/***********************************************************************/
-
-SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {globaldata = GlobalData::getInstance();}
+SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {}
/***********************************************************************/
SharedRAbundVector::~SharedRAbundVector() {
/***********************************************************************/
SharedRAbundVector::SharedRAbundVector(int n) : DataVector(), maxRank(0), numBins(n), numSeqs(0) {
- globaldata = GlobalData::getInstance();
individual newGuy;
//initialize data
for (int i=0; i< n; i++) {
//reads a shared file
SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
try {
- globaldata = GlobalData::getInstance();
-
- if (globaldata->gGroupmap == NULL) { groupmap = new GroupMap(); }
-
+ m->namesOfGroups.clear();
+
int num, inputData, count;
count = 0;
string holdLabel, nextLabel, groupN;
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } lookup.clear();
- if (globaldata->saveNextLabel == "") { f >> label; }
- else { label = globaldata->saveNextLabel; }
+ //are we at the beginning of the file??
+ if (m->saveNextLabel == "") {
+ f >> label;
+
+ //is this a shared file that has headers
+ if (label == "label") {
+ //gets "group"
+ f >> label; m->gobble(f);
+
+ //gets "numOtus"
+ f >> label; m->gobble(f);
+
+ //eat rest of line
+ label = m->getline(f); m->gobble(f);
+
+ //parse labels to save
+ istringstream iStringStream(label);
+ m->binLabelsInFile.clear();
+ while(!iStringStream.eof()){
+ if (m->control_pressed) { break; }
+ string temp;
+ iStringStream >> temp; m->gobble(iStringStream);
+
+ m->binLabelsInFile.push_back(temp);
+ }
+
+ f >> label;
+ }
+ }else { label = m->saveNextLabel; }
+
+ //reset labels, currentLabels may have gotten changed as otus were eliminated because of group choices or sampling
+ m->currentBinLabels = m->binLabelsInFile;
//read in first row since you know there is at least 1 group.
f >> groupN >> num;
lookup[0]->setLabel(label);
lookup[0]->setGroup(groupN);
- if (globaldata->gGroupmap == NULL) {
- //save group in groupmap
- groupmap->namesOfGroups.push_back(groupN);
- groupmap->groupIndex[groupN] = 0;
- }
+ m->namesOfGroups.push_back(groupN);
//fill vector. data = first sharedrabund in file
for(int i=0;i<num;i++){
lookup[0]->push_back(inputData, groupN); //abundance, bin, group
push_back(inputData, groupN);
- //numSeqs += inputData;
- //numBins++;
+
if (inputData > maxRank) { maxRank = inputData; }
}
f >> groupN >> num;
count++;
- if (globaldata->gGroupmap == NULL) {
- //save group in groupmap
-
- groupmap->namesOfGroups.push_back(groupN);
- groupmap->groupIndex[groupN] = count;
- }
+ m->namesOfGroups.push_back(groupN);
//add new vector to lookup
temp = new SharedRAbundVector();
//fill vector.
for(int i=0;i<num;i++){
f >> inputData;
+
lookup[count]->push_back(inputData, groupN); //abundance, bin, group
}
if (f.eof() != true) { f >> nextLabel; }
}
-
- globaldata->saveNextLabel = nextLabel;
-
- if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap; }
+ m->saveNextLabel = nextLabel;
}
catch(exception& e) {
return data.size();
}
+
+/***********************************************************************/
+void SharedRAbundVector::printHeaders(ostream& output){
+ try {
+
+ output << "label\tGroup\tnumOtus\t";
+ if (m->sharedHeaderMode == "tax") {
+ for (int i = 0; i < numBins; i++) {
+
+ //if there is a bin label use it otherwise make one
+ string binLabel = "PhyloType" + toString(i+1);
+ if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; }
+
+ output << binLabel << '\t';
+ }
+ output << endl;
+ }else {
+ for (int i = 0; i < numBins; i++) {
+ //if there is a bin label use it otherwise make one
+ string mybinLabel = "Otu" + toString(i+1);
+ if (i < m->currentBinLabels.size()) { mybinLabel = m->currentBinLabels[i]; }
+
+ output << mybinLabel << '\t';
+ }
+
+ output << endl;
+ }
+ m->printedHeaders = true;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundVector", "printHeaders");
+ exit(1);
+ }
+}
/***********************************************************************/
-void SharedRAbundVector::print(ostream& output){
+void SharedRAbundVector::print(ostream& output) {
try {
output << numBins << '\t';
SharedUtil* util;
util = new SharedUtil();
- util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
+ util->setGroups(m->Groups, m->namesOfGroups);
bool remove = false;
for (int i = 0; i < lookup.size(); i++) {
//if this sharedrabund is not from a group the user wants then delete it.
- if (util->isValidGroup(lookup[i]->getGroup(), globaldata->Groups) == false) {
+ if (util->isValidGroup(lookup[i]->getGroup(), m->Groups) == false) {
remove = true;
delete lookup[i]; lookup[i] = NULL;
lookup.erase(lookup.begin()+i);
}
//for each bin
+ vector<string> newBinLabels;
for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
for (int j = 0; j < thislookup.size(); j++) {
newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
}
+
+ //if there is a bin label use it otherwise make one
+ string binLabel = "Otu" + (i+1);
+ if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; }
+
+ newBinLabels.push_back(binLabel);
}
}
for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
thislookup = newLookup;
+ m->currentBinLabels = newBinLabels;
return 0;
projects / mothur.git / blobdiff