+++ /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);
- }
-}
-
-/***********************************************************************/
-
projects / mothur.git / blobdiff