) && (!rarefy) && (!summary)) { m->mothurOut("No outputs selected. You must set either collect, rarefy or summary to true, summary=T by default."); m->mothurOutEndLine(); abort=true; }
+
+ if (namefile == "") {
+ vector<string> files; files.push_back(treefile);
+ parser.getNameFile(files);
+ }
}
}
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- //read in group map info.
- tmap = new TreeMap(groupfile);
- tmap->readMap();
+ m->setTreeFile(treefile);
+
+ if (groupfile != "") {
+ //read in group map info.
+ tmap = new TreeMap(groupfile);
+ tmap->readMap();
+ }else{ //fake out by putting everyone in one group
+ Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
+ tmap = new TreeMap();
+
+ for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
+ }
if (namefile != "") { readNamesFile(); }
if (m->control_pressed) {
delete tmap; for (int i = 0; i < trees.size(); i++) { delete trees[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;
}
}
SharedUtil* util = new SharedUtil();
- util->setGroups(m->Groups, tmap->namesOfGroups, "treegroup"); //sets the groups the user wants to analyze
+ vector<string> mGroups = m->getGroups();
+ vector<string> tGroups = tmap->getNamesOfGroups();
+ util->setGroups(mGroups, tGroups, "phylo.diversity"); //sets the groups the user wants to analyze
delete util;
//incase the user had some mismatches between the tree and group files we don't want group xxx to be analyzed
- for (int i = 0; i < m->Groups.size(); i++) { if (m->Groups[i] == "xxx") { m->Groups.erase(m->Groups.begin()+i); break; } }
+ for (int i = 0; i < mGroups.size(); i++) { if (mGroups[i] == "xxx") { mGroups.erase(mGroups.begin()+i); break; } }
+ m->setGroups(mGroups);
vector<string> outputNames;
//for each of the users trees
for(int i = 0; i < trees.size(); i++) {
- if (m->control_pressed) { delete tmap; for (int j = 0; j < trees.size(); j++) { delete trees[j]; } for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
+ if (m->control_pressed) { delete tmap; for (int j = 0; j < trees.size(); j++) { delete trees[j]; } for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
ofstream outSum, outRare, outCollect;
string outSumFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(i+1) + ".phylodiv.summary";
//create a vector containing indexes of leaf nodes, randomize it, select nodes to send to calculator
vector<int> randomLeaf;
for (int j = 0; j < numLeafNodes; j++) {
- if (m->inUsersGroups(trees[i]->tree[j].getGroup(), m->Groups) == true) { //is this a node from the group the user selected.
+ if (m->inUsersGroups(trees[i]->tree[j].getGroup(), mGroups) == true) { //is this a node from the group the user selected.
randomLeaf.push_back(j);
}
}
//find largest group total
int largestGroup = 0;
- for (int j = 0; j < m->Groups.size(); j++) {
- if (tmap->seqsPerGroup[m->Groups[j]] > largestGroup) { largestGroup = tmap->seqsPerGroup[m->Groups[j]]; }
+ for (int j = 0; j < mGroups.size(); j++) {
+ if (tmap->seqsPerGroup[mGroups[j]] > largestGroup) { largestGroup = tmap->seqsPerGroup[mGroups[j]]; }
//initialize diversity
- diversity[m->Groups[j]].resize(tmap->seqsPerGroup[m->Groups[j]]+1, 0.0); //numSampled
+ diversity[mGroups[j]].resize(tmap->seqsPerGroup[mGroups[j]]+1, 0.0); //numSampled
//groupA 0.0 0.0
//initialize sumDiversity
- sumDiversity[m->Groups[j]].resize(tmap->seqsPerGroup[m->Groups[j]]+1, 0.0);
+ sumDiversity[mGroups[j]].resize(tmap->seqsPerGroup[mGroups[j]]+1, 0.0);
}
//convert freq percentage to number
if(largestGroup % increment != 0){ numSampledList.insert(largestGroup); }
//add other groups ending points
- for (int j = 0; j < m->Groups.size(); j++) {
- if (numSampledList.count(diversity[m->Groups[j]].size()-1) == 0) { numSampledList.insert(diversity[m->Groups[j]].size()-1); }
+ for (int j = 0; j < mGroups.size(); j++) {
+ if (numSampledList.count(diversity[mGroups[j]].size()-1) == 0) { numSampledList.insert(diversity[mGroups[j]].size()-1); }
}
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
if(processors == 1){
driver(trees[i], diversity, sumDiversity, iters, increment, randomLeaf, numSampledList, outCollect, outSum, true);
}else{
}
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
//**********************************************************************************************************************
int PhyloDiversityCommand::createProcesses(vector<int>& procIters, Tree* t, map< string, vector<float> >& div, map<string, vector<float> >& sumDiv, int numIters, int increment, vector<int>& randomLeaf, set<int>& numSampledList, ofstream& outCollect, ofstream& outSum){
try {
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
int process = 1;
vector<int> processIDS;
}
in.close();
- remove(inTemp.c_str());
+ m->mothurRemove(inTemp);
}
#endif
int PhyloDiversityCommand::driver(Tree* t, map< string, vector<float> >& div, map<string, vector<float> >& sumDiv, int numIters, int increment, vector<int>& randomLeaf, set<int>& numSampledList, ofstream& outCollect, ofstream& outSum, bool doSumCollect){
try {
int numLeafNodes = randomLeaf.size();
+ vector<string> mGroups = m->getGroups();
for (int l = 0; l < numIters; l++) {
random_shuffle(randomLeaf.begin(), randomLeaf.end());
//initialize counts
map<string, int> counts;
map< string, set<int> > countedBranch;
- for (int j = 0; j < m->Groups.size(); j++) { counts[m->Groups[j]] = 0; countedBranch[m->Groups[j]].insert(-2); } //add dummy index to initialize countedBranch sets
+ for (int j = 0; j < mGroups.size(); j++) { counts[mGroups[j]] = 0; countedBranch[mGroups[j]].insert(-2); } //add dummy index to initialize countedBranch sets
for(int k = 0; k < numLeafNodes; k++){
if (rarefy) {
//add this diversity to the sum
- for (int j = 0; j < m->Groups.size(); j++) {
- for (int g = 0; g < div[m->Groups[j]].size(); g++) {
- sumDiv[m->Groups[j]][g] += div[m->Groups[j]][g];
+ for (int j = 0; j < mGroups.size(); j++) {
+ for (int g = 0; g < div[mGroups[j]].size(); g++) {
+ sumDiv[mGroups[j]][g] += div[mGroups[j]][g];
}
}
}
out << "Groups\tnumSampled\tphyloDiversity" << endl;
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-
- for (int j = 0; j < m->Groups.size(); j++) {
- int numSampled = (div[m->Groups[j]].size()-1);
- out << m->Groups[j] << '\t' << numSampled << '\t';
+
+ vector<string> mGroups = m->getGroups();
+ for (int j = 0; j < mGroups.size(); j++) {
+ int numSampled = (div[mGroups[j]].size()-1);
+ out << mGroups[j] << '\t' << numSampled << '\t';
float score;
- if (scale) { score = (div[m->Groups[j]][numSampled] / (float)numIters) / (float)numSampled; }
- else { score = div[m->Groups[j]][numSampled] / (float)numIters; }
+ if (scale) { score = (div[mGroups[j]][numSampled] / (float)numIters) / (float)numSampled; }
+ else { score = div[mGroups[j]][numSampled] / (float)numIters; }
out << setprecision(4) << score << endl;
}
try {
out << "numSampled\t";
- for (int i = 0; i < m->Groups.size(); i++) { out << m->Groups[i] << '\t'; }
+ vector<string> mGroups = m->getGroups();
+ for (int i = 0; i < mGroups.size(); i++) { out << mGroups[i] << '\t'; }
out << endl;
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
int numSampled = *it;
out << numSampled << '\t';
-
- for (int j = 0; j < m->Groups.size(); j++) {
- if (numSampled < div[m->Groups[j]].size()) {
+
+ for (int j = 0; j < mGroups.size(); j++) {
+ if (numSampled < div[mGroups[j]].size()) {
float score;
- if (scale) { score = (div[m->Groups[j]][numSampled] / (float)numIters) / (float)numSampled; }
- else { score = div[m->Groups[j]][numSampled] / (float)numIters; }
+ if (scale) { score = (div[mGroups[j]][numSampled] / (float)numIters) / (float)numSampled; }
+ else { score = div[mGroups[j]][numSampled] / (float)numIters; }
out << setprecision(4) << score << '\t';
}else { out << "NA" << '\t'; }
projects / mothur.git / blobdiff