//**********************************************************************************************************************
vector<string> IndicatorCommand::setParameters(){
try {
- CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pdesign);
- CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(pshared);
- CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(prelabund);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pdesign("design", "InputTypes", "", "", "TreeDesign", "TreeDesign", "none","summary",false,false,true); parameters.push_back(pdesign);
+ CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none","summary",false,false,true); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none","summary",false,false); parameters.push_back(prelabund);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter ptree("tree", "InputTypes", "", "", "TreeDesign", "TreeDesign", "none","tree-summary",false,false,true); parameters.push_back(ptree);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pprocessors);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
string IndicatorCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The indicator command reads a shared or relabund file and a tree file, and outputs a .indicator.tre and .indicator.summary file. \n";
+ helpString += "The indicator command can be run in 3 ways: with a shared or relabund file and a design file, or with a shared or relabund file and a tree file, or with a shared or relabund file, tree file and design file. \n";
+ helpString += "The indicator command outputs a .indicator.summary file and a .indicator.tre if a tree is given. \n";
helpString += "The new tree contains labels at each internal node. The label is the node number so you can relate the tree to the summary file.\n";
helpString += "The summary file lists the indicator value for each OTU for each node.\n";
- helpString += "The indicator command parameters are tree, groups, shared, relabund, design and label. The tree parameter is required as well as either shared or relabund.\n";
- helpString += "The design parameter allows you to provide a design file to relate the tree to the shared or relabund file.\n";
+ helpString += "The indicator command parameters are tree, groups, shared, relabund, design and label. \n";
+ helpString += "The design parameter allows you to relate the tree to the shared or relabund file, if your tree contains the grouping names, or if no tree is provided to group your groups into groupings.\n";
helpString += "The groups parameter allows you to specify which of the groups in your shared or relabund you would like analyzed, or if you provide a design file the groups in your design file. The groups may be entered separated by dashes.\n";
helpString += "The label parameter indicates at what distance your tree relates to the shared or relabund.\n";
+ helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
+ helpString += "The iters parameter allows you to set number of randomization for the P value. The default is 1000.";
helpString += "The indicator command should be used in the following format: indicator(tree=test.tre, shared=test.shared, label=0.03)\n";
helpString += "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n";
return helpString;
exit(1);
}
}
-
+//**********************************************************************************************************************
+string IndicatorCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "tree") { pattern = "[filename],indicator.tre"; }
+ else if (type == "summary") { pattern = "[filename],indicator.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, "IndicatorCommand", "getOutputPattern");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
IndicatorCommand::IndicatorCommand(){
try {
}
m->runParse = true;
- m->Groups.clear();
- m->namesOfGroups.clear();
+ m->clearGroups();
+ m->clearAllGroups();
m->Treenames.clear();
- m->names.clear();
vector<string> tempOutNames;
outputTypes["tree"] = tempOutNames;
//check for required parameters
treefile = validParameter.validFile(parameters, "tree", true);
- if (treefile == "not open") { 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; }
- }
+ if (treefile == "not open") { treefile = ""; abort = true; }
+ else if (treefile == "not found") { treefile = ""; }
+ else { m->setTreeFile(treefile); }
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
- else { inputFileName = sharedfile; }
+ else { inputFileName = sharedfile; m->setSharedFile(sharedfile); }
relabundfile = validParameter.validFile(parameters, "relabund", true);
if (relabundfile == "not open") { abort = true; }
else if (relabundfile == "not found") { relabundfile = ""; }
- else { inputFileName = relabundfile; }
+ else { inputFileName = relabundfile; m->setRelAbundFile(relabundfile); }
designfile = validParameter.validFile(parameters, "design", true);
- if (designfile == "not open") { abort = true; }
+ if (designfile == "not open") { designfile = ""; abort = true; }
else if (designfile == "not found") { designfile = ""; }
+ else { m->setDesignFile(designfile); }
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; Groups.push_back("all"); }
else { m->splitAtDash(groups, Groups); }
- m->Groups = Groups;
+ m->setGroups(Groups);
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; }
+ string temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ m->mothurConvert(temp, iters);
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
+
if ((relabundfile == "") && (sharedfile == "")) {
//is there are current file available for either of these?
//give priority to shared, then relabund
}
}
- if ((relabundfile != "") && (sharedfile != "")) { m->mothurOut("You may not use both a shared and relabund file."); m->mothurOutEndLine(); abort = true; }
+
+ if ((designfile == "") && (treefile == "")) {
+ treefile = m->getTreeFile();
+ if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
+ else {
+ designfile = m->getDesignFile();
+ if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("[ERROR]: You must provide either a tree or design file."); m->mothurOutEndLine(); abort = true;
+ }
+ }
+ }
+
+ if ((relabundfile != "") && (sharedfile != "")) { m->mothurOut("[ERROR]: You may not use both a shared and relabund file."); m->mothurOutEndLine(); abort = true; }
+
}
}
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
+
+ int start = time(NULL);
- //read designfile if given and set up globaldatas groups for read of sharedfiles
+ //read designfile if given and set up groups for read of sharedfiles
if (designfile != "") {
designMap = new GroupMap(designfile);
designMap->readDesignMap();
//fill Groups - checks for "all" and for any typo groups
- SharedUtil* util = new SharedUtil();
- util->setGroups(Groups, designMap->namesOfGroups);
- delete util;
+ SharedUtil util;
+ vector<string> nameGroups = designMap->getNamesOfGroups();
+ util.setGroups(Groups, nameGroups);
+ designMap->setNamesOfGroups(nameGroups);
- //loop through the Groups and fill Globaldata's Groups with the design file info
- m->Groups = designMap->getNamesSeqs(Groups);
+ vector<string> namesSeqs = designMap->getNamesSeqs(Groups);
+ m->setGroups(namesSeqs);
}
/***************************************************/
if (lookupFloat[0] == NULL) { m->mothurOut("[ERROR] reading relabund file."); m->mothurOutEndLine(); return 0; }
}
- //reset Globaldatas groups if needed
- if (designfile != "") { m->Groups = Groups; }
+ //reset groups if needed
+ if (designfile != "") { m->setGroups(Groups); }
/***************************************************/
// reading tree info //
/***************************************************/
- string groupfile = "";
- m->setTreeFile(treefile);
- Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
- treeMap = new TreeMap();
- bool mismatch = false;
-
- for (int i = 0; i < m->Treenames.size(); i++) {
- //sanity check - is this a group that is not in the sharedfile?
- if (designfile == "") {
- if (!(m->inUsersGroups(m->Treenames[i], m->namesOfGroups))) {
- m->mothurOut("[ERROR]: " + m->Treenames[i] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
- mismatch = true;
- }
- treeMap->addSeq(m->Treenames[i], "Group1");
- }else{
- vector<string> myGroups; myGroups.push_back(m->Treenames[i]);
- vector<string> myNames = designMap->getNamesSeqs(myGroups);
-
- for(int k = 0; k < myNames.size(); k++) {
- if (!(m->inUsersGroups(myNames[k], m->namesOfGroups))) {
- m->mothurOut("[ERROR]: " + myNames[k] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
+ if (treefile != "") {
+ string groupfile = "";
+ m->setTreeFile(treefile);
+ Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
+ ct = new CountTable();
+ bool mismatch = false;
+
+ set<string> nameMap;
+ map<string, string> groupMap;
+ set<string> gps;
+ for (int i = 0; i < m->Treenames.size(); i++) {
+ nameMap.insert(m->Treenames[i]);
+ //sanity check - is this a group that is not in the sharedfile?
+ if (i == 0) { gps.insert("Group1"); }
+ if (designfile == "") {
+ if (!(m->inUsersGroups(m->Treenames[i], m->getAllGroups()))) {
+ m->mothurOut("[ERROR]: " + m->Treenames[i] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
mismatch = true;
}
+ groupMap[m->Treenames[i]] = "Group1";
+ }else{
+ vector<string> myGroups; myGroups.push_back(m->Treenames[i]);
+ vector<string> myNames = designMap->getNamesSeqs(myGroups);
+
+ for(int k = 0; k < myNames.size(); k++) {
+ if (!(m->inUsersGroups(myNames[k], m->getAllGroups()))) {
+ m->mothurOut("[ERROR]: " + myNames[k] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
+ mismatch = true;
+ }
+ }
+ groupMap[m->Treenames[i]] = "Group1";
}
- treeMap->addSeq(m->Treenames[i], "Group1");
+ }
+ ct->createTable(nameMap, groupMap, gps);
+
+ if ((designfile != "") && (m->Treenames.size() != Groups.size())) { cout << Groups.size() << '\t' << m->Treenames.size() << endl; m->mothurOut("[ERROR]: You design file does not match your tree, aborting."); m->mothurOutEndLine(); mismatch = true; }
+
+ if (mismatch) { //cleanup and exit
+ if (designfile != "") { delete designMap; }
+ if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
+ else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
+ delete ct;
+ return 0;
}
- }
-
- if ((designfile != "") && (m->Treenames.size() != Groups.size())) { m->mothurOut("[ERROR]: You design file does not match your tree, aborting."); m->mothurOutEndLine(); mismatch = true; }
-
- if (mismatch) { //cleanup and exit
- if (designfile != "") { delete designMap; }
- if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
- else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
- delete treeMap;
- return 0;
- }
-
- read = new ReadNewickTree(treefile);
- int readOk = read->read(treeMap);
-
- if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete treeMap; delete read; return 0; }
-
- vector<Tree*> T = read->getTrees();
-
- delete read;
-
- if (m->control_pressed) {
- if (designfile != "") { delete designMap; }
- if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
- else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
- for (int i = 0; i < T.size(); i++) { delete T[i]; } delete treeMap; return 0;
- }
+
+ read = new ReadNewickTree(treefile);
+ int readOk = read->read(ct);
- T[0]->assembleTree();
-
- /***************************************************/
- // create ouptut tree - respecting pickedGroups //
- /***************************************************/
- Tree* outputTree = new Tree(m->Groups.size(), treeMap);
-
- outputTree->getSubTree(T[0], m->Groups);
- outputTree->assembleTree();
+ if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete ct; delete read; return 0; }
- //no longer need original tree, we have output tree to use and label
- for (int i = 0; i < T.size(); i++) { delete T[i]; }
-
+ vector<Tree*> T = read->getTrees();
+
+ delete read;
+
+ if (m->control_pressed) {
+ if (designfile != "") { delete designMap; }
+ if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
+ else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
+ for (int i = 0; i < T.size(); i++) { delete T[i]; } delete ct; return 0;
+ }
+
+ T[0]->assembleTree();
+
+ /***************************************************/
+ // create ouptut tree - respecting pickedGroups //
+ /***************************************************/
+ Tree* outputTree = new Tree(m->getNumGroups(), ct);
+
+ outputTree->getSubTree(T[0], m->getGroups());
+ outputTree->assembleTree();
- if (m->control_pressed) {
- if (designfile != "") { delete designMap; }
- if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
- else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
- delete outputTree; delete treeMap; return 0;
+ //no longer need original tree, we have output tree to use and label
+ for (int i = 0; i < T.size(); i++) { delete T[i]; }
+
+ if (m->control_pressed) {
+ if (designfile != "") { delete designMap; }
+ if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
+ else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
+ delete outputTree; delete ct; return 0;
+ }
+
+ /***************************************************/
+ // get indicator species values //
+ /***************************************************/
+ GetIndicatorSpecies(outputTree);
+ delete outputTree; delete ct;
+
+ }else { //run with design file only
+ //get indicator species
+ GetIndicatorSpecies();
}
- /***************************************************/
- // get indicator species values //
- /***************************************************/
- GetIndicatorSpecies(outputTree);
-
if (designfile != "") { delete designMap; }
if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
- delete outputTree; delete treeMap;
-
- 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; }
//set tree file as new current treefile
- string current = "";
- itTypes = outputTypes.find("tree");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
+ if (treefile != "") {
+ string current = "";
+ itTypes = outputTypes.find("tree");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
+ }
}
+ m->mothurOutEndLine(); m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to find the indicator species."); m->mothurOutEndLine();
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
}
}
//**********************************************************************************************************************
+//divide shared or relabund file by groupings in the design file
+//report all otu values to file
+int IndicatorCommand::GetIndicatorSpecies(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(inputFileName); }
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName));
+ string outputFileName = getOutputFileName("summary", variables);
+ outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+ m->mothurOutEndLine(); m->mothurOut("Species\tIndicator_Groups\tIndicatorValue\tpValue\n");
+
+ int numBins = 0;
+ if (sharedfile != "") { numBins = lookup[0]->getNumBins(); }
+ else { numBins = lookupFloat[0]->getNumBins(); }
+
+ if (m->control_pressed) { out.close(); return 0; }
+
+ /*****************************************************/
+ //create vectors containing rabund info //
+ /*****************************************************/
+
+ vector<float> indicatorValues; //size of numBins
+ vector<float> pValues;
+ vector<string> indicatorGroups;
+ map< vector<int>, vector<int> > randomGroupingsMap; //maps location in groupings to location in groupings, ie, [0][0] -> [1][2]. This is so we don't have to actually move the sharedRabundVectors.
+
+ if (sharedfile != "") {
+ vector< vector<SharedRAbundVector*> > groupings;
+ set<string> groupsAlreadyAdded;
+ vector<SharedRAbundVector*> subset;
+
+ //for each grouping
+ for (int i = 0; i < (designMap->getNamesOfGroups()).size(); i++) {
+
+ for (int k = 0; k < lookup.size(); k++) {
+ //are you from this grouping?
+ if (designMap->getGroup(lookup[k]->getGroup()) == (designMap->getNamesOfGroups())[i]) {
+ subset.push_back(lookup[k]);
+ groupsAlreadyAdded.insert(lookup[k]->getGroup());
+ }
+ }
+ if (subset.size() != 0) { groupings.push_back(subset); }
+ subset.clear();
+ }
+
+ if (groupsAlreadyAdded.size() != lookup.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
+
+ indicatorValues = getValues(groupings, indicatorGroups, randomGroupingsMap);
+
+ pValues = getPValues(groupings, lookup.size(), indicatorValues);
+ }else {
+ vector< vector<SharedRAbundFloatVector*> > groupings;
+ set<string> groupsAlreadyAdded;
+ vector<SharedRAbundFloatVector*> subset;
+
+ //for each grouping
+ for (int i = 0; i < (designMap->getNamesOfGroups()).size(); i++) {
+ for (int k = 0; k < lookupFloat.size(); k++) {
+ //are you from this grouping?
+ if (designMap->getGroup(lookupFloat[k]->getGroup()) == (designMap->getNamesOfGroups())[i]) {
+ subset.push_back(lookupFloat[k]);
+ groupsAlreadyAdded.insert(lookupFloat[k]->getGroup());
+ }
+ }
+ if (subset.size() != 0) { groupings.push_back(subset); }
+ subset.clear();
+ }
+
+ if (groupsAlreadyAdded.size() != lookupFloat.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
+
+ indicatorValues = getValues(groupings, indicatorGroups, randomGroupingsMap);
+
+ pValues = getPValues(groupings, lookupFloat.size(), indicatorValues);
+ }
+
+ if (m->control_pressed) { out.close(); return 0; }
+
+
+ /******************************************************/
+ //output indicator values to table form //
+ /*****************************************************/
+ out << "OTU\tIndicator_Groups\tIndicator_Value\tpValue" << endl;
+ for (int j = 0; j < indicatorValues.size(); j++) {
+
+ if (m->control_pressed) { out.close(); return 0; }
+
+ out << m->currentBinLabels[j] << '\t' << indicatorGroups[j] << '\t' << indicatorValues[j] << '\t';
+
+ if (pValues[j] > (1/(float)iters)) { out << pValues[j] << endl; }
+ else { out << "<" << (1/(float)iters) << endl; }
+
+ if (pValues[j] <= 0.05) {
+ cout << m->currentBinLabels[j] << '\t' << indicatorGroups[j] << '\t' << indicatorValues[j] << '\t';
+ string pValueString = "<" + toString((1/(float)iters));
+ if (pValues[j] > (1/(float)iters)) { pValueString = toString(pValues[j]); cout << pValues[j];}
+ else { cout << "<" << (1/(float)iters); }
+ m->mothurOutJustToLog(m->currentBinLabels[j] + "\t" + indicatorGroups[j] + "\t" + toString(indicatorValues[j]) + "\t" + pValueString);
+ m->mothurOutEndLine();
+ }
+ }
+
+ out.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "GetIndicatorSpecies");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
//traverse tree finding indicator species values for each otu at each node
//label node with otu number that has highest indicator value
//report all otu values to file
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(inputFileName); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName));
+ string outputFileName = getOutputFileName("summary",variables);
outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
ofstream out;
//print headings
out << "TreeNode\t";
- for (int i = 0; i < numBins; i++) { out << "OTU-" << (i+1) << '\t'; }
+ for (int i = 0; i < numBins; i++) { out << m->currentBinLabels[i] << "_IndGroups" << '\t' << m->currentBinLabels[i] << "_IndValue" << '\t' << "pValue" << '\t'; }
out << endl;
+ m->mothurOutEndLine(); m->mothurOut("Node\tSpecies\tIndicator_Groups\tIndicatorValue\tpValue\n");
+
string treeOutputDir = outputDir;
if (outputDir == "") { treeOutputDir += m->hasPath(treefile); }
- string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + "indicator.tre";
+ variables["[filename]"] = treeOutputDir + m->getRootName(m->getSimpleName(treefile));
+ string outputTreeFileName = getOutputFileName("tree", variables);
//create a map from tree node index to names of descendants, save time later to know which sharedRabund you need
//for each node
for (int i = T->getNumLeaves(); i < T->getNumNodes(); i++) {
-
+ //cout << endl << i+1 << endl;
if (m->control_pressed) { out.close(); return 0; }
/*****************************************************/
/*****************************************************/
vector<float> indicatorValues; //size of numBins
+ vector<float> pValues;
+ vector<string> indicatorGroups;
+ map< vector<int>, vector<int> > randomGroupingsMap; //maps location in groupings to location in groupings, ie, [0][0] -> [1][2]. This is so we don't have to actually move the sharedRabundVectors.
if (sharedfile != "") {
vector< vector<SharedRAbundVector*> > groupings;
if (groupsAlreadyAdded.size() != lookup.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
- indicatorValues = getValues(groupings);
+ indicatorValues = getValues(groupings, indicatorGroups, randomGroupingsMap);
+ pValues = getPValues(groupings, lookup.size(), indicatorValues);
}else {
vector< vector<SharedRAbundFloatVector*> > groupings;
if (groupsAlreadyAdded.size() != lookupFloat.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
- indicatorValues = getValues(groupings);
+ indicatorValues = getValues(groupings, indicatorGroups, randomGroupingsMap);
+
+ pValues = getPValues(groupings, lookupFloat.size(), indicatorValues);
}
if (m->control_pressed) { out.close(); return 0; }
if (m->control_pressed) { out.close(); return 0; }
- out << indicatorValues[j] << '\t';
+ if (pValues[j] < (1/(float)iters)) {
+ out << indicatorGroups[j] << '\t' << indicatorValues[j] << '\t' << '<' << (1/(float)iters) << '\t';
+ }else {
+ out << indicatorGroups[j] << '\t' << indicatorValues[j] << '\t' << pValues[j] << '\t';
+ }
+
+ if (pValues[j] <= 0.05) {
+ cout << i+1 << '\t' << m->currentBinLabels[j] << '\t' << indicatorGroups[j] << '\t' << indicatorValues[j] << '\t';
+ string pValueString = "<" + toString((1/(float)iters));
+ if (pValues[j] > (1/(float)iters)) { pValueString = toString(pValues[j]); cout << pValues[j];}
+ else { cout << "<" << (1/(float)iters); }
+ m->mothurOutJustToLog(toString(i) + "\t" + m->currentBinLabels[j] + "\t" + indicatorGroups[j] + "\t" + toString(indicatorValues[j]) + "\t" + pValueString);
+ m->mothurOutEndLine();
+ }
}
out << endl;
T->tree[i].setLabel((i+1));
-
}
out.close();
}
}
//**********************************************************************************************************************
-vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundFloatVector*> >& groupings){
+vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundFloatVector*> >& groupings, vector<string>& indicatorGroupings, map< vector<int>, vector<int> > groupingsMap){
try {
vector<float> values;
-
+ map< vector<int>, vector<int> >::iterator it;
+
+ indicatorGroupings.clear();
+
+ //create grouping strings
+ vector<string> groupingsGroups;
+ for (int j = 0; j < groupings.size(); j++) {
+ string tempGrouping = "";
+ for (int k = 0; k < groupings[j].size()-1; k++) {
+ tempGrouping += groupings[j][k]->getGroup() + "-";
+ }
+ tempGrouping += groupings[j][groupings[j].size()-1]->getGroup();
+ groupingsGroups.push_back(tempGrouping);
+ }
+
+
//for each otu
for (int i = 0; i < groupings[0][0]->getNumBins(); i++) {
vector<float> terms;
float AijDenominator = 0.0;
vector<float> Bij;
+
//get overall abundance of each grouping
for (int j = 0; j < groupings.size(); j++) {
float totalAbund = 0;
int numNotZero = 0;
for (int k = 0; k < groupings[j].size(); k++) {
- totalAbund += groupings[j][k]->getAbundance(i);
- if (groupings[j][k]->getAbundance(i) != 0) { numNotZero++; }
+ vector<int> temp; temp.push_back(j); temp.push_back(k);
+ it = groupingsMap.find(temp);
+
+ if (it == groupingsMap.end()) { //this one didnt get moved
+ totalAbund += groupings[j][k]->getAbundance(i);
+ if (groupings[j][k]->getAbundance(i) != 0.0) { numNotZero++; }
+ }else {
+ totalAbund += groupings[(it->second)[0]][(it->second)[1]]->getAbundance(i);
+ if (groupings[(it->second)[0]][(it->second)[1]]->getAbundance(i) != 0.0) { numNotZero++; }
+ }
+
}
+ //mean abundance
float Aij = (totalAbund / (float) groupings[j].size());
terms.push_back(Aij);
}
float maxIndVal = 0.0;
+ string maxGrouping = "";
for (int j = 0; j < terms.size(); j++) {
- float thisAij = (terms[j] / AijDenominator);
+ float thisAij = (terms[j] / AijDenominator); //relative abundance
float thisValue = thisAij * Bij[j] * 100.0;
//save largest
- if (thisValue > maxIndVal) { maxIndVal = thisValue; }
+ if (thisValue > maxIndVal) { maxIndVal = thisValue; maxGrouping = groupingsGroups[j]; }
}
values.push_back(maxIndVal);
+ indicatorGroupings.push_back(maxGrouping);
}
return values;
}
//**********************************************************************************************************************
//same as above, just data type difference
-vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundVector*> >& groupings){
+vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundVector*> >& groupings, vector<string>& indicatorGroupings, map< vector<int>, vector<int> > groupingsMap){
try {
vector<float> values;
+ map< vector<int>, vector<int> >::iterator it;
+
+ indicatorGroupings.clear();
+
+ //create grouping strings
+ vector<string> groupingsGroups;
+ for (int j = 0; j < groupings.size(); j++) {
+ string tempGrouping = "";
+ for (int k = 0; k < groupings[j].size()-1; k++) {
+ tempGrouping += groupings[j][k]->getGroup() + "-";
+ }
+ tempGrouping += groupings[j][groupings[j].size()-1]->getGroup();
+ groupingsGroups.push_back(tempGrouping);
+ }
+
- /*for (int j = 0; j < groupings.size(); j++) {
- cout << "grouping " << j << endl;
- for (int k = 0; k < groupings[j].size(); k++) {
- cout << groupings[j][k]->getGroup() << endl;
- }
- }*/
//for each otu
for (int i = 0; i < groupings[0][0]->getNumBins(); i++) {
vector<float> terms;
int totalAbund = 0.0;
int numNotZero = 0;
for (int k = 0; k < groupings[j].size(); k++) {
- totalAbund += groupings[j][k]->getAbundance(i);
- if (groupings[j][k]->getAbundance(i) != 0.0) { numNotZero++; }
+ vector<int> temp; temp.push_back(j); temp.push_back(k);
+ it = groupingsMap.find(temp);
- }
+ if (it == groupingsMap.end()) { //this one didnt get moved
+ totalAbund += groupings[j][k]->getAbundance(i);
+ if (groupings[j][k]->getAbundance(i) != 0.0) { numNotZero++; }
+ }else {
+ totalAbund += groupings[(it->second)[0]][(it->second)[1]]->getAbundance(i);
+ if (groupings[(it->second)[0]][(it->second)[1]]->getAbundance(i) != 0.0) { numNotZero++; }
+ }
+ }
+
+ //mean abundance
float Aij = (totalAbund / (float) groupings[j].size());
terms.push_back(Aij);
}
float maxIndVal = 0.0;
+ string maxGrouping = "";
for (int j = 0; j < terms.size(); j++) {
- float thisAij = (terms[j] / AijDenominator);
+ float thisAij = (terms[j] / AijDenominator); //relative abundance
float thisValue = thisAij * Bij[j] * 100.0;
//save largest
- if (thisValue > maxIndVal) { maxIndVal = thisValue; }
+ if (thisValue > maxIndVal) { maxIndVal = thisValue; maxGrouping = groupingsGroups[j]; }
}
values.push_back(maxIndVal);
+ indicatorGroupings.push_back(maxGrouping);
}
return values;
m->errorOut(e, "IndicatorCommand", "getShared");
exit(1);
}
-}
+}
+//**********************************************************************************************************************
+vector<float> IndicatorCommand::driver(vector< vector<SharedRAbundFloatVector*> >& groupings, int num, vector<float> indicatorValues, int numIters){
+ try {
+ vector<float> pvalues;
+ pvalues.resize(indicatorValues.size(), 0);
+ vector<string> notUsedGroupings; //we dont care about the grouping for the pvalues since they are randomized, but we need to pass the function something to make it work.
+
+ for(int i=0;i<numIters;i++){
+ if (m->control_pressed) { break; }
+ map< vector<int>, vector<int> > groupingsMap = randomizeGroupings(groupings, num);
+ vector<float> randomIndicatorValues = getValues(groupings, notUsedGroupings, groupingsMap);
+
+ for (int j = 0; j < indicatorValues.size(); j++) {
+ if (randomIndicatorValues[j] >= indicatorValues[j]) { pvalues[j]++; }
+ }
+ }
+
+ return pvalues;
+
+ }catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "driver");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<float> IndicatorCommand::getPValues(vector< vector<SharedRAbundFloatVector*> >& groupings, int num, vector<float> indicatorValues){
+ try {
+ vector<float> pvalues;
+
+ if(processors == 1){
+ pvalues = driver(groupings, num, indicatorValues, iters);
+ for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
+ }else{
+ //divide iters between processors
+ vector<int> procIters;
+ int numItersPerProcessor = iters / processors;
+
+ //divide iters between processes
+ for (int h = 0; h < processors; h++) {
+ if(h == processors - 1){ numItersPerProcessor = iters - h * numItersPerProcessor; }
+ procIters.push_back(numItersPerProcessor);
+ }
+
+ vector<int> processIDS;
+ int process = 1;
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ pvalues = driver(groupings, num, indicatorValues, procIters[process]);
+
+ //pass pvalues to parent
+ ofstream out;
+ string tempFile = toString(getpid()) + ".pvalues.temp";
+ m->openOutputFile(tempFile, out);
+
+ //pass values
+ for (int i = 0; i < pvalues.size(); i++) {
+ out << pvalues[i] << '\t';
+ }
+ out << endl;
+
+ out.close();
+
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
+ }
+
+ //do my part
+ pvalues = driver(groupings, num, indicatorValues, procIters[0]);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ //combine results
+ for (int i = 0; i < processIDS.size(); i++) {
+ ifstream in;
+ string tempFile = toString(processIDS[i]) + ".pvalues.temp";
+ m->openInputFile(tempFile, in);
+
+ ////// to do ///////////
+ int numTemp; numTemp = 0;
+ for (int j = 0; j < pvalues.size(); j++) {
+ in >> numTemp; m->gobble(in);
+ pvalues[j] += numTemp;
+ }
+ in.close(); m->mothurRemove(tempFile);
+ }
+ for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
+#else
+
+ //fill in functions
+ vector<indicatorData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=1; i<processors; i++ ){
+
+ //make copy of lookup so we don't get access violations
+ vector< vector<SharedRAbundFloatVector*> > newGroupings;
+
+ for (int k = 0; k < groupings.size(); k++) {
+ vector<SharedRAbundFloatVector*> newLookup;
+ for (int l = 0; l < groupings[k].size(); l++) {
+ SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
+ temp->setLabel(groupings[k][l]->getLabel());
+ temp->setGroup(groupings[k][l]->getGroup());
+ newLookup.push_back(temp);
+ }
+ newGroupings.push_back(newLookup);
+ }
+
+ //for each bin
+ for (int l = 0; l < groupings.size(); l++) {
+ for (int k = 0; k < groupings[l][0]->getNumBins(); k++) {
+ if (m->control_pressed) { for (int j = 0; j < newGroupings.size(); j++) { for (int u = 0; u < newGroupings[j].size(); u++) { delete newGroupings[j][u]; } } return pvalues; }
+
+ for (int j = 0; j < groupings[l].size(); j++) { newGroupings[l][j]->push_back(groupings[l][j]->getAbundance(k), groupings[l][j]->getGroup()); }
+ }
+ }
+
+ vector<float> copyIValues = indicatorValues;
+
+ indicatorData* temp = new indicatorData(m, procIters[i], newGroupings, num, copyIValues);
+ pDataArray.push_back(temp);
+ processIDS.push_back(i);
+
+ hThreadArray[i-1] = CreateThread(NULL, 0, MyIndicatorThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+ }
+
+ //do my part
+ pvalues = driver(groupings, num, indicatorValues, procIters[0]);
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ for (int j = 0; j < pDataArray[i]->pvalues.size(); j++) { pvalues[j] += pDataArray[i]->pvalues[j]; }
+
+ for (int l = 0; l < pDataArray[i]->groupings.size(); l++) {
+ for (int j = 0; j < pDataArray[i]->groupings[l].size(); j++) { delete pDataArray[i]->groupings[l][j]; }
+ }
+
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+
+ for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
+#endif
+ }
+
+
+ return pvalues;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "getPValues");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+//same as above, just data type difference
+vector<float> IndicatorCommand::driver(vector< vector<SharedRAbundVector*> >& groupings, int num, vector<float> indicatorValues, int numIters){
+ try {
+ vector<float> pvalues;
+ pvalues.resize(indicatorValues.size(), 0);
+ vector<string> notUsedGroupings; //we dont care about the grouping for the pvalues since they are randomized, but we need to pass the function something to make it work.
+
+ for(int i=0;i<numIters;i++){
+ if (m->control_pressed) { break; }
+ map< vector<int>, vector<int> > groupingsMap = randomizeGroupings(groupings, num);
+ vector<float> randomIndicatorValues = getValues(groupings, notUsedGroupings, groupingsMap);
+
+ for (int j = 0; j < indicatorValues.size(); j++) {
+ if (randomIndicatorValues[j] >= indicatorValues[j]) { pvalues[j]++; }
+ }
+ }
+
+ return pvalues;
+
+ }catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "driver");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//same as above, just data type difference
+vector<float> IndicatorCommand::getPValues(vector< vector<SharedRAbundVector*> >& groupings, int num, vector<float> indicatorValues){
+ try {
+ vector<float> pvalues;
+
+ if(processors == 1){
+ pvalues = driver(groupings, num, indicatorValues, iters);
+ for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
+ }else{
+ //divide iters between processors
+ vector<int> procIters;
+ int numItersPerProcessor = iters / processors;
+
+ //divide iters between processes
+ for (int h = 0; h < processors; h++) {
+ if(h == processors - 1){ numItersPerProcessor = iters - h * numItersPerProcessor; }
+ procIters.push_back(numItersPerProcessor);
+ }
+
+ vector<int> processIDS;
+ int process = 1;
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ pvalues = driver(groupings, num, indicatorValues, procIters[process]);
+
+ //pass pvalues to parent
+ ofstream out;
+ string tempFile = toString(getpid()) + ".pvalues.temp";
+ m->openOutputFile(tempFile, out);
+
+ //pass values
+ for (int i = 0; i < pvalues.size(); i++) {
+ out << pvalues[i] << '\t';
+ }
+ out << endl;
+
+ out.close();
+
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
+ }
+
+ //do my part
+ pvalues = driver(groupings, num, indicatorValues, procIters[0]);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ //combine results
+ for (int i = 0; i < processIDS.size(); i++) {
+ ifstream in;
+ string tempFile = toString(processIDS[i]) + ".pvalues.temp";
+ m->openInputFile(tempFile, in);
+
+ ////// to do ///////////
+ int numTemp; numTemp = 0;
+ for (int j = 0; j < pvalues.size(); j++) {
+ in >> numTemp; m->gobble(in);
+ pvalues[j] += numTemp;
+ }
+ in.close(); m->mothurRemove(tempFile);
+ }
+ for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
+#else
+
+ //fill in functions
+ vector<indicatorData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=1; i<processors; i++ ){
+
+ //make copy of lookup so we don't get access violations
+ vector< vector<SharedRAbundFloatVector*> > newGroupings;
+
+ for (int k = 0; k < groupings.size(); k++) {
+ vector<SharedRAbundFloatVector*> newLookup;
+ for (int l = 0; l < groupings[k].size(); l++) {
+ SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
+ temp->setLabel(groupings[k][l]->getLabel());
+ temp->setGroup(groupings[k][l]->getGroup());
+ newLookup.push_back(temp);
+ }
+ newGroupings.push_back(newLookup);
+ }
+
+ //for each bin
+ for (int l = 0; l < groupings.size(); l++) {
+ for (int k = 0; k < groupings[l][0]->getNumBins(); k++) {
+ if (m->control_pressed) { for (int j = 0; j < newGroupings.size(); j++) { for (int u = 0; u < newGroupings[j].size(); u++) { delete newGroupings[j][u]; } } return pvalues; }
+
+ for (int j = 0; j < groupings[l].size(); j++) { newGroupings[l][j]->push_back((float)(groupings[l][j]->getAbundance(k)), groupings[l][j]->getGroup()); }
+ }
+ }
+
+ vector<float> copyIValues = indicatorValues;
+
+ indicatorData* temp = new indicatorData(m, procIters[i], newGroupings, num, copyIValues);
+ pDataArray.push_back(temp);
+ processIDS.push_back(i);
+
+ hThreadArray[i-1] = CreateThread(NULL, 0, MyIndicatorThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+ }
+
+ //do my part
+ pvalues = driver(groupings, num, indicatorValues, procIters[0]);
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ for (int j = 0; j < pDataArray[i]->pvalues.size(); j++) { pvalues[j] += pDataArray[i]->pvalues[j]; }
+
+ for (int l = 0; l < pDataArray[i]->groupings.size(); l++) {
+ for (int j = 0; j < pDataArray[i]->groupings[l].size(); j++) { delete pDataArray[i]->groupings[l][j]; }
+ }
+
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+
+ for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
+#endif
+ }
+
+
+ return pvalues;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "getPValues");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//swap groups between groupings, in essence randomizing the second column of the design file
+map< vector<int>, vector<int> > IndicatorCommand::randomizeGroupings(vector< vector<SharedRAbundVector*> >& groupings, int numLookupGroups){
+ try {
+
+ map< vector<int>, vector<int> > randomGroupings;
+
+ for (int i = 0; i < numLookupGroups; i++) {
+ if (m->control_pressed) {break;}
+
+ //get random groups to swap to switch with
+ //generate random int between 0 and groupings.size()-1
+ int z = m->getRandomIndex(groupings.size()-1);
+ int x = m->getRandomIndex(groupings.size()-1);
+ int a = m->getRandomIndex(groupings[z].size()-1);
+ int b = m->getRandomIndex(groupings[x].size()-1);
+ //cout << i << '\t' << z << '\t' << x << '\t' << a << '\t' << b << endl;
+ //if ((z < 0) || (z > 1) || x<0 || x>1 || a <0 || a>groupings[z].size()-1 || b<0 || b>groupings[x].size()-1) { cout << "probelm" << i << '\t' << z << '\t' << x << '\t' << a << '\t' << b << endl; }
+
+ vector<int> from;
+ vector<int> to;
+
+ from.push_back(z); from.push_back(a);
+ to.push_back(x); to.push_back(b);
+
+ randomGroupings[from] = to;
+ }
+ //cout << "done" << endl;
+ return randomGroupings;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "randomizeGroupings");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//swap groups between groupings, in essence randomizing the second column of the design file
+map< vector<int>, vector<int> > IndicatorCommand::randomizeGroupings(vector< vector<SharedRAbundFloatVector*> >& groupings, int numLookupGroups){
+ try {
+
+ map< vector<int>, vector<int> > randomGroupings;
+
+ for (int i = 0; i < numLookupGroups; i++) {
+
+ //get random groups to swap to switch with
+ //generate random int between 0 and groupings.size()-1
+ int z = m->getRandomIndex(groupings.size()-1);
+ int x = m->getRandomIndex(groupings.size()-1);
+ int a = m->getRandomIndex(groupings[z].size()-1);
+ int b = m->getRandomIndex(groupings[x].size()-1);
+ //cout << i << '\t' << z << '\t' << x << '\t' << a << '\t' << b << endl;
+
+ vector<int> from;
+ vector<int> to;
+
+ from.push_back(z); from.push_back(a);
+ to.push_back(x); to.push_back(b);
+
+ randomGroupings[from] = to;
+ }
+
+ return randomGroupings;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "randomizeGroupings");
+ exit(1);
+ }
+}
+
/*****************************************************************/
projects / mothur.git / blobdiff