+++ /dev/null
-/*
- * consensuscommand.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 4/29/09.
- * Copyright 2009 Schloss Lab UMASS AMherst. All rights reserved.
- *
- */
-
-#include "consensuscommand.h"
-
-//**********************************************************************************************************************
-vector<string> ConcensusCommand::setParameters(){
- try {
- vector<string> myArray;
- for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "ConcensusCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string ConcensusCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The consensus command can only be executed after a successful read.tree command.\n";
- helpString += "The consensus command has no parameters.\n";
- helpString += "The consensus command should be in the following format: consensus().\n";
- helpString += "The consensus command output two files: .consensus.tre and .consensuspairs.\n";
- helpString += "The .consensus.tre file contains the consensus tree of the trees in your input file.\n";
- helpString += "The branch lengths are the percentage of trees in your input file that had the given pair.\n";
- helpString += "The .consensuspairs file contains a list of the internal nodes in your tree. For each node, the pair that was used in the consensus tree \n";
- helpString += "is reported with its percentage, as well as the other pairs that were seen for that node but not used and their percentages.\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "ConcensusCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-ConcensusCommand::ConcensusCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["tree"] = tempOutNames;
- outputTypes["nodepairs"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "ConcensusCommand", "ConcensusCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-ConcensusCommand::ConcensusCommand(string fileroot) {
- try {
- abort = false; calledHelp = false;
-
- setParameters();
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["tree"] = tempOutNames;
- outputTypes["nodepairs"] = tempOutNames;
-
- filename = fileroot;
-
- }
- catch(exception& e) {
- m->errorOut(e, "ConcensusCommand", "ConcensusCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int ConcensusCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
-
- m->mothurOut("This command is not currently in use."); m->mothurOutEndLine();
- /*
- t = globaldata->gTree;
- numNodes = t[0]->getNumNodes();
- numLeaves = t[0]->getNumLeaves();
-
-
- //get the possible pairings
- getSets();
-
- if (m->control_pressed) { return 0; }
-
- //open file for pairing not included in the tree
- notIncluded = filename + ".cons.pairs"; outputNames.push_back(notIncluded); outputTypes["nodepairs"].push_back(notIncluded);
- m->openOutputFile(notIncluded, out2);
-
- consensusTree = new Tree();
-
- it2 = nodePairs.find(treeSet);
-
- nodePairsInTree[treeSet] = it2->second;
-
- //erase treeset because you are adding it
- nodePairs.erase(treeSet);
-
- //set count to numLeaves;
- count = numLeaves;
-
- buildConcensusTree(treeSet);
-
- if (m->control_pressed) { delete consensusTree; return 0; }
-
- consensusTree->assembleTree();
-
- if (m->control_pressed) { delete consensusTree; return 0; }
-
- //output species in order
- out2 << "Species in Order: " << endl << endl;
- for (int i = 0; i < treeSet.size(); i++) { out2 << i+1 << ". " << treeSet[i] << endl; }
-
- //output sets included
- out2 << endl << "Sets included in the consensus tree:" << endl << endl;
-
- if (m->control_pressed) { delete consensusTree; return 0; }
-
- vector<string> temp;
- for (it2 = nodePairsInTree.begin(); it2 != nodePairsInTree.end(); it2++) {
-
- if (m->control_pressed) { delete consensusTree; return 0; }
-
- //only output pairs not leaves
- if (it2->first.size() > 1) {
- temp.clear();
- //initialize temp to all "."
- temp.resize(treeSet.size(), ".");
-
- //set the spot in temp that represents it2->first[i] to a "*"
- for (int i = 0; i < it2->first.size(); i++) {
- //find spot
- int index = findSpot(it2->first[i]);
- temp[index] = "*";
- //temp[index] = it2->first[i] + " ";
- }
-
- //output temp
- for (int j = 0; j < temp.size(); j++) {
- out2 << temp[j];
- }
- out2 << '\t' << it2->second << endl;
- }
- }
-
- //output sets not included
- out2 << endl << "Sets NOT included in the consensus tree:" << endl << endl;
- for (it2 = nodePairs.begin(); it2 != nodePairs.end(); it2++) {
-
- if (m->control_pressed) { delete consensusTree; return 0; }
-
- temp.clear();
- //initialize temp to all "."
- temp.resize(treeSet.size(), ".");
-
- //set the spot in temp that represents it2->first[i] to a "*"
- for (int i = 0; i < it2->first.size(); i++) {
- //find spot
- int index = findSpot(it2->first[i]);
- temp[index] = "*";
- }
-
- //output temp
- for (int j = 0; j < temp.size(); j++) {
- out2 << temp[j];
- }
- out2 << '\t' << it2->second << endl;
- }
-
- outputFile = filename + ".cons.tre"; outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
- m->openOutputFile(outputFile, out);
-
- consensusTree->print(out, "boot");
-
- out.close(); out2.close();
-
- delete consensusTree;
-
- //set first tree file as new current treefile
- string currentTree = "";
- itTypes = outputTypes.find("tree");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { currentTree = (itTypes->second)[0]; m->setTreeFile(currentTree); }
- }
- */
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "ConcensusCommand", "execute");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-int ConcensusCommand::buildConcensusTree(vector<string> nodeSet) {
- try {
- vector<string> leftChildSet;
- vector<string> rightChildSet;
-
- if (m->control_pressed) { return 1; }
-
- //if you are at a leaf
- if (nodeSet.size() == 1) {
- //return the vector index of the leaf you are at
- return consensusTree->getIndex(nodeSet[0]);
- //terminate recursion
- }else if (count == numNodes) { return 0; }
- else {
- //finds best child pair
- leftChildSet = getNextAvailableSet(nodeSet, rightChildSet);
- int left = buildConcensusTree(leftChildSet);
- int right = buildConcensusTree(rightChildSet);
- consensusTree->tree[count].setChildren(left, right);
- consensusTree->tree[count].setLabel(nodePairsInTree[nodeSet]);
- consensusTree->tree[left].setParent(count);
- consensusTree->tree[right].setParent(count);
- count++;
- return (count-1);
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "ConcensusCommand", "buildConcensusTree");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-int ConcensusCommand::getSets() {
- try {
- vector<string> temp;
- treeSet.clear();
-
- //for each tree add the possible pairs you find
- for (int i = 0; i < t.size(); i++) {
-
- //for each non-leaf node get descendant info.
- for (int j = numLeaves; j < numNodes; j++) {
-
- if (m->control_pressed) { return 1; }
-
- temp.clear();
- //go through pcounts and pull out descendants
- for (it = t[i]->tree[j].pcount.begin(); it != t[i]->tree[j].pcount.end(); it++) {
- temp.push_back(it->first);
- }
-
- //sort temp
- sort(temp.begin(), temp.end());
-
- it2 = nodePairs.find(temp);
- if (it2 != nodePairs.end()) {
- nodePairs[temp]++;
- }else{
- nodePairs[temp] = 1;
- }
- }
- }
-
-
- //add each leaf to terminate recursion in consensus
- //you want the leaves in there but with insignifigant sightings value so it is added last
- //for each leaf node get descendant info.
- for (int j = 0; j < numLeaves; j++) {
-
- if (m->control_pressed) { return 1; }
-
- //only need the first one since leaves have no descendants but themselves
- it = t[0]->tree[j].pcount.begin();
- temp.clear(); temp.push_back(it->first);
-
- //fill treeSet
- treeSet.push_back(it->first);
-
- //add leaf to list but with sighting value less then all non leaf pairs
- nodePairs[temp] = 0;
- }
-
- sort(treeSet.begin(), treeSet.end());
-
-
- map< vector<string>, int> nodePairsCopy = nodePairs;
-
-
- //set initial rating on pairs to sightings + subgroup sightings
- while (nodePairsCopy.size() != 0) {
- if (m->control_pressed) { return 1; }
-
- vector<string> smallOne = getSmallest(nodePairsCopy);
-
- int subgrouprate = getSubgroupRating(smallOne);
-
- nodePairsInitialRate[smallOne] = nodePairs[smallOne] + subgrouprate;
-
- nodePairsCopy.erase(smallOne);
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "ConcensusCommand", "getSets");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> ConcensusCommand::getSmallest(map< vector<string>, int> nodes) {
- try{
- vector<string> smallest = nodes.begin()->first;
- int smallsize = smallest.size();
-
- for(it2 = nodes.begin(); it2 != nodes.end(); it2++) {
- if(it2->first.size() < smallsize) { smallsize = it2->first.size(); smallest = it2->first; }
- }
-
- return smallest;
- }
- catch(exception& e) {
- m->errorOut(e, "ConcensusCommand", "getSmallest");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-vector<string> ConcensusCommand::getNextAvailableSet(vector<string> bigset, vector<string>& rest) {
- try {
-//cout << "new call " << endl << endl << endl;
- vector<string> largest; largest.clear();
- rest.clear();
-
- //if you are just 2 groups
- if (bigset.size() == 2) {
- rest.push_back(bigset[0]);
- largest.push_back(bigset[1]);
- }else{
- rest = bestSplit[bigset][0];
- largest = bestSplit[bigset][1];
- }
-
-
- //save for printing out later and for branch lengths
- nodePairsInTree[rest] = nodePairs[rest];
-
- //delete whatever set you return because it is no longer available
- nodePairs.erase(rest);
-
- //save for printing out later and for branch lengths
- nodePairsInTree[largest] = nodePairs[largest];
-
- //delete whatever set you return because it is no longer available
- nodePairs.erase(largest);
-
- return largest;
-
- }
- catch(exception& e) {
- m->errorOut(e, "ConcensusCommand", "getNextAvailableSet");
- exit(1);
- }
-}
-
-/**********************************************************************************************************************/
-int ConcensusCommand::getSubgroupRating(vector<string> group) {
- try {
- map< vector<string>, int>::iterator ittemp;
- map< vector< vector<string> > , int >::iterator it3;
- int rate = 0;
-
- // ***********************************************************************************//
- //1. this function must be called passing it littlest sets to biggest
- // since it the rating is made from your sighting plus you best splits rating
- //2. it saves the top pair to use later
- // ***********************************************************************************//
-
-
- if (group.size() < 3) { return rate; }
-
- map< vector<string>, int> possiblePairing; //this is all the subsets of group
-
- //go through the sets
- for (it2 = nodePairs.begin(); it2 != nodePairs.end(); it2++) {
- //are you a subset of bigset, then save in possiblePairings
- if (isSubset(group, it2->first) == true) { possiblePairing[it2->first] = it2->second; }
- }
-
- map< vector< vector<string> > , int > rating;
-
- while (possiblePairing.size() != 0) {
-
- it2 = possiblePairing.begin();
- vector<string> temprest = getRestSet(group, it2->first);
-
- //is the rest a set available in possiblePairings
- ittemp = possiblePairing.find(temprest);
- if (ittemp != possiblePairing.end()) { //if the rest is in the possible pairings then add this pair to rating map
- vector< vector<string> > temprate;
- temprate.push_back(it2->first); temprate.push_back(temprest);
-
- rating[temprate] = (nodePairsInitialRate[it2->first] + nodePairsInitialRate[temprest]);
-
- //erase so you dont add 1,2 and 2,1.
- possiblePairing.erase(temprest);
- }
-
- possiblePairing.erase(it2);
- }
-
-
- it3 = rating.begin();
- rate = it3->second;
- vector< vector<string> > topPair = it3->first;
-
- //choose the split with the best rating
- for (it3 = rating.begin(); it3 != rating.end(); it3++) {
-
- if (it3->second > rate) { rate = it3->second; topPair = it3->first; }
- }
-
- bestSplit[group] = topPair;
-
- return rate;
- }
- catch(exception& e) {
- m->errorOut(e, "ConcensusCommand", "getSubgroupRating");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-vector<string> ConcensusCommand::getRestSet(vector<string> bigset, vector<string> subset) {
- try {
- vector<string> rest;
-
- for (int i = 0; i < bigset.size(); i++) {
- bool inSubset = false;
- for (int j = 0; j < subset.size(); j++) {
- if (bigset[i] == subset[j]) { inSubset = true; break; }
- }
-
- //its not in the subset so put it in the rest
- if (inSubset == false) { rest.push_back(bigset[i]); }
- }
-
- return rest;
-
- }
- catch(exception& e) {
- m->errorOut(e, "ConcensusCommand", "getRestSet");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-bool ConcensusCommand::isSubset(vector<string> bigset, vector<string> subset) {
- try {
-
-
- if (subset.size() > bigset.size()) { return false; }
-
- //check if each guy in suset is also in bigset
- for (int i = 0; i < subset.size(); i++) {
- bool match = false;
- for (int j = 0; j < bigset.size(); j++) {
- if (subset[i] == bigset[j]) { match = true; break; }
- }
-
- //you have a guy in subset that had no match in bigset
- if (match == false) { return false; }
- }
-
- return true;
-
- }
- catch(exception& e) {
- m->errorOut(e, "ConcensusCommand", "isSubset");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int ConcensusCommand::findSpot(string node) {
- try {
- int spot;
-
- //check if each guy in suset is also in bigset
- for (int i = 0; i < treeSet.size(); i++) {
- if (treeSet[i] == node) { spot = i; break; }
- }
-
- return spot;
-
- }
- catch(exception& e) {
- m->errorOut(e, "ConcensusCommand", "findSpot");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-
-
-
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