#include "unifracweightedcommand.h"
#include "consensus.h"
#include "subsample.h"
+#include "treereader.h"
//**********************************************************************************************************************
vector<string> UnifracWeightedCommand::setParameters(){
}
}
- m->runParse = true;
- m->clearGroups();
- m->clearAllGroups();
- m->Treenames.clear();
- m->names.clear();
-
//check for required parameters
treefile = validParameter.validFile(parameters, "tree", true);
if (treefile == "not open") { treefile = ""; abort = true; }
m->setTreeFile(treefile);
- readTrees(); if (m->control_pressed) { delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } return 0; }
+ TreeReader* reader = new TreeReader(treefile, groupfile, namefile);
+ T = reader->getTrees();
+ tmap = T[0]->getTreeMap();
+ map<string, string> nameMap = reader->getNames();
+ delete reader;
+
+ if (m->control_pressed) { delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } return 0; }
sumFile = outputDir + m->getSimpleName(treefile) + ".wsummary";
m->openOutputFile(sumFile, outSum);
if (m->control_pressed) { delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } return 0; }
- Weighted weighted(tmap, includeRoot);
+ Weighted weighted(includeRoot);
int start = time(NULL);
if (m->control_pressed) { break; }
- //copy to preserve old one - would do this in subsample but tree needs it and memory cleanup becomes messy.
+ //copy to preserve old one - would do this in subsample but memory cleanup becomes messy.
TreeMap* newTmap = new TreeMap();
- newTmap->getCopy(tmap);
+ newTmap->getCopy(*tmap);
SubSample sample;
Tree* subSampleTree = sample.getSample(T[i], newTmap, nameMap, subsampleSize);
//call new weighted function
vector<double> iterData; iterData.resize(numComp,0);
- Weighted thisWeighted(newTmap, includeRoot);
+ Weighted thisWeighted(includeRoot);
iterData = thisWeighted.getValues(subSampleTree, processors, outputDir); //userData[0] = weightedscore
//save data to make ave dist, std dist
delete newTmap;
delete subSampleTree;
+
+ if((thisIter+1) % 100 == 0){ m->mothurOut(toString(thisIter+1)); m->mothurOutEndLine(); }
}
if (m->control_pressed) { delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; } if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
m->runParse = false;
//create treemap class from groupmap for tree class to use
- TreeMap* newTmap = new TreeMap();
- newTmap->makeSim(m->getGroups());
+ TreeMap newTmap;
+ newTmap.makeSim(m->getGroups());
//clear old tree names if any
m->Treenames.clear();
vector<Tree*> newTrees = buildTrees(dists, treeNum, newTmap); //also creates .all.tre file containing the trees created
- if (m->control_pressed) { delete newTmap; return 0; }
+ if (m->control_pressed) { return 0; }
Consensus con;
- Tree* conTree = con.getTree(newTrees, newTmap);
+ Tree* conTree = con.getTree(newTrees);
//create a new filename
string conFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(treeNum+1) + ".weighted.cons.tre";
if (conTree != NULL) { conTree->print(outTree, "boot"); delete conTree; }
outTree.close();
- delete newTmap;
return 0;
}
/**************************************************************************************************/
-vector<Tree*> UnifracWeightedCommand::buildTrees(vector< vector<double> >& dists, int treeNum, TreeMap* mytmap) {
+vector<Tree*> UnifracWeightedCommand::buildTrees(vector< vector<double> >& dists, int treeNum, TreeMap& mytmap) {
try {
vector<Tree*> trees;
}
//create tree
- Tree* tempTree = new Tree(mytmap, sims);
- tempTree->assembleTree();
+ Tree* tempTree = new Tree(&mytmap, sims);
+ map<string, string> empty;
+ tempTree->assembleTree(empty);
trees.push_back(tempTree);
}
/**************************************************************************************************/
-int UnifracWeightedCommand::readTrees() {
- try {
-
- if (groupfile != "") {
- //read in group map info.
- tmap = new TreeMap(groupfile);
- tmap->readMap();
- }else{ //fake out by putting everyone in one group
- Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
- tmap = new TreeMap();
-
- for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
- }
-
- if (namefile != "") { readNamesFile(); }
-
- read = new ReadNewickTree(treefile);
- int readOk = read->read(tmap);
-
- if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete tmap; delete read; return 0; }
-
- read->AssembleTrees();
- T = read->getTrees();
- delete read;
-
- //make sure all files match
- //if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size.
- int numNamesInTree;
- if (namefile != "") {
- if (numUniquesInName == m->Treenames.size()) { numNamesInTree = nameMap.size(); }
- else { numNamesInTree = m->Treenames.size(); }
- }else { numNamesInTree = m->Treenames.size(); }
-
-
- //output any names that are in group file but not in tree
- if (numNamesInTree < tmap->getNumSeqs()) {
- for (int i = 0; i < tmap->namesOfSeqs.size(); i++) {
- //is that name in the tree?
- int count = 0;
- for (int j = 0; j < m->Treenames.size(); j++) {
- if (tmap->namesOfSeqs[i] == m->Treenames[j]) { break; } //found it
- count++;
- }
-
- if (m->control_pressed) {
- delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
- for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
- m->clearGroups();
- return 0;
- }
-
- //then you did not find it so report it
- if (count == m->Treenames.size()) {
- //if it is in your namefile then don't remove
- map<string, string>::iterator it = nameMap.find(tmap->namesOfSeqs[i]);
-
- if (it == nameMap.end()) {
- m->mothurOut(tmap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
- tmap->removeSeq(tmap->namesOfSeqs[i]);
- i--; //need this because removeSeq removes name from namesOfSeqs
- }
- }
- }
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "UnifracWeightedCommand", "readTrees");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
int UnifracWeightedCommand::runRandomCalcs(Tree* thisTree, vector<double> usersScores) {
try {
try {
Tree* randT = new Tree(tmap);
- Weighted weighted(tmap, includeRoot);
+ Weighted weighted(includeRoot);
for (int h = start; h < (start+num); h++) {
exit(1);
}
}
-/*****************************************************************/
-int UnifracWeightedCommand::readNamesFile() {
- try {
- m->names.clear();
- numUniquesInName = 0;
-
- ifstream in;
- m->openInputFile(namefile, in);
-
- string first, second;
- map<string, string>::iterator itNames;
-
- while(!in.eof()) {
- in >> first >> second; m->gobble(in);
-
- numUniquesInName++;
-
- itNames = m->names.find(first);
- if (itNames == m->names.end()) {
- m->names[first] = second;
-
- //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
- vector<string> dupNames;
- m->splitAtComma(second, dupNames);
-
- for (int i = 0; i < dupNames.size(); i++) {
- nameMap[dupNames[i]] = first;
- if ((groupfile == "") && (i != 0)) { tmap->addSeq(dupNames[i], "Group1"); }
- }
- }else { m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); m->names.clear(); namefile = ""; return 1; }
- }
- in.close();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "UnifracWeightedCommand", "readNamesFile");
- exit(1);
- }
-}
/***********************************************************/
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