*
*/
-
-using namespace std;
-
-
#include "sabundvector.hpp"
#include "rabundvector.hpp"
#include "ordervector.hpp"
#include "sharedlistvector.h"
#include "sharedordervector.h"
+#include "sharedutilities.h"
/***********************************************************************/
-SharedListVector::SharedListVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){};
+SharedListVector::SharedListVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){ groupmap = NULL; }
/***********************************************************************/
-SharedListVector::SharedListVector(int n): DataVector(), data(n, "") , maxRank(0), numBins(0), numSeqs(0){};
+SharedListVector::SharedListVector(int n): DataVector(), data(n, "") , maxRank(0), numBins(0), numSeqs(0){ groupmap = NULL; }
/***********************************************************************/
SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
try {
- globaldata = GlobalData::getInstance();
-
//set up groupmap for later.
- groupmap = new GroupMap(globaldata->getGroupFile());
- groupmap->readMap();
+ groupmap = new GroupMap(m->getGroupFile());
+ groupmap->readMap();
int hold;
string inputData;
f >> label >> hold;
data.assign(hold, "");
-
+
for(int i=0;i<hold;i++){
f >> inputData;
set(i, inputData);
}
-
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function SharedListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedListVector class function SharedListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedListVector", "SharedListVector");
exit(1);
}
}
/***********************************************************************/
void SharedListVector::set(int binNumber, string seqNames){
try {
- int nNames_old = getNumNames(data[binNumber]);
+ int nNames_old = m->getNumNames(data[binNumber]);
data[binNumber] = seqNames;
- int nNames_new = getNumNames(seqNames);
+ int nNames_new = m->getNumNames(seqNames);
if(nNames_old == 0) { numBins++; }
if(nNames_new == 0) { numBins--; }
if(nNames_new > maxRank) { maxRank = nNames_new; }
numSeqs += (nNames_new - nNames_old);
+
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedListVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedListVector", "set");
exit(1);
}
}
void SharedListVector::push_back(string seqNames){
try {
data.push_back(seqNames);
- int nNames = getNumNames(seqNames);
+ int nNames = m->getNumNames(seqNames);
numBins++;
numSeqs += nNames;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedListVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedListVector", "push_back");
exit(1);
}
}
output << endl;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedListVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedListVector", "print");
exit(1);
}
}
RAbundVector rav;
for(int i=0;i<data.size();i++){
- int binSize = getNumNames(data[i]);
+ int binSize = m->getNumNames(data[i]);
rav.push_back(binSize);
}
return rav;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedListVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedListVector", "getRAbundVector");
exit(1);
}
}
SAbundVector sav(maxRank+1);
for(int i=0;i<data.size();i++){
- int binSize = getNumNames(data[i]);
+ int binSize = m->getNumNames(data[i]);
sav.set(binSize, sav.get(binSize) + 1);
}
sav.set(0, 0);
return sav;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedListVector class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedListVector", "getSAbundVector");
exit(1);
}
}
order->setLabel(label);
for(int i=0;i<numBins;i++){
- int binSize = getNumNames(get(i)); //find number of individual in given bin
+ int binSize = m->getNumNames(get(i)); //find number of individual in given bin
names = get(i);
while (names.find_first_of(',') != -1) {
name = names.substr(0,names.find_first_of(','));
names = names.substr(names.find_first_of(',')+1, names.length());
groupName = groupmap->getGroup(name);
+
+ if(groupName == "not found") { m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
+
order->push_back(i, binSize, groupName); //i represents what bin you are in
}
//get last name
groupName = groupmap->getGroup(names);
+ if(groupName == "not found") { m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
order->push_back(i, binSize, groupName);
}
+
random_shuffle(order->begin(), order->end());
+ order->updateStats();
+
return order;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedListVector", "getSharedOrderVector");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SharedListVector class function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
/***********************************************************************/
SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) {
name = names.substr(0,names.find_first_of(','));
names = names.substr(names.find_first_of(',')+1, names.length());
group = groupmap->getGroup(name);
+ if(group == "not found") { m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
if (group == groupName) { //this name is in the group you want the vector for.
rav.set(i, rav.getAbundance(i) + 1, group); //i represents what bin you are in
}
//get last name
groupName = groupmap->getGroup(names);
+ if(groupName == "not found") { m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
if (group == groupName) { //this name is in the group you want the vector for.
rav.set(i, rav.getAbundance(i) + 1, group); //i represents what bin you are in
}
rav.setLabel(label);
rav.setGroup(groupName);
+
return rav;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedListVector", "getSharedRAbundVector");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SharedListVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/***********************************************************************/
+vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
+ try {
+ SharedUtil* util;
+ util = new SharedUtil();
+ vector<SharedRAbundVector*> lookup; //contains just the groups the user selected
+ map<string, SharedRAbundVector*> finder; //contains all groups in groupmap
+ string group, names, name;
+
+ vector<string> Groups = m->getGroups();
+ vector<string> allGroups = groupmap->getNamesOfGroups();
+ util->setGroups(Groups, allGroups);
+ m->setGroups(Groups);
+ delete util;
+
+ for (int i = 0; i < allGroups.size(); i++) {
+ SharedRAbundVector* temp = new SharedRAbundVector(data.size());
+ finder[allGroups[i]] = temp;
+ finder[allGroups[i]]->setLabel(label);
+ finder[allGroups[i]]->setGroup(allGroups[i]);
+ if (m->inUsersGroups(allGroups[i], m->getGroups())) { //if this group is in user groups
+ lookup.push_back(finder[allGroups[i]]);
+ }
+ }
+
+ //fill vectors
+ for(int i=0;i<numBins;i++){
+ names = get(i);
+ int nameLength = names.size();
+ string seqName = "";
+
+ for(int j=0;j<nameLength;j++){
+ if(names[j] == ','){
+ group = groupmap->getGroup(seqName);
+ if(group == "not found") { m->mothurOut("Error: Sequence '" + seqName + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
+ finder[group]->set(i, finder[group]->getAbundance(i) + 1, group); //i represents what bin you are in
+
+ seqName = "";
+ }
+ else{
+ seqName += names[j];
+ }
+ }
+ group = groupmap->getGroup(seqName);
+ if(group == "not found") { m->mothurOut("Error: Sequence '" + seqName + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
+ finder[group]->set(i, finder[group]->getAbundance(i) + 1, group); //i represents what bin you are in
+
+
+
+// while (names.find_first_of(',') != -1) {
+// name = names.substr(0,names.find_first_of(','));
+// names = names.substr(names.find_first_of(',')+1, names.length());
+// group = groupmap->getGroup(name);
+// if(group == "not found") { m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
+// finder[group]->set(i, finder[group]->getAbundance(i) + 1, group); //i represents what bin you are in
+// }
+
+ //get last name
+// group = groupmap->getGroup(names);
+// if(group == "not found") { m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
+// finder[group]->set(i, finder[group]->getAbundance(i) + 1, group); //i represents what bin you are in
+
+ }
+
+ return lookup;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedListVector", "getSharedRAbundVector");
exit(1);
}
}
return sav;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedListVector class function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedListVector", "getSharedSAbundVector");
exit(1);
}
}
OrderVector ov;
for(int i=0;i<data.size();i++){
- int binSize = getNumNames(data[i]);
+ int binSize = m->getNumNames(data[i]);
for(int j=0;j<binSize;j++){
ov.push_back(i);
}
}
else{
if(orderMap->count(seqName) == 0){
- cerr << seqName << " not found, check *.names file\n";
+ m->mothurOut(seqName + " not found, check *.names file\n");
exit(1);
}
}
if(orderMap->count(seqName) == 0){
- cerr << seqName << " not found, check *.names file\n";
+ m->mothurOut(seqName + " not found, check *.names file\n");
exit(1);
}
ov.set((*orderMap)[seqName], i);
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedListVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SharedListVector", "getOrderVector");
exit(1);
}
}
projects / mothur.git / blobdiff