//initialize outputTypes
vector<string> tempOutNames;
outputTypes["csv"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["csv"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
+ createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel());
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete read; delete input; globaldata->ginput = NULL; delete sabund; return 0; }
outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
+ createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel());
+
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete read; delete input; globaldata->ginput = NULL; delete sabund; return 0; }
processedLabels.insert(sabund->getLabel());
outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
- outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
+ outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
+
+ createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel());
delete sabund;
}
exit(1);
}
}
+//**********************************************************************************************************************
+string CatchAllCommand::createSummaryFile(string file1, string label) {
+ try {
+ string filename = outputDir + m->getRootName(m->getSimpleName(sabundfile)) + label + ".catchall.summary";
+ filename = m->getFullPathName(filename);
+ outputNames.push_back(filename); outputTypes["summary"].push_back(filename);
+
+ ofstream out;
+ m->openOutputFile(filename, out);
+
+ out << "group\tmodel\testimate\tlci\tuci" << endl;
+
+ ifstream in;
+ m->openInputFile(file1, in);
+
+ if (!in.eof()) {
+
+ string header = m->getline(in); m->gobble(in);
+
+ int pos = header.find("Total Number of Observed Species =");
+ cout << pos << '\t' << header.length() << endl; exit(1);
+ if (pos == string::npos) { m->mothurOut("[ERROR]: cannot parse " + file1); m->mothurOutEndLine(); }
+ else {
+ //pos will be the position of the T in total, so we want to count to the position of =
+ pos += 34;
+ char c=header[pos];
+ string numString = "";
+ while (c != ','){
+ if (c != ' ') {
+ numString += c;
+ }
+ }
+
+ int numOtus; convert(numString, numOtus);
+ cout << numOtus << endl;
+ }
+ }
+
+ in.close();
+ out.close();
+
+ return filename;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CatchAllCommand", "createSummaryFile");
+ exit(1);
+ }
+}
/**************************************************************************************/
map< string, vector<string> > outputTypes;
string process(SAbundVector*);
+ string createSummaryFile(string, string);
};
/****************************************************************************/
//**********************************************************************************************************************
vector<string> GetOTURepCommand::getValidParameters(){
try {
- string Array[] = {"fasta","list","label","name", "group", "sorted", "phylip","column","large","cutoff","precision","groups","outputdir","inputdir"};
+ string Array[] = {"fasta","list","label","name", "group", "weighted","sorted", "phylip","column","large","cutoff","precision","groups","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
return myArray;
}
help(); abort = true;
} else {
//valid paramters for this command
- string Array[] = {"fasta","list","label","name", "group", "sorted", "phylip","column","large","cutoff","precision","groups","outputdir","inputdir"};
+ string Array[] = {"fasta","list","label","name","weighted", "group", "sorted", "phylip","column","large","cutoff","precision","groups","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
string temp = validParameter.validFile(parameters, "large", false); if (temp == "not found") { temp = "F"; }
large = m->isTrue(temp);
+ temp = validParameter.validFile(parameters, "weighted", false); if (temp == "not found") { if (namefile == "") { temp = "F"; } else { temp = "t"; } }
+ weighted = m->isTrue(temp);
+
+ if ((weighted) && (namefile == "")) { m->mothurOut("You cannot set weighted to true unless you provide a namesfile."); m->mothurOutEndLine(); abort = true; }
+
temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
convert(temp, precision);
void GetOTURepCommand::help(){
try {
- m->mothurOut("The get.oturep command parameters are phylip, column, list, fasta, name, group, large, cutoff, precision, groups, sorted and label. The fasta and list parameters are required, as well as phylip or column and name.\n");
+ m->mothurOut("The get.oturep command parameters are phylip, column, list, fasta, name, group, large, weighted, cutoff, precision, groups, sorted and label. The fasta and list parameters are required, as well as phylip or column and name.\n");
m->mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and is separated by dashes.\n");
m->mothurOut("The phylip or column parameter is required, but only one may be used. If you use a column file the name filename is required. \n");
m->mothurOut("If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n");
m->mothurOut("The default value for label is all labels in your inputfile.\n");
m->mothurOut("The sorted parameter allows you to indicate you want the output sorted. You can sort by sequence name, bin number, bin size or group. The default is no sorting, but your options are name, number, size, or group.\n");
m->mothurOut("The large parameter allows you to indicate that your distance matrix is too large to fit in RAM. The default value is false.\n");
+ m->mothurOut("The weighted parameter allows you to indicate that want to find the weighted representative. You must provide a namesfile to set weighted to true. The default value is false with no namesfile and true when a name file is provided.\n");
+ m->mothurOut("The representative is found by selecting the sequence that has the smallest total distance to all other sequences in the OTU. If a tie occurs the smallest average distance is used.\n");
+ m->mothurOut("For weighted = false, mothur assumes the distance file contains only unique sequences, the list file may contain all sequences, but only the uniques are considered to become the representative. If your distance file contains all the sequences it would become weighted=true.\n");
+ m->mothurOut("For weighted = true, mothur assumes the distance file contains only unique sequences, the list file must contain all sequences, all sequences are considered to become the representative, but unique name will be used in the output for consistency.\n");
+ m->mothurOut("If your distance file contains all the sequence and you do not provide a name file, the weighted representative will be given, unless your listfile is unique. If you provide a namefile, then you can select weighted or unweighted.\n");
m->mothurOut("The group parameter allows you provide a group file.\n");
m->mothurOut("The groups parameter allows you to indicate that you want representative sequences for each group specified for each OTU, group name should be separated by dashes. ex. groups=A-B-C.\n");
m->mothurOut("The get.oturep command outputs a .fastarep and .rep.names file for each distance you specify, selecting one OTU representative for each bin.\n");
if (m->control_pressed) { delete readMatrix; return 0; }
seqVec[currentCell->row][currentCell->column] = currentCell->dist;
}
+ //add dummy map for unweighted calc
+ SeqMap dummy;
+ seqVec.push_back(dummy);
delete matrix;
delete readMatrix;
//positions in file where the distances for each sequence begin
//rowPositions[1] = position in file where distance related to sequence 1 start.
rowPositions = formatMatrix->getRowPositions();
+ rowPositions.push_back(-1); //dummy row for unweighted calc
delete formatMatrix;
delete nameMap;
if (large) { inRow.close(); remove(distFile.c_str()); }
delete read; delete input; delete list; globaldata->gListVector = NULL; return 0;
}
-
+
+ if (!weighted) { readNamesFile(weighted); }
+
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (allLines == 1 || labels.count(list->getLabel()) == 1){
delete input; globaldata->ginput = NULL;
delete read;
+ if (!weighted) { nameFileMap.clear(); }
+
//read fastafile
fasta = new FastaMap();
fasta->readFastaFile(fastafile);
}
}
//**********************************************************************************************************************
+//read names file to find the weighted rep for each bin
+void GetOTURepCommand::readNamesFile(bool w) {
+ try {
+ vector<string> dupNames;
+ m->openInputFile(namefile, inNames);
+
+ string name, names, sequence;
+
+ while(inNames){
+ inNames >> name; m->gobble(inNames); //read from first column A
+ inNames >> names; //read from second column A,B,C,D
+
+ dupNames.clear();
+
+ //parse names into vector
+ m->splitAtComma(names, dupNames);
+
+ for (int i = 0; i < dupNames.size(); i++) {
+ nameFileMap[dupNames[i]] = name;
+ }
+
+ m->gobble(inNames);
+ }
+ inNames.close();
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOTURepCommand", "readNamesFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
string GetOTURepCommand::findRep(vector<string> names) {
try{
// if only 1 sequence in bin or processing the "unique" label, then
// the first sequence of the OTU is the representative one
- if ((names.size() == 2) || (names.size() == 1) || (list->getLabel() == "unique")) {
+ if ((names.size() == 1) || (list->getLabel() == "unique")) {
return names[0];
}else{
vector<int> seqIndex(names.size());
vector<float> max_dist(names.size());
vector<float> total_dist(names.size());
+ map<string, string>::iterator itNameFile;
+ map<string, int>::iterator itNameIndex;
//fill seqIndex and initialize sums
for (size_t i = 0; i < names.size(); i++) {
- seqIndex[i] = nameToIndex[names[i]];
+ if (weighted) {
+ seqIndex[i] = nameToIndex[names[i]];
+ }else {
+ if (namefile == "") {
+ itNameIndex = nameToIndex.find(names[i]);
+
+ if (itNameIndex == nameToIndex.end()) { // you are not in the distance file and no namesfile, then assume you are not unique
+ if (large) { seqIndex[i] = (rowPositions.size()-1); }
+ else { seqIndex[i] = (seqVec.size()-1); }
+ }else {
+ seqIndex[i] = itNameIndex->second;
+ }
+
+ }else {
+ itNameFile = nameFileMap.find(names[i]);
+
+ if (itNameFile == nameFileMap.end()) {
+ m->mothurOut("[ERROR]: " + names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true;
+ }else{
+ string name1 = itNameFile->first;
+ string name2 = itNameFile->second;
+
+ if (name1 == name2) { //then you are unique so add your real dists
+ seqIndex[i] = nameToIndex[names[i]];
+ }else { //add dummy
+ if (large) { seqIndex[i] = (rowPositions.size()-1); }
+ else { seqIndex[i] = (seqVec.size()-1); }
+ }
+ }
+ }
+ }
max_dist[i] = 0.0;
total_dist[i] = 0.0;
}
string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir, groups;
ofstream out;
ifstream in, inNames, inRow;
- bool abort, allLines, groupError, large;
+ bool abort, allLines, groupError, large, weighted;
set<string> labels; //holds labels to be used
map<string, int> nameToIndex; //maps sequence name to index in sparsematrix
+ map<string, string> nameFileMap;
vector<string> outputNames, Groups;
map<string, string> outputNameFiles;
float cutoff;
map<string, vector<string> > outputTypes;
void readNamesFile();
+ void readNamesFile(bool);
int process(ListVector*);
SeqMap getMap(int);
string findRep(vector<string>); // returns the name of the "representative" sequence of given bin or subset of a bin, for groups
//**********************************************************************************************************************
vector<string> IndicatorCommand::getRequiredParameters(){
try {
- string Array[] = {"label","tree"};
+ string Array[] = {"tree"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
return myArray;
}
else { inputFileName = relabundfile; }
groups = validParameter.validFile(parameters, "groups", false);
- if (groups == "not found") { groups = ""; pickedGroups = false; }
- else {
- pickedGroups = true;
- m->splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
- }
+ if (groups == "not found") { groups = ""; Groups.push_back("all"); }
+ else { m->splitAtDash(groups, Groups); }
+ globaldata->Groups = Groups;
label = validParameter.validFile(parameters, "label", false);
- if (label == "not found") { label = ""; m->mothurOut("You must provide a label to process."); m->mothurOutEndLine(); abort = true; }
+ 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=""; }
if ((relabundfile == "") && (sharedfile == "")) { m->mothurOut("You must provide either a shared or relabund file."); m->mothurOutEndLine(); abort = true; }
void IndicatorCommand::help(){
try {
m->mothurOut("The indicator command reads a shared or relabund file and a tree file, and outputs a .indicator.tre and .indicator.summary file. \n");
- m->mothurOut("The new tree contains labels at each internal node. The label is the OTU number of the indicator OTU.\n");
+ m->mothurOut("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");
m->mothurOut("The summary file lists the indicator value for each OTU for each node.\n");
- m->mothurOut("The indicator command parameters are tree, groups, shared, relabund and label. The tree and label parameter are required as well as either shared or relabund.\n");
+ m->mothurOut("The indicator command parameters are tree, groups, shared, relabund and label. The tree parameter is required as well as either shared or relabund.\n");
m->mothurOut("The groups parameter allows you to specify which of the groups in your shared or relabund you would like analyzed. The groups may be entered separated by dashes.\n");
m->mothurOut("The label parameter indicates at what distance your tree relates to the shared or relabund.\n");
m->mothurOut("The indicator command should be used in the following format: indicator(tree=test.tre, shared=test.shared, label=0.03)\n");
/***************************************************/
Tree* outputTree = new Tree(globaldata->Groups.size());
- if (pickedGroups) {
- outputTree->getSubTree(T[0], globaldata->Groups);
- outputTree->assembleTree();
- }else{
- outputTree->getCopy(T[0]);
- outputTree->assembleTree();
- }
-
+ outputTree->getSubTree(T[0], globaldata->Groups);
+ outputTree->assembleTree();
+
//no longer need original tree, we have output tree to use and label
for (int i = 0; i < T.size(); i++) { delete T[i]; } globaldata->gTree.clear();
+
if (m->control_pressed) {
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]; } }
//report all otu values to file
int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
try {
+
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(inputFileName); }
string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
ofstream out;
m->openOutputFile(outputFileName, out);
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
out << "Node\tOTU#\tIndVal" << endl;
string treeOutputDir = outputDir;
//you are valid if you are not one of my descendants
//AND your distToLeaf is <= mine
//AND your distToLeaf is >= my smallest childs
- //AND you were not added as part of a larger grouping
+ //AND you were not added as part of a larger groupings
+
set<string> groupsAlreadyAdded;
+ //create a grouping with my grouping
+ vector<SharedRAbundVector*> subset;
+ int count = 0;
+ int doneCount = nodeToDescendants[i].size();
+ for (int k = 0; k < lookup.size(); k++) {
+ //is this descendant of i
+ if ((nodeToDescendants[i].count(lookup[k]->getGroup()) != 0)) {
+ subset.push_back(lookup[k]);
+ groupsAlreadyAdded.insert(lookup[k]->getGroup());
+ count++;
+ }
+ if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
+ }
+ if (subset.size() != 0) { groupings.push_back(subset); }
+
+
for (int j = (T->getNumNodes()-1); j >= 0; j--) {
if ((descendantNodes[i].count(j) == 0) && (distToLeaf[j] <= distToLeaf[i]) && ((distToLeaf[j] >= distToLeaf[T->tree[i].getLChild()]) || (distToLeaf[j] >= distToLeaf[T->tree[i].getRChild()]))) {
vector<SharedRAbundVector*> subset;
}
}
- if (groupsAlreadyAdded.size() != lookup.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
+ if (groupsAlreadyAdded.size() != lookup.size()) { cout << i << '\t' << groupsAlreadyAdded.size() << '\t' << lookup.size() << endl; m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
+ for (int k = 0; k < lookup.size(); k++) {
+ if (groupsAlreadyAdded.count(lookup[k]->getGroup()) == 0) { cout << lookup[k]->getGroup() << endl; }
+ }
indicatorValues = getValues(groupings);
//AND your distToLeaf is <= mine
//AND your distToLeaf is >= my smallest childs
//AND you were not added as part of a larger grouping
+
set<string> groupsAlreadyAdded;
+ //create a grouping with my grouping
+ vector<SharedRAbundFloatVector*> subset;
+ int count = 0;
+ int doneCount = nodeToDescendants[i].size();
+ for (int k = 0; k < lookupFloat.size(); k++) {
+ //is this descendant of i
+ if ((nodeToDescendants[i].count(lookupFloat[k]->getGroup()) != 0)) {
+ subset.push_back(lookupFloat[k]);
+ groupsAlreadyAdded.insert(lookupFloat[k]->getGroup());
+ count++;
+ }
+ if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
+ }
+ if (subset.size() != 0) { groupings.push_back(subset); }
+
for (int j = (T->getNumNodes()-1); j >= 0; j--) {
if ((descendantNodes[i].count(j) == 0) && (distToLeaf[j] <= distToLeaf[i]) && ((distToLeaf[j] >= distToLeaf[T->tree[i].getLChild()]) || (distToLeaf[j] >= distToLeaf[T->tree[i].getRChild()]))) {
vector<SharedRAbundFloatVector*> subset;
/******************************************************/
//output indicator values to table form + label tree //
/*****************************************************/
- vector<int> indicatorOTUs;
- float largestValue = 0.0;
for (int j = 0; j < indicatorValues.size(); j++) {
if (m->control_pressed) { out.close(); return 0; }
out << (i+1) << '\t' << (j+1) << '\t' << indicatorValues[j] << endl;
-
- //show no favortism
- if (indicatorValues[j] > largestValue) {
- largestValue = indicatorValues[j];
- indicatorOTUs.clear();
- indicatorOTUs.push_back(j+1);
- }else if (indicatorValues[j] == largestValue) {
- indicatorOTUs.push_back(j+1);
- }
-
- random_shuffle(indicatorOTUs.begin(), indicatorOTUs.end());
-
- T->tree[i].setLabel(indicatorOTUs[0]);
}
+ T->tree[i].setLabel((i+1));
+
}
out.close();
if (lc == -1) { // you are a leaf
//if you are a leaf set you priliminary length to 1.0, this may adjust later
T->tree[i].setBranchLength(1.0);
- dists[i] = 0.0;
+ dists[i] = 1.0;
}else{ // you are an internal node
//look at your children's length to leaf
float ldist = dists[lc];
float rdist = dists[rc];
- float greater;
- if (rdist > greater) { greater = rdist; }
- else { greater = ldist; }
+ float greater = ldist;
+ if (rdist > greater) { greater = rdist; dists[i] = ldist; }
+ else { dists[i] = rdist; }
//branch length = difference + 1
T->tree[lc].setBranchLength((abs(ldist-greater) + 1.0));
T->tree[rc].setBranchLength((abs(rdist-greater) + 1.0));
-
- dists[i] = dists[lc] + (abs(ldist-greater) + 1.0);
}
}else{
- if (lc == -1) { dists[i] = 0.0; }
- else { dists[i] = dists[lc] + T->tree[lc].getBranchLength(); }
+ if (lc == -1) { dists[i] = T->tree[i].getBranchLength(); }
+ else { //smaller of my two children distances plus my branch length
+ //look at your children's length to leaf
+ float ldist = dists[lc];
+ float rdist = dists[rc];
+
+ float smaller = ldist;
+ if (rdist < smaller) { smaller = rdist; }
+
+ dists[i] = smaller + T->tree[i].getBranchLength();
+ }
}
}
for (set<int>::iterator itNum = nodes[rc].begin(); itNum != nodes[rc].end(); itNum++) {
nodes[i].insert(*itNum);
}
+ //you are your own descendant
+ nodes[i].insert(i);
}
return names;
lookup = input->getSharedRAbundVectors();
string lastLabel = lookup[0]->getLabel();
+ if (label == "") { label = lastLabel; delete input; return 0; }
+
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> labels; labels.insert(label);
set<string> processedLabels;
lookupFloat = input->getSharedRAbundFloatVectors();
string lastLabel = lookupFloat[0]->getLabel();
+ if (label == "") { label = lastLabel; delete input; return 0; }
+
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> labels; labels.insert(label);
set<string> processedLabels;
ReadTree* read;
TreeMap* treeMap;
string treefile, sharedfile, relabundfile, groups, label, inputFileName, outputDir;
- bool abort, pickedGroups;
+ bool abort;
vector<string> outputNames, Groups;
map<string, vector<string> > outputTypes;
vector<SharedRAbundVector*> lookup;
files[outputNames[i]] = thisFilesLines;
temp.close();
+ remove(outputNames[i].c_str());
}
//output label line to new file
//initialize leaf nodes
if (i <= (numLeaves-1)) {
tree[i].setName(Groups[i]);
-
+
//save group info
string group = globaldata->gTreemap->getGroup(Groups[i]);
vector<string> tempGroups; tempGroups.push_back(group);
int parent = copy->tree[i].getParent();
if (parent != -1) {
+
if (m->inUsersGroups(copy->tree[i].getName(), Groups)) {
//find my siblings name
int parentRC = copy->tree[parent].getRChild();
//so set our parents sib to our great-grandparent
int parent = copy->tree[i].getParent();
int grandparent = copy->tree[parent].getParent();
-
+ int parentsSibIndex;
if (grandparent != -1) {
int greatgrandparent = copy->tree[grandparent].getParent();
int greatgrandparentLC = copy->tree[greatgrandparent].getLChild();
int grandparentLC = copy->tree[grandparent].getLChild();
int grandparentRC = copy->tree[grandparent].getRChild();
- int parentsSibIndex = grandparentLC;
- if (grandparentRC == parent) { parentsSibIndex = grandparentLC; }
+ parentsSibIndex = grandparentLC;
+ if (grandparentLC == parent) { parentsSibIndex = grandparentRC; }
//whichever of my greatgrandparents children was my grandparent
if (greatgrandparentLC == grandparent) { greatgrandparentLC = parentsSibIndex; }
int nextSpot = numLeaves;
populateNewTree(copy->tree, root, nextSpot);
-
}
catch(exception& e) {
m->errorOut(e, "Tree", "getCopy");
if (oldtree[node].getLChild() != -1) {
int rc = populateNewTree(oldtree, oldtree[node].getLChild(), index);
int lc = populateNewTree(oldtree, oldtree[node].getRChild(), index);
-
+
tree[index].setChildren(lc, rc);
- index++;
+ tree[rc].setParent(index);
+ tree[lc].setParent(index);
- return (index-1);
+ return (index++);
}else { //you are a leaf
int indexInNewTree = globaldata->gTreemap->getIndex(oldtree[node].getName());
-
- tree[indexInNewTree].setParent(index);
return indexInNewTree;
-
}
}
catch(exception& e) {
exit(1);
}
}
-
+/*****************************************************************/
+void Tree::printBranch(int node, ostream& out, string mode, vector<Node>& theseNodes) {
+ try {
+
+ // you are not a leaf
+ if (theseNodes[node].getLChild() != -1) {
+ out << "(";
+ printBranch(theseNodes[node].getLChild(), out, mode);
+ out << ",";
+ printBranch(theseNodes[node].getRChild(), out, mode);
+ out << ")";
+ if (mode == "branch") {
+ //if there is a branch length then print it
+ if (theseNodes[node].getBranchLength() != -1) {
+ out << ":" << theseNodes[node].getBranchLength();
+ }
+ }else if (mode == "boot") {
+ //if there is a label then print it
+ if (theseNodes[node].getLabel() != -1) {
+ out << theseNodes[node].getLabel();
+ }
+ }else if (mode == "both") {
+ if (theseNodes[node].getLabel() != -1) {
+ out << theseNodes[node].getLabel();
+ }
+ //if there is a branch length then print it
+ if (theseNodes[node].getBranchLength() != -1) {
+ out << ":" << theseNodes[node].getBranchLength();
+ }
+ }
+ }else { //you are a leaf
+ string leafGroup = globaldata->gTreemap->getGroup(theseNodes[node].getName());
+
+ if (mode == "branch") {
+ out << leafGroup;
+ //if there is a branch length then print it
+ if (theseNodes[node].getBranchLength() != -1) {
+ out << ":" << theseNodes[node].getBranchLength();
+ }
+ }else if (mode == "boot") {
+ out << leafGroup;
+ //if there is a label then print it
+ if (theseNodes[node].getLabel() != -1) {
+ out << theseNodes[node].getLabel();
+ }
+ }else if (mode == "both") {
+ out << theseNodes[node].getName();
+ if (theseNodes[node].getLabel() != -1) {
+ out << theseNodes[node].getLabel();
+ }
+ //if there is a branch length then print it
+ if (theseNodes[node].getBranchLength() != -1) {
+ out << ":" << theseNodes[node].getBranchLength();
+ }
+ }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "printBranch");
+ exit(1);
+ }
+}
/*****************************************************************/
void Tree::printTree() {
//only takes names from the first tree in the tree file and assumes that all trees use the same names.
int readTreeString(ifstream&);
int populateNewTree(vector<Node>&, int, int&);
+ void printBranch(int, ostream&, string, vector<Node>&);
MothurOut* m;
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