*
*/
-using namespace std;
-
-
#include "sharedordervector.h"
-#include "utilities.hpp"
-
+#include "sharedutilities.h"
/***********************************************************************/
//This function is used to read a .shared file for the collect.shared, rarefaction.shared and summary.shared commands
//if you don't use a list and groupfile.
-SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {
+SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() { //reads in a shared file
try {
- globaldata = GlobalData::getInstance();
maxRank = 0; numBins = 0; numSeqs = 0;
+
+ groupmap = new GroupMap();
- if (globaldata->gGroupmap == NULL) { groupmap = new GroupMap(); }
-
- int num, inputData, pos, count;
+ int num, inputData, count;
count = 0; numSeqs = 0;
string holdLabel, nextLabel, groupN;
individual newguy;
//read in first row since you know there is at least 1 group.
- f >> label >> groupN >> num;
+ //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->sharedBinLabelsInFile.clear();
+ while(!iStringStream.eof()){
+ if (m->control_pressed) { break; }
+ string temp;
+ iStringStream >> temp; m->gobble(iStringStream);
+
+ m->sharedBinLabelsInFile.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->currentSharedBinLabels = m->sharedBinLabelsInFile;
+
+ //read in first row since you know there is at least 1 group.
+ f >> groupN >> num;
+
holdLabel = label;
- if (globaldata->gGroupmap == NULL) {
- //save group in groupmap
- groupmap->namesOfGroups.push_back(groupN);
- groupmap->groupIndex[groupN] = 0;
- }
+
+ vector<string> allGroups;
+ //save group in groupmap
+ allGroups.push_back(groupN);
+ groupmap->groupIndex[groupN] = 0;
+
for(int i=0;i<num;i++){
f >> inputData;
for (int j = 0; j < inputData; j++) {
- push_back(i+1, i+1, groupN);
+ push_back(i, i, groupN);
numSeqs++;
}
}
- //save position in file in case next line is a new label.
- pos = f.tellg();
+ m->gobble(f);
- if (f.eof() != true) { f >> nextLabel; }
+ if (!(f.eof())) { f >> nextLabel; }
//read the rest of the groups info in
while ((nextLabel == holdLabel) && (f.eof() != true)) {
f >> groupN >> num;
count++;
- if (globaldata->gGroupmap == NULL) {
- //save group in groupmap
- groupmap->namesOfGroups.push_back(groupN);
- groupmap->groupIndex[groupN] = count;
- }
+
+ //save group in groupmap
+ allGroups.push_back(groupN);
+ groupmap->groupIndex[groupN] = count;
+
for(int i=0;i<num;i++){
f >> inputData;
for (int j = 0; j < inputData; j++) {
- push_back(i+1, i+1, groupN);
+ push_back(i, i, groupN);
numSeqs++;
}
}
- //save position in file in case next line is a new label.
- pos = f.tellg();
-
+ m->gobble(f);
+
if (f.eof() != true) { f >> nextLabel; }
}
- //put file pointer back since you are now at a new distance label
- f.seekg(pos, ios::beg);
-
- if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap; }
-
+ m->saveNextLabel = nextLabel;
+
+ groupmap->setNamesOfGroups(allGroups);
+ m->setAllGroups(allGroups);
+
updateStats();
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function SharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedOrderVector class function SharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedOrderVector", "SharedOrderVector");
exit(1);
}
}
/***********************************************************************/
int SharedOrderVector::getNumBins(){
- if(needToUpdate == 1){ updateStats(); }
return numBins;
}
/***********************************************************************/
int SharedOrderVector::getNumSeqs(){
- if(needToUpdate == 1){ updateStats(); }
return numSeqs;
}
/***********************************************************************/
int SharedOrderVector::getMaxRank(){
- if(needToUpdate == 1){ updateStats(); }
return maxRank;
}
data[index].group = groupName;
data[index].bin = binNumber;
data[index].abundance = abund;
- needToUpdate = 1;
-
+ //if (abund > maxRank) { maxRank = abund; }
+ updateStats();
}
/***********************************************************************/
/***********************************************************************/
-
+//commented updateStats out to improve speed, but whoever calls this must remember to update when they are done with all the pushbacks they are doing
void SharedOrderVector::push_back(int binNumber, int abund, string groupName){
individual newGuy;
newGuy.group = groupName;
newGuy.abundance = abund;
newGuy.bin = binNumber;
data.push_back(newGuy);
- needToUpdate = 1;
+ //numSeqs++;
+ //numBins++;
+ //if (abund > maxRank) { maxRank = abund; }
+ //updateStats();
}
/***********************************************************************/
output << endl;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedOrderVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedOrderVector", "print");
exit(1);
}
}
+/***********************************************************************/
+void SharedOrderVector::clear(){
+ numBins = 0;
+ maxRank = 0;
+ numSeqs = 0;
+ data.clear();
+}
/***********************************************************************/
void SharedOrderVector::resize(int){
- cout << "resize() did nothing in class SharedOrderVector";
+ m->mothurOut("resize() did nothing in class SharedOrderVector");
}
/***********************************************************************/
return rav;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedOrderVector", "getRAbundVector");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SharedOrderVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************************/
return ov;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedOrderVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedOrderVector", "getOrderVector");
exit(1);
}
}
return sharedRav;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedOrderVector", "getSharedRAbundVector");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SharedOrderVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/***********************************************************************/
+vector<SharedRAbundVector*> SharedOrderVector::getSharedRAbundVector() {
+ try {
+ SharedUtil* util;
+ util = new SharedUtil();
+ vector<SharedRAbundVector*> lookup;
+
+ vector<string> Groups = m->getGroups();
+ vector<string> allGroups = m->getAllGroups();
+ util->setGroups(Groups, allGroups);
+ util->getSharedVectors(Groups, lookup, this);
+ m->setGroups(Groups);
+ m->setAllGroups(allGroups);
+
+ return lookup;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedOrderVector", "getSharedRAbundVector");
exit(1);
}
-
}
/***********************************************************************/
SharedSAbundVector SharedOrderVector::getSharedSAbundVector(string group) {
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedOrderVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedOrderVector", "getSharedSAbundVector");
exit(1);
}
-
}
/***********************************************************************/
SharedOrderVector SharedOrderVector::getSharedOrderVector(){
+ random_shuffle(data.begin(), data.end());
return *this;
}
numBins = 0;
maxRank = 0;
- for(int i=0;i<data.size();i++){
- if(data[i].bin != -1){
- numSeqs++;
- }
- }
-
- vector<individual> hold(numSeqs);
-
+ numSeqs = data.size();
+
+ vector<int> hold(numSeqs, 0);
for(int i=0;i<numSeqs;i++){
- if(data[i].bin != -1){
- hold[data[i].bin].bin = hold[data[i].bin].bin+1;
- }
+ hold[data[i].bin] = hold[data[i].bin]+1;
}
-
+
for(int i=0;i<numSeqs;i++){
- if(data[i].bin > numBins) { numBins = data[i].bin; }
- if(data[i].abundance > maxRank) { maxRank = data[i].abundance; }
+ if(hold[i] > 0) { numBins++; }
+ if(hold[i] > maxRank) { maxRank = hold[i]; }
}
- numBins++; //if you have 10 bins largest .bin is 9 since we start at 0.
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function updateStats. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedOrderVector", "updateStats");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SharedOrderVector class function updateStats. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************************/
projects / mothur.git / blobdiff