*
*/
-using namespace std;
-
-
#include "sharedordervector.h"
#include "sharedutilities.h"
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;
f >> label >> 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;
}
}
- //save position in file in case next line is a new label.
- pos = f.tellg();
+ m->gobble(f);
if (f.eof() != true) { f >> nextLabel; }
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;
}
}
- //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; }
+ for (int i = 0; i < nextLabel.length(); i++) { f.unget(); }
+
+ 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);
}
}
/***********************************************************************/
-
+//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;
//numSeqs++;
//numBins++;
//if (abund > maxRank) { maxRank = abund; }
- updateStats();
+
+ //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";
- exit(1);
- }
-
}
/***********************************************************************/
vector<SharedRAbundVector*> SharedOrderVector::getSharedRAbundVector() {
util = new SharedUtil();
vector<SharedRAbundVector*> lookup;
- util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
- util->getSharedVectors(globaldata->Groups, lookup, this);
+ 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) {
- 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";
- 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";
+ m->errorOut(e, "SharedOrderVector", "getSharedSAbundVector");
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";
- exit(1);
- }
-
}
/***********************************************************************/
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