--- /dev/null
+/*
+ * sharedSharedListVector.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 1/22/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#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){ groupmap = NULL; }
+
+/***********************************************************************/
+
+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 {
+ //set up groupmap for later.
+ 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) {
+ m->errorOut(e, "SharedListVector", "SharedListVector");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+void SharedListVector::set(int binNumber, string seqNames){
+ try {
+ int nNames_old = m->getNumNames(data[binNumber]);
+ data[binNumber] = 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) {
+ m->errorOut(e, "SharedListVector", "set");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+string SharedListVector::get(int index){
+ return data[index];
+}
+
+/***********************************************************************/
+
+void SharedListVector::push_back(string seqNames){
+ try {
+ data.push_back(seqNames);
+ int nNames = m->getNumNames(seqNames);
+
+ numBins++;
+
+ if(nNames > maxRank) { maxRank = nNames; }
+
+ numSeqs += nNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedListVector", "push_back");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void SharedListVector::resize(int size){
+ data.resize(size);
+}
+
+/***********************************************************************/
+
+int SharedListVector::size(){
+ return data.size();
+}
+/***********************************************************************/
+
+void SharedListVector::clear(){
+ numBins = 0;
+ maxRank = 0;
+ numSeqs = 0;
+ return data.clear();
+
+}
+
+/***********************************************************************/
+
+void SharedListVector::print(ostream& output){
+ try {
+ output << label << '\t' << numBins << '\t';
+
+ for(int i=0;i<data.size();i++){
+ if(data[i] != ""){
+ output << data[i] << '\t';
+ }
+ }
+ output << endl;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedListVector", "print");
+ exit(1);
+ }
+}
+
+
+/***********************************************************************/
+
+RAbundVector SharedListVector::getRAbundVector(){
+ try {
+ RAbundVector rav;
+
+ for(int i=0;i<data.size();i++){
+ int binSize = m->getNumNames(data[i]);
+ rav.push_back(binSize);
+ }
+
+ // This was here before to output data in a nice format, but it screws up the name mapping steps
+ // sort(rav.rbegin(), rav.rend());
+ //
+ // for(int i=data.size()-1;i>=0;i--){
+ // if(rav.get(i) == 0){ rav.pop_back(); }
+ // else{
+ // break;
+ // }
+ // }
+ rav.setLabel(label);
+
+ return rav;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedListVector", "getRAbundVector");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+SAbundVector SharedListVector::getSAbundVector(){
+ try {
+ SAbundVector sav(maxRank+1);
+
+ for(int i=0;i<data.size();i++){
+ int binSize = m->getNumNames(data[i]);
+ sav.set(binSize, sav.get(binSize) + 1);
+ }
+ sav.set(0, 0);
+ sav.setLabel(label);
+
+ return sav;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedListVector", "getSAbundVector");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+SharedOrderVector* SharedListVector::getSharedOrderVector(){
+ try {
+ string groupName, names, name;
+
+ SharedOrderVector* order = new SharedOrderVector();
+ order->setLabel(label);
+
+ for(int i=0;i<numBins;i++){
+ 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) {
+ m->errorOut(e, "SharedListVector", "getSharedOrderVector");
+ exit(1);
+ }
+}
+/***********************************************************************/
+SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) {
+ try {
+ SharedRAbundVector rav(data.size());
+ string group, names, name;
+
+ for(int i=0;i<numBins;i++){
+ 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());
+ 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) {
+ m->errorOut(e, "SharedListVector", "getSharedRAbundVector");
+ exit(1);
+ }
+}
+/***********************************************************************/
+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);
+ }
+}
+
+/***********************************************************************/
+SharedSAbundVector SharedListVector::getSharedSAbundVector(string groupName) {
+ try {
+ SharedSAbundVector sav;
+ SharedRAbundVector rav;
+
+ rav = this->getSharedRAbundVector(groupName);
+ sav = rav.getSharedSAbundVector();
+
+ return sav;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedListVector", "getSharedSAbundVector");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+OrderVector SharedListVector::getOrderVector(map<string,int>* orderMap = NULL){
+
+ try {
+ if(orderMap == NULL){
+ OrderVector ov;
+
+ for(int i=0;i<data.size();i++){
+ int binSize = m->getNumNames(data[i]);
+ for(int j=0;j<binSize;j++){
+ ov.push_back(i);
+ }
+ }
+ random_shuffle(ov.begin(), ov.end());
+ ov.setLabel(label);
+ ov.getNumBins();
+
+ return ov;
+
+ }
+ else{
+ OrderVector ov(numSeqs);
+
+ for(int i=0;i<data.size();i++){
+ string listOTU = data[i];
+ int length = listOTU.size();
+
+ string seqName="";
+
+ for(int j=0;j<length;j++){
+
+ if(listOTU[j] != ','){
+ seqName += listOTU[j];
+ }
+ else{
+ if(orderMap->count(seqName) == 0){
+ m->mothurOut(seqName + " not found, check *.names file\n");
+ exit(1);
+ }
+
+ ov.set((*orderMap)[seqName], i);
+ seqName = "";
+ }
+ }
+
+ if(orderMap->count(seqName) == 0){
+ m->mothurOut(seqName + " not found, check *.names file\n");
+ exit(1);
+ }
+ ov.set((*orderMap)[seqName], i);
+ }
+
+ ov.setLabel(label);
+ ov.getNumBins();
+
+ return ov;
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedListVector", "getOrderVector");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
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