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+ 3792948A0F2E258500B9034A /* parsimony.cpp in Sources */,
+ 374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */,
+ 3746107E0F4064D100460C57 /* weighted.cpp in Sources */,
+ 374610830F40652400460C57 /* unweighted.cpp in Sources */,
+ 3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */,
);
runOnlyForDeploymentPostprocessing = 0;
};
ppc,
i386,
);
- GCC_OPTIMIZATION_LEVEL = 3;
+ GCC_OPTIMIZATION_LEVEL = 0;
GCC_WARN_ABOUT_RETURN_TYPE = YES;
GCC_WARN_UNUSED_VARIABLE = YES;
PREBINDING = NO;
#include "rabundvector.hpp"
#include "uvest.h"
-/* The calculator class is the parent class for all the different estimators implemented in mothur.
+/* The calculator class is the parent class for all the different estimators implemented in mothur except the tree calculators.
It has 2 pure functions EstOutput getValues(SAbundVector*), which works on a single group, and
EstOutput getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2), which compares 2 groups. */
* Dotur
*
* Created by Sarah Westcott on 11/18/08.
- * Copyright 2008 __MyCompanyName__. All rights reserved.
+ * Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "helpcommand.h"
#include "commandfactory.hpp"
#include "deconvolutecommand.h"
+#include "parsimonycommand.h"
+#include "unifracunweightedcommand.h"
+#include "unifracweightedcommand.h"
#include <exception>
try {
delete command; //delete the old command
- if(commandName == "read.dist") { command = new ReadDistCommand(); }
- else if(commandName == "read.otu") { command = new ReadOtuCommand(); }
- //else if(commandName == "read.tree") { command = new ReadTreeCommand(); }
- else if(commandName == "cluster") { command = new ClusterCommand(); }
- else if(commandName == "deconvolute") { command = new DeconvoluteCommand(); }
- else if(commandName == "help") { command = new HelpCommand(); }
- else if(commandName == "quit") { command = new QuitCommand(); }
- else if(commandName == "collect.single") { command = new CollectCommand(); }
- else if(commandName == "collect.shared") { command = new CollectSharedCommand(); }
- else if(commandName == "rarefaction.single") { command = new RareFactCommand(); }
- else if(commandName == "rarefaction.shared") { command = new RareFactSharedCommand(); }
- else if(commandName == "summary.single") { command = new SummaryCommand(); }
- else if(commandName == "summary.shared") { command = new SummarySharedCommand(); }
- else { command = new NoCommand(); }
-
+ if(commandName == "read.dist") { command = new ReadDistCommand(); }
+ else if(commandName == "read.otu") { command = new ReadOtuCommand(); }
+ else if(commandName == "read.tree") { command = new ReadTreeCommand(); }
+ else if(commandName == "cluster") { command = new ClusterCommand(); }
+ else if(commandName == "deconvolute") { command = new DeconvoluteCommand(); }
+ else if(commandName == "parsimony") { command = new ParsimonyCommand(); }
+ else if(commandName == "help") { command = new HelpCommand(); }
+ else if(commandName == "quit") { command = new QuitCommand(); }
+ else if(commandName == "collect.single") { command = new CollectCommand(); }
+ else if(commandName == "collect.shared") { command = new CollectSharedCommand(); }
+ else if(commandName == "rarefaction.single") { command = new RareFactCommand(); }
+ else if(commandName == "rarefaction.shared") { command = new RareFactSharedCommand(); }
+ else if(commandName == "summary.single") { command = new SummaryCommand(); }
+ else if(commandName == "summary.shared") { command = new SummarySharedCommand(); }
+ else if(commandName == "unifrac.weighted") { command = new UnifracWeightedCommand(); }
+ else if(commandName == "unifrac.unweighted") { command = new UnifracUnweightedCommand(); }
+ else { command = new NoCommand(); }
+
return command;
}
catch(exception& e) {
validCommand = new ValidCommands();
validParameter = new ValidParameters();
validCalculator = new ValidCalculators();
+}
+/*******************************************************/
+
+/******************************************************/
+
+void ErrorCheck::refresh() {
columnfile = globaldata->getColumnFile();
phylipfile = globaldata->getPhylipFile();
listfile = globaldata->getListFile();
cutoff = globaldata->getCutOff();
format = globaldata->getFormat();
method = globaldata->getMethod();
-
+ randomtree = globaldata->getRandomTree();
}
+
/*******************************************************/
/******************************************************/
bool ErrorCheck::checkInput(string input) {
errorFree = true;
clear();
-
+
+ //refresh variable
+ refresh();
+
//get command name and parameters
int openParen = input.find_first_of('(');
int closeParen = input.find_last_of(')');
if (parameter == "fileroot" ) { fileroot = value; }
if (parameter == "line" ) { line = value; }
if (parameter == "label" ) { label = value; }
+ if (parameter == "randomtree" ) { randomtree = value; }
if (parameter == "single") {//stores estimators in a vector
singleEsimators.clear(); //clears out old values
if (parameter == "fileroot" ) { fileroot = value; }
if (parameter == "line" ) { line = value; }
if (parameter == "label" ) { label = value; }
+ if (parameter == "randomtree" ) { randomtree = value; }
if (parameter == "single") {//stores estimators in a vector
singleEsimators.clear(); //clears out old values
errorFree = false;
}
+ if (commandName == "parsimony") {
+ //are you trying to use parsimony without reading a tree or saying you want random distribution
+ if (randomtree == "0") {
+ if ((globaldata->getTreeFile() == "") || (globaldata->getGroupFile() == "")) {
+ cout << "You must read a treefile and a groupfile or set the randomtree parameter to 1, before you may execute the parsimony command." << endl; return false; }
+ }
+ }
+
//check for valid method
if (commandName == "cluster") {
if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
void validateParseFiles();
void validateTreeFiles();
void clear();
+ void refresh();
string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, cutoff, format;
- string precision, method, fileroot, label, line, iters, jumble, freq, single, rarefaction, shared, summary;
+ string precision, method, fileroot, label, line, iters, jumble, freq, single, rarefaction, shared, summary, randomtree;
string commandName, optionText;
bool errorFree;
vector<string> singleEsimators, sharedEstimators, rareEstimators, summaryEstimators, sharedRareEstimators;
if (key == "freq" ) { freq = value; }
if (key == "method" ) { method = value; }
if (key == "fileroot" ) { fileroot = value; }
+ if (key == "randomtree" ) { randomtree = value; }
+ if (key == "groups" ) { groups = value; }
if (key == "single") {//stores estimators in a vector
singleEstimators.clear(); //clears out old values
if (value == "default") { value = "sharedobserved"; }
splitAtDash(value, sharedRareEstimators);
}
- if (key == "line") {//stores lines to be used in a vector
+ if (key == "line") {//stores lines to be used in a set
lines.clear();
line = value;
label = "";
splitAtDash(value, lines);
allLines = 0;
}
- if (key == "label") {//stores lines to be used in a vector
+ if (key == "label") {//stores lines to be used in a set
labels.clear();
label = value;
line = "";
splitAtDash(value, labels);
allLines = 0;
}
+ if (key == "groups") {//stores lines to be used in a vector
+ Groups.clear();
+ groups = value;
+ splitAtDash(value, Groups);
+ }
+
}
//saves the last parameter
if (key == "freq" ) { freq = value; }
if (key == "method" ) { method = value; }
if (key == "fileroot" ) { fileroot = value; }
-
+ if (key == "randomtree" ) { randomtree = value; }
+
if (key == "single") {//stores estimators in a vector
singleEstimators.clear(); //clears out old values
if (value == "default") { value = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction"; }
string GlobalData::getIters() { return iters; }
string GlobalData::getJumble() { return jumble; }
string GlobalData::getFreq() { return freq; }
+string GlobalData::getRandomTree() { return randomtree; }
void GlobalData::setListFile(string file) { listfile = file; inputFileName = file;}
void GlobalData::setRabundFile(string file) { rabundfile = file; inputFileName = file;}
void GlobalData::setSabundFile(string file) { sabundfile = file; inputFileName = file;}
void GlobalData::setPhylipFile(string file) { phylipfile = file; inputFileName = file;}
void GlobalData::setColumnFile(string file) { columnfile = file; inputFileName = file;}
-//void GlobalData::setGroupFile(string file) { groupfile = file; }
-void GlobalData::setNameFile(string file) { namefile = file; }
-void GlobalData::setFormat(string Format) { format = Format; }
+//void GlobalData::setGroupFile(string file) { groupfile = file; }
+void GlobalData::setNameFile(string file) { namefile = file; }
+void GlobalData::setFormat(string Format) { format = Format; }
+void GlobalData::setRandomTree(string Random) { randomtree = Random; }
/*******************************************************/
iters = "1000";
line = "";
label = "";
- jumble = "1";
+ jumble = "1"; //0 means don't jumble, 1 means jumble.
+ randomtree = "0"; //0 means user will enter some user trees, 1 means they just want the random tree distribution.
freq = "100";
method = "furthest";
fileroot = "";
InputData* ginput;
OrderVector* gorder;
ListVector* glist;
- Tree* gTree;
+ vector<Tree*> gTree;
SharedListVector* gSharedList;
SAbundVector* sabund;
GroupMap* gGroupmap;
vector<string> singleEstimators, summaryEstimators, sharedEstimators, rareEstimators, sharedRareEstimators, sharedSummaryEstimators; //holds estimators to be used
set<int> lines; //hold lines to be used
set<string> labels; //holds labels to be used
+ vector<string> Groups;
string getPhylipFile();
string getColumnFile();
string getIters();
string getJumble();
string getFreq();
+ string getRandomTree();
void setListFile(string);
void setPhylipFile(string);
void setColumnFile(string);
void setRabundFile(string);
void setSabundFile(string);
void setFormat(string);
+ void setRandomTree(string);
void setListVector(ListVector*);
void splitAtDash(string&, set<string>&);
private:
- string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, line, label;
+ string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, line, label, randomtree, groups;
string cutoff, format, precision, method, fileroot, iters, jumble, freq, single, rarefaction, shared, summary, sharedsummary, sharedrarefaction;
static GlobalData* _uniqueInstance;
GlobalData( const GlobalData& ); // Disable copy constructor
* Dotur
*
* Created by Sarah Westcott on 11/18/08.
- * Copyright 2008 __MyCompanyName__. All rights reserved.
+ * Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
* Dotur
*
* Created by John Westcott on 1/7/09.
- * Copyright 2009 __MyCompanyName__. All rights reserved.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
--- /dev/null
+/*
+ * parsimony.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 1/26/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "parsimony.h"
+
+/**************************************************************************************************/
+EstOutput Parsimony::getValues(Tree* t) {
+ try {
+ data.resize(1,0);
+
+ int score = 0;
+
+ for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
+ int lc = t->tree[i].getLChild();
+ int rc = t->tree[i].getRChild();
+
+ if(t->tree[i].pGroups.size() > t->tree[rc].pGroups.size() || t->tree[i].pGroups.size() > t->tree[lc].pGroups.size()){
+ score++;
+ }
+ }
+
+ data[0] = score;
+
+ return data;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Parsimony class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Parsimony class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+/**************************************************************************************************/
--- /dev/null
+#ifndef PARSIMONY_H
+#define PARSIMONY_H
+
+
+/*
+ * parsimony.h
+ * Mothur
+ *
+ * Created by Sarah Westcott on 1/26/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "treecalculator.h"
+#include "treemap.h"
+
+/***********************************************************************/
+
+class Parsimony : public TreeCalculator {
+
+ public:
+ Parsimony(TreeMap* t) : tmap(t) {};
+ ~Parsimony() {};
+ EstOutput getValues(Tree*);
+
+ private:
+ EstOutput data;
+ TreeMap* tmap;
+};
+
+/***********************************************************************/
+#endif
\ No newline at end of file
--- /dev/null
+/*
+ * parsimonycommand.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 1/26/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "parsimonycommand.h"
+
+/***********************************************************/
+ParsimonyCommand::ParsimonyCommand() {
+ try {
+ globaldata = GlobalData::getInstance();
+
+ //randomtree will tell us if user had their own treefile or if they just want the random distribution
+ convert(globaldata->getRandomTree(), randomtree);
+
+ //user has entered their own tree
+ if (randomtree == 0) {
+ T = globaldata->gTree;
+ tmap = globaldata->gTreemap;
+ parsFile = globaldata->getTreeFile() + ".parsimony";
+ openOutputFile(parsFile, out);
+ sumFile = globaldata->getTreeFile() + ".psummary";
+ openOutputFile(sumFile, outSum);
+ distFile = globaldata->getTreeFile() + ".pdistrib";
+ openOutputFile(distFile, outDist);
+
+ }else { //user wants random distribution
+ getUserInput();
+ parsFile = "rd_parsimony";
+ openOutputFile(parsFile, out);
+ }
+
+ convert(globaldata->getIters(), iters); //how many random trees to generate
+ pars = new Parsimony(tmap);
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function ParsimonyCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ParsimonyCommand class function ParsimonyCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************/
+int ParsimonyCommand::execute() {
+ try {
+
+ //get pscore for users tree
+ userData.resize(1,0); //data[0] = pscore.
+ randomData.resize(1,0); //data[0] = pscore.
+
+ //format output
+ outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
+ outDist << "RandomTree#" << '\t' << "ParsScore" << endl;
+
+ if (randomtree == 0) {
+ //get pscores for users trees
+ for (int i = 0; i < T.size(); i++) {
+ cout << "Processing tree " << i+1 << endl;
+ userData = pars->getValues(T[i]); //userData[0] = pscore
+ //update uscoreFreq
+ it = uscoreFreq.find(userData[0]);
+ if (it == uscoreFreq.end()) {//new score
+ uscoreFreq[userData[0]] = 1;
+ }else{ uscoreFreq[userData[0]]++; }
+
+ //add users score to valid scores
+ validScores[userData[0]] = userData[0];
+
+ //save score for summary file
+ userTreeScores.push_back(userData[0]);
+
+ }
+
+ //get pscores for random trees
+ for (int j = 0; j < iters; j++) {
+ //create new tree with same num nodes and leaves as users
+ randT = new Tree();
+ //create random relationships between nodes
+ randT->assembleRandomTree();
+ //get pscore of random tree
+ randomData = pars->getValues(randT);
+
+ //add trees pscore to map of scores
+ it2 = rscoreFreq.find(randomData[0]);
+ if (it2 != rscoreFreq.end()) {//already have that score
+ rscoreFreq[randomData[0]]++;
+ }else{//first time we have seen this score
+ rscoreFreq[randomData[0]] = 1;
+ }
+
+ //add randoms score to validscores
+ validScores[randomData[0]] = randomData[0];
+
+ //output info to pdistrib file
+ outDist << j+1 << '\t'<< '\t' << randomData[0] << endl;
+
+ delete randT;
+ }
+ }else {
+ //get pscores for random trees
+ for (int j = 0; j < iters; j++) {
+ //create new tree with same num nodes and leaves as users
+ randT = new Tree();
+ //create random relationships between nodes
+ randT->assembleRandomTree();
+ //get pscore of random tree
+ randomData = pars->getValues(randT);
+
+ //add trees pscore to map of scores
+ it2 = rscoreFreq.find(randomData[0]);
+ if (it2 != rscoreFreq.end()) {//already have that score
+ rscoreFreq[randomData[0]]++;
+ }else{//first time we have seen this score
+ rscoreFreq[randomData[0]] = 1;
+ }
+
+ //add randoms score to validscores
+ validScores[randomData[0]] = randomData[0];
+
+ delete randT;
+ }
+ }
+
+ float rcumul = 0.0000;
+ float ucumul = 0.0000;
+
+ //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
+ for (it = validScores.begin(); it != validScores.end(); it++) {
+ if (randomtree == 0) {
+ it2 = uscoreFreq.find(it->first);
+ //user data has that score
+ if (it2 != uscoreFreq.end()) { uscoreFreq[it->first] /= T.size(); ucumul+= it2->second; }
+ else { uscoreFreq[it->first] = 0.0000; } //no user trees with that score
+ //make uCumul map
+ uCumul[it->first] = ucumul;
+ }
+
+ //make rscoreFreq map and rCumul
+ it2 = rscoreFreq.find(it->first);
+ //get percentage of random trees with that info
+ if (it2 != rscoreFreq.end()) { rscoreFreq[it->first] /= iters; rcumul+= it2->second; }
+ else { rscoreFreq[it->first] = 0.0000; } //no random trees with that score
+ rCumul[it->first] = rcumul;
+ }
+
+ //find the signifigance of each user trees score when compared to the random trees and save for printing the summary file
+ for (int h = 0; h < userTreeScores.size(); h++) {
+ UScoreSig.push_back(rCumul[userTreeScores[h]]);
+ }
+
+ printParsimonyFile();
+ printUSummaryFile();
+
+ //reset randomTree parameter to 0
+ globaldata->setRandomTree("0");
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ParsimonyCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************/
+void ParsimonyCommand::printParsimonyFile() {
+ try {
+ //column headers
+ if (randomtree == 0) {
+ out << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
+ }else {
+ out << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
+ }
+
+ //format output
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ //print each line
+ for (it = validScores.begin(); it != validScores.end(); it++) {
+ if (randomtree == 0) {
+ out << setprecision(6) << it->first << '\t' << '\t' << uscoreFreq[it->first] << '\t' << uCumul[it->first] << '\t' << rscoreFreq[it->first] << '\t' << rCumul[it->first] << endl;
+ }else{
+ out << setprecision(6) << it->first << '\t' << '\t' << rscoreFreq[it->first] << '\t' << rCumul[it->first] << endl;
+ }
+ }
+
+ out.close();
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function printParsimonyFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ParsimonyCommand class function printParsimonyFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************/
+void ParsimonyCommand::printUSummaryFile() {
+ try {
+ //column headers
+ outSum << "Tree#" << '\t' << "ParsScore" << '\t' << '\t' << "ParsSig" << endl;
+
+ //format output
+ outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
+
+ //print each line
+ for (int i = 0; i< T.size(); i++) {
+ outSum << setprecision(6) << i+1 << '\t' << '\t' << userTreeScores[i] << '\t' << UScoreSig[i] << endl;
+ }
+
+ outSum.close();
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function printUSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ParsimonyCommand class function printUSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************/
+void ParsimonyCommand::getUserInput() {
+ try {
+
+ //create treemap
+ tmap = new TreeMap();
+
+ cout << "Please enter the number of groups you would like to analyze: ";
+ cin >> numGroups;
+
+ int num, count;
+ count = 1;
+ numEachGroup.resize(numGroups, 0);
+
+ for (int i = 1; i <= numGroups; i++) {
+ cout << "Please enter the number of sequences in group " << i << ": ";
+ cin >> num;
+
+ //set tmaps seqsPerGroup
+ tmap->seqsPerGroup[toString(i)] = num;
+
+ //set tmaps namesOfSeqs
+ for (int j = 0; j < num; j++) {
+ tmap->namesOfSeqs.push_back(toString(count));
+ tmap->treemap[toString(count)].groupname = toString(i);
+ count++;
+ }
+ }
+
+ //clears buffer so next command doesn't have error
+ string s;
+ getline(cin, s);
+
+ //save tmap for later
+ globaldata->gTreemap = tmap;
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function getUserInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ParsimonyCommand class function getUserInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************/
+
--- /dev/null
+#ifndef PARSIMONYCOMMAND_H
+#define PARSIMONYCOMMAND_H
+/*
+ * parsimonycommand.h
+ * Mothur
+ *
+ * Created by Sarah Westcott on 1/26/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include <iostream>
+#include <fstream>
+#include <vector>
+#include <map>
+#include <cmath>
+#include "command.hpp"
+#include "parsimony.h"
+#include "treemap.h"
+
+using namespace std;
+
+class GlobalData;
+
+class ParsimonyCommand : public Command {
+
+ public:
+ ParsimonyCommand();
+ ~ParsimonyCommand() { delete pars; }
+ int execute();
+
+ private:
+ GlobalData* globaldata;
+ vector<Tree*> T; //user trees
+ Tree* randT; //random tree
+ TreeMap* tmap;
+ Parsimony* pars;
+ string parsFile, sumFile, distFile;
+ int iters, randomtree, numGroups;
+ vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
+ vector<float> userTreeScores; //scores for users trees
+ vector<float> UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
+ EstOutput userData; //pscore info for user tree
+ EstOutput randomData; //pscore info for random trees
+ map<int, float> validScores; //contains scores from both user and random
+ map<int, float> rscoreFreq; //pscore, number of random trees with that score.
+ map<int, float> uscoreFreq; //pscore, number of user trees with that score.
+ map<int, float> rCumul; //pscore, cumulative percentage of number of random trees with that score or lower.
+ map<int, float> uCumul; //pscore, cumulative percentage of number of user trees with that score or lower .
+ map<int, float>::iterator it;
+ map<int, float>::iterator it2;
+
+ ofstream out, outSum, outDist;
+
+ void printParsimonyFile();
+ void printUSummaryFile();
+ void getUserInput();
+
+};
+
+
+#endif
* Dotur
*
* Created by Sarah Westcott on 11/18/08.
- * Copyright 2008 __MyCompanyName__. All rights reserved.
+ * Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "readtree.h"
/***********************************************************************/
-//Parent Class
-// The following functions are used by all reading formats.
-/***********************************************************************/
-ReadTree::ReadTree() {
+ReadTree::ReadTree() {
try {
- globaldata = GlobalData::getInstance();
- T = new Tree();
- numNodes = T->getNumNodes();
- numLeaves = T->getNumLeaves();
+ globaldata = GlobalData::getInstance();
+ globaldata->gTree.clear();
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
void ReadNewickTree::read() {
try {
+ int c;
+ int comment = 0;
+
+ //if you are not a nexus file
+ if ((c = filehandle.peek()) != '#') {
+ while((c = filehandle.peek()) != EOF) {
+ //make new tree
+ T = new Tree();
+ numNodes = T->getNumNodes();
+ numLeaves = T->getNumLeaves();
+
+ readTreeString();
+ //save trees for later commands
+ globaldata->gTree.push_back(T);
+ }
+ //if you are a nexus file
+ }else if ((c = filehandle.peek()) == '#') {
+ nexusTranslation(); //reads file through the translation and updates treemap
+ while((c = filehandle.peek()) != EOF) {
+ // get past comments
+ while ((c = filehandle.peek()) != EOF) {
+ if(holder == "[" || holder == "[!"){
+ comment = 1;
+ }
+ if(holder == "]"){
+ comment = 0;
+ }
+ if((holder == "tree" || holder == "end;") && comment != 1){ holder = ""; comment = 0; break;}
+ filehandle >> holder;
+ }
+
+ //pass over the "tree rep.6878900 = "
+ while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF) ) {;}
+
+ if (c == EOF ) { break; }
+ filehandle.putback(c); //put back first ( of tree.
+
+ //make new tree
+ T = new Tree();
+ numNodes = T->getNumNodes();
+ numLeaves = T->getNumLeaves();
+
+ //read tree info
+ readTreeString();
+ //save trees for later commands
+ globaldata->gTree.push_back(T);
+ }
+ }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ReadNewickTree class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+//This function read the file through the translation of the sequences names and updates treemap.
+void ReadNewickTree::nexusTranslation() {
+ try {
+
+ holder = "";
+ int numSeqs = globaldata->gTreemap->getNumSeqs(); //must save this some when we clear old names we can still know how many sequences there were
+ int comment = 0;
+
+ // get past comments
+ while(holder != "translate" && holder != "Translate"){
+ if(holder == "[" || holder == "[!"){
+ comment = 1;
+ }
+ if(holder == "]"){
+ comment = 0;
+ }
+ filehandle >> holder;
+ if(holder == "tree" && comment != 1){return;}
+ }
+
+ //update treemap
+ globaldata->gTreemap->namesOfSeqs.clear();
+ for(int i=0;i<numSeqs;i++){
+ string number, name;
+ filehandle >> number;
+ filehandle >> name;
+ name.erase(name.end()-1); //erase the comma
+ //insert new one with new name
+ globaldata->gTreemap->treemap[toString(number)].groupname = globaldata->gTreemap->treemap[name].groupname;
+ globaldata->gTreemap->treemap[toString(number)].vectorIndex = globaldata->gTreemap->treemap[name].vectorIndex;
+ //erase old one. so treemap[sarah].groupnumber is now treemap[1].groupnumber. if number is 1 and name is sarah.
+ globaldata->gTreemap->treemap.erase(name);
+ globaldata->gTreemap->namesOfSeqs.push_back(number);
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function nexus. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ReadNewickTree class function nexus. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+void ReadNewickTree::readTreeString() {
+ try {
+
int n = 0;
int lc, rc;
}
}
//note: treeclimber had the code below added - not sure why?
- else{
+ else{
filehandle.putback(ch);
char name[MAX_LINE];
filehandle.get(name, MAX_LINE,'\n');
if(lc!=-1){ T->tree[lc].setParent(n); }
if(rc!=-1){ T->tree[rc].setParent(n); }
}
-
- //save tree for later commands
- globaldata->gTree = T;
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function readTreeString. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
catch(...) {
- cout << "An unknown error has occurred in the ReadNewickTree class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the ReadNewickTree class function readTreeString. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
+
}
/**************************************************************************************************/
int readSpecialChar(istream&, char, string);
int readNodeChar(istream& f);
float readBranchLength(istream& f);
-
-
- Tree* getTree() { return T; }
- int numNodes, numLeaves;
+ protected:
GlobalData* globaldata;
+ int numNodes, numLeaves;
- protected:
- Tree* T;
};
/****************************************************************************/
class ReadNewickTree : public ReadTree {
public:
- ReadNewickTree(string file) : treeFile(file) { openInputFile(file, filehandle); }
+ ReadNewickTree(string file) : treeFile(file) { openInputFile(file, filehandle); }
~ReadNewickTree() {};
void read();
private:
+ Tree* T;
int readNewickInt(istream&, int&, Tree*);
+ void readTreeString();
+ void nexusTranslation();
ifstream filehandle;
string treeFile;
+ string holder;
};
/****************************************************************************/
read->read();
- Tree* T = globaldata->gTree;
-// T->createNewickFile();
+ vector<Tree*> T = globaldata->gTree;
+
+ //assemble users trees
+ for (int i = 0; i < T.size(); i++) {
+ T[i]->assembleTree();
+ }
return 0;
}
* Dotur
*
* Created by Sarah Westcott on 12/10/08.
- * Copyright 2008 __MyCompanyName__. All rights reserved.
+ * Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
/*****************************************************************/
Tree::Tree() {
try {
+
globaldata = GlobalData::getInstance();
-
numLeaves = globaldata->gTreemap->getNumSeqs();
numNodes = 2*numLeaves - 1;
//initialize tree with correct number of nodes, name and group info.
for (int i = 0; i < numNodes; i++) {
-
//initialize leaf nodes
if (i <= (numLeaves-1)) {
tree[i].setName(globaldata->gTreemap->namesOfSeqs[i]);
tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i]));
//the node knows its index
tree[i].setIndex(i);
+ //set pcount and pGroup for groupname to 1.
+ tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
+ tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
//Treemap knows name, group and index to speed up search
globaldata->gTreemap->setIndex(globaldata->gTreemap->namesOfSeqs[i], i);
+
//intialize non leaf nodes
}else if (i > (numLeaves-1)) {
tree[i].setName("");
exit(1);
}
}
+/*****************************************************************/
+void Tree::assembleTree() {
+ try {
+ //build the pGroups in non leaf nodes to be used in the parsimony calcs.
+ for (int i = numLeaves; i < numNodes; i++) {
+ tree[i].pGroups = (mergeGroups(i));
+ tree[i].pcount = (mergeGcounts(i));
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function assembleTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function assembleTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/*****************************************************************/
+void Tree::getCopy(Tree* copy) {
+ try {
+
+ //for each node in the tree copy its info
+ for (int i = 0; i < numNodes; i++) {
+ //copy name
+ tree[i].setName(copy->tree[i].getName());
+
+ //copy group
+ tree[i].setGroup(copy->tree[i].getGroup());
+
+ //copy branch length
+ tree[i].setBranchLength(copy->tree[i].getBranchLength());
+
+ //copy parent
+ tree[i].setParent(copy->tree[i].getParent());
+
+ //copy children
+ tree[i].setChildren(copy->tree[i].getLChild(), copy->tree[i].getRChild());
+
+ //copy index in node and tmap
+ tree[i].setIndex(copy->tree[i].getIndex());
+ setIndex(copy->tree[i].getName(), getIndex(copy->tree[i].getName()));
+
+ //copy pGroups
+ tree[i].pGroups = copy->tree[i].pGroups;
+
+ //copy pcount
+ tree[i].pcount = copy->tree[i].pcount;
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function getCopy. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function getCopy. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/*****************************************************************/
+//returns a map with a groupname and the number of times that group was seen in the children
+//for instance if your children are white and black then it would return a map with 2 entries
+// p[white] = 1 and p[black] = 1. Now go up a level and merge that with a node who has p[white] = 1
+//and you get p[white] = 2, p[black] = 1, but you erase the p[black] because you have a p value higher than 1.
+
+map<string, int> Tree::mergeGroups(int i) {
+ try {
+
+ int lc = tree[i].getLChild();
+ int rc = tree[i].getRChild();
+
+ //set parsimony groups to left child
+ map<string,int> parsimony = tree[lc].pGroups;
+
+ int maxPars = 1;
+
+ //look at right child groups and update maxPars if right child has something higher for that group.
+ for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();it++){
+ parsimony[it->first]++;
+
+ if(parsimony[it->first] > maxPars){
+ maxPars = parsimony[it->first];
+ }
+ }
+
+ // this is true if right child had a greater parsimony for a certain group
+ if(maxPars > 1){
+ //erase all the groups that are only 1 because you found something with 2.
+ for(it=parsimony.begin();it!=parsimony.end();it++){
+ if(it->second == 1){
+ parsimony.erase(it->first);
+ it--;
+ }
+ }
+ //set one remaining groups to 1
+ //so with our above example p[white] = 2 would be left and it would become p[white] = 1
+ for(it=parsimony.begin();it!=parsimony.end();it++){
+ parsimony[it->first] = 1;
+ }
+
+ }
+
+ return parsimony;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+map<string,int> Tree::mergeGcounts(int position) {
+ try{
+ map<string,int>::iterator pos;
+
+ int lc = tree[position].getLChild();
+ int rc = tree[position].getRChild();
+
+ map<string,int> sum = tree[lc].pcount;
+
+ for(it=tree[rc].pcount.begin();it!=tree[rc].pcount.end();it++){
+ sum[it->first] += it->second;
+ }
+ return sum;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function mergeGcounts. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function mergeGcounts. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+void Tree::randomLabels() {
+ try {
+ for(int i=numLeaves-1;i>=0;i--){
+ if(tree[i].pGroups.size() == 0){
+ continue;
+ }
+
+ int escape = 1;
+ int z;
+
+ while(escape == 1){
+ z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
+
+ if(tree[z].pGroups.size() != 0){
+ escape = 0;
+ }
+ }
+
+
+ map<string,int> lib_hold = tree[z].pGroups;
+ tree[z].pGroups = (tree[i].pGroups);
+ tree[i].pGroups = (lib_hold);
+
+ tree[z].setGroup(tree[z].pGroups.begin()->first);
+ tree[i].setGroup(tree[i].pGroups.begin()->first);
+
+ map<string,int> gcount_hold = tree[z].pcount;
+ tree[z].pcount = (tree[i].pcount);
+ tree[i].pcount = (gcount_hold);
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+void Tree::randomBlengths() {
+ try {
+ for(int i=numNodes-1;i>=0;i--){
+ int z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
+
+ float bl_hold = tree[z].getBranchLength();
+ tree[z].setBranchLength(tree[i].getBranchLength());
+ tree[i].setBranchLength(bl_hold);
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomBlengths. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function randomBlengths. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/*************************************************************************************************/
+void Tree::assembleRandomUnifracTree() {
+ randomLabels();
+ assembleTree();
+}
+
+/*************************************************************************************************/
+//for now it's just random topology but may become random labels as well later that why this is such a simple function now...
+void Tree::assembleRandomTree() {
+ randomTopology();
+ assembleTree();
+}
+/**************************************************************************************************/
+
+void Tree::randomTopology() {
+ try {
+ for(int i=0;i<numNodes;i++){
+ tree[i].setParent(-1);
+ }
+ for(int i=numLeaves;i<numNodes;i++){
+ tree[i].setChildren(-1, -1);
+ }
+
+ for(int i=numLeaves;i<numNodes;i++){
+ int escape =0;
+ int rnd_index1, rnd_index2;
+ while(escape == 0){
+ rnd_index1 = (int)(((double)rand() / (double) RAND_MAX)*i);
+ if(tree[rnd_index1].getParent() == -1){escape = 1;}
+ }
+
+ escape = 0;
+ while(escape == 0){
+ rnd_index2 = (int)(((double)rand() / (double) RAND_MAX)*i);
+ if(rnd_index2 != rnd_index1 && tree[rnd_index2].getParent() == -1){
+ escape = 1;
+ }
+ }
+
+ tree[i].setChildren(rnd_index1,rnd_index2);
+ tree[i].setParent(-1);
+ tree[rnd_index1].setParent(i);
+ tree[rnd_index2].setParent(i);
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomTopology. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function randomTopology. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
/*****************************************************************/
// This prints out the tree in Newick form.
#include <string>
#include <iostream>
#include <vector>
+#include <fstream>
+#include <iomanip>
+#include <sstream>
+#include <map>
+
#include "treenode.h"
#include "globaldata.hpp"
/* This class represents the treefile. */
-
-
class Tree {
public:
- Tree();
+ Tree(); //to generate a tree from a file
~Tree() {};
- Tree generateRandomTree();
+
+ void getCopy(Tree*); //makes tree a copy of the one passed in.
+ void assembleRandomTree();
+ void assembleRandomUnifracTree();
void createNewickFile();
int getIndex(string);
void setIndex(string, int);
int getNumNodes() { return numNodes; }
- int getNumLeaves(){ return numLeaves;}
+ int getNumLeaves(){ return numLeaves; }
+
+ //this function takes the leaf info and populates the non leaf nodes
+ void assembleTree();
+
vector<Node> tree; //the first n nodes are the leaves, where n is the number of sequences.
private:
GlobalData* globaldata;
- int findRoot(); //return index of root node
- void printBranch(int); //recursively print out tree
int numNodes, numLeaves;
ofstream out;
string filename;
+
+ map<string, int>::iterator it;
+ map<string, int> mergeGroups(int); //returns a map with a groupname and the number of times that group was seen in the children
+ map<string,int> Tree::mergeGcounts(int);
+ void randomTopology();
+ void randomBlengths();
+ void randomLabels();
+ int findRoot(); //return index of root node
+ void printBranch(int); //recursively print out tree
};
#endif
--- /dev/null
+#ifndef TREECALCULATOR_H
+#define TREECALCULATOR_H
+
+/*
+ * treecalculator.h
+ * Mothur
+ *
+ * Created by Sarah Westcott on 1/26/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+using namespace std;
+
+#include <vector>
+#include <cmath>
+#include <math.h>
+#include <string>
+#include <map>
+#include <algorithm>
+#include "utilities.hpp"
+#include "tree.h"
+
+/* The tree calculator class is the parent class for tree calculators in mothur. */
+
+typedef vector<double> EstOutput;
+
+/***********************************************************************/
+
+class TreeCalculator {
+
+public:
+ TreeCalculator(){};
+ TreeCalculator(string n) : name(n) {};
+ ~TreeCalculator(){};
+ virtual EstOutput getValues(Tree*) = 0;
+
+ virtual string getName() { return name; }
+
+protected:
+ EstOutput data;
+ string name;
+
+};
+
+/***********************************************************************/
+
+#endif
\ No newline at end of file
setNamesOfGroups(seqGroup);
treemap[seqName].groupname = seqGroup; //store data in map
-
+
+ it2 = seqsPerGroup.find(seqGroup);
+ if (it2 == seqsPerGroup.end()) { //if it's a new group
+ seqsPerGroup[seqGroup] = 1;
+ }else {//it's a group we already have
+ seqsPerGroup[seqGroup]++;
+ }
+
gobble(fileHandle);
}
fileHandle.close();
int TreeMap::getNumGroups() {
- return namesOfGroups.size();
+ return seqsPerGroup.size();
}
/************************************************************/
class TreeMap {
public:
+ TreeMap() {};
TreeMap(string);
~TreeMap();
void readMap();
string getGroup(string);
vector<string> namesOfGroups;
vector<string> namesOfSeqs;
+ map<string,int> seqsPerGroup; //groupname, number of seqs in that group.
+ map<string, GroupIndex> treemap; //sequence name and groupname
void print(ostream&);
private:
string groupFileName;
int numGroups;
map<string, GroupIndex>::iterator it;
+ map<string, int>::iterator it2;
void setNamesOfGroups(string);
- map<string, GroupIndex> treemap; //sequence name and groupname
+
};
#endif
/****************************************************************/
void Node::setName(string Name) { name = Name; }
/****************************************************************/
-//non leaf nodes will belong to multiple groups, leaf nodes will only belong to one.
-void Node::setGroup(string groups) { group.push_back(groups); }
+void Node::setGroup(string groups) { group =groups; }
/****************************************************************/
void Node::setBranchLength(float l) { branchLength = l; }
/****************************************************************/
/****************************************************************/
string Node::getName() { return name; }
/****************************************************************/
-vector<string> Node::getGroup() { return group; }
+string Node::getGroup() { return group; }
/****************************************************************/
float Node::getBranchLength() { return branchLength; }
/****************************************************************/
#include <fstream>
#include <iomanip>
#include <vector>
+#include <map>
/* This class represents a node on a tree. */
~Node() {};
void setName(string);
- void setGroup(string); //non leaf nodes will belong to multiple groups, leaf nodes will only belong to one.
+ void setGroup(string);
void setBranchLength(float);
void setParent(int);
void setChildren(int, int); //leftchild, rightchild
void setIndex(int);
string getName();
- vector<string> getGroup(); //leaf nodes will only have 1 group, but branch nodes may have multiple groups.
+ string getGroup();
float getBranchLength();
int getParent();
int getLChild();
int getRChild();
int getIndex();
-
void printNode(ostream&); //prints out the name and the branch length
+
+ //pGroup is the parsimony group info. i.e. for a leaf node it would contain 1 enter pGroup["groupname"] = 1;
+ //but for a branch node it may contain several entries so if the nodes children are from different groups it
+ //would have at least two entries pgroup["groupnameOfLeftChild"] = 1, pgroup["groupnameOfRightChild"] = 1.
+ //pCount is the nodes descendant group infomation. i.e. pCount["black"] = 20 would mean that 20 of the nodes
+ //descendant are from group black.
+
+ map<string, int> pGroups; //leaf nodes will only have 1 group, but branch nodes may have multiple groups.
+ map<string, int> pcount;
+
private:
string name;
- vector<string> group;
+ string group;
float branchLength;
int parent;
int lchild;
--- /dev/null
+/*
+ * unifracunweightedcommand.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 2/9/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "unifracunweightedcommand.h"
+
+/***********************************************************/
+UnifracUnweightedCommand::UnifracUnweightedCommand() {
+ try {
+ globaldata = GlobalData::getInstance();
+
+ T = globaldata->gTree;
+ tmap = globaldata->gTreemap;
+ unweightedFile = globaldata->getTreeFile() + ".unweighted";
+ openOutputFile(unweightedFile, out);
+ sumFile = globaldata->getTreeFile() + ".uwsummary";
+ openOutputFile(sumFile, outSum);
+ distFile = globaldata->getTreeFile() + ".uwdistrib";
+ openOutputFile(distFile, outDist);
+
+ convert(globaldata->getIters(), iters); //how many random trees to generate
+ unweighted = new Unweighted(tmap);
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function UnifracUnweightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracUnweightedCommand class function UnifracUnweightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************/
+int UnifracUnweightedCommand::execute() {
+ try {
+
+ //get unweighted for users tree
+ userData.resize(1,0); //data[0] = unweightedscore
+ randomData.resize(1,0); //data[0] = unweightedscore
+
+ //format output
+ outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
+ outDist << "Tree#" << '\t' << "Iter" << '\t' << "UWScore" << endl;
+
+ //create new tree with same num nodes and leaves as users
+ randT = new Tree();
+
+ //get pscores for users trees
+ for (int i = 0; i < T.size(); i++) {
+ cout << "Processing tree " << i+1 << endl;
+ userData = unweighted->getValues(T[i]); //userData[0] = unweightedscore
+
+ //update uscoreFreq
+ it = uscoreFreq.find(userData[0]);
+ if (it == uscoreFreq.end()) {//new score
+ uscoreFreq[userData[0]] = 1;
+ }else{ uscoreFreq[userData[0]]++; }
+
+ //add users score to valid scores
+ validScores[userData[0]] = userData[0];
+
+ //saves users score
+ utreeScores.push_back(userData[0]);
+
+ //copy T[i]'s info.
+ randT->getCopy(T[i]);
+
+ //get unweighted scores for random trees
+ for (int j = 0; j < iters; j++) {
+ //create a random tree with same topology as T[i], but different labels
+ randT->assembleRandomUnifracTree();
+ //get pscore of random tree
+ randomData = unweighted->getValues(randT);
+
+ //add trees unweighted score to map of scores
+ it2 = rscoreFreq.find(randomData[0]);
+ if (it2 != rscoreFreq.end()) {//already have that score
+ rscoreFreq[randomData[0]]++;
+ }else{//first time we have seen this score
+ rscoreFreq[randomData[0]] = 1;
+ }
+
+ //add randoms score to validscores
+ validScores[randomData[0]] = randomData[0];
+
+ //output info to uwdistrib file
+ outDist << i+1 << '\t' << '\t'<< j+1 << '\t' << '\t' << randomData[0] << endl;
+ }
+
+ //find the signifigance of the score
+ float rcumul = 0.0000;
+ for (it = rscoreFreq.begin(); it != rscoreFreq.end(); it++) {
+ //get percentage of random trees with that info
+ rscoreFreq[it->first] /= iters;
+ rcumul+= it->second;
+ rCumul[it->first] = rcumul;
+ }
+
+ //save the signifigance of the users score for printing later
+ UWScoreSig.push_back(rCumul[userData[0]]);
+
+ saveRandomScores(); //save all random scores for unweighted file
+
+ //clear random data
+ rscoreFreq.clear(); //you clear this because in the summary file you want the unweighted signifinance to be relative to these 1000 trees.
+ rCumul.clear();
+ }
+
+ float ucumul = 0.0000;
+ float rcumul = 0.0000;
+ //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
+ for (it = validScores.begin(); it != validScores.end(); it++) {
+ it2 = uscoreFreq.find(it->first);
+ //user data has that score
+ if (it2 != uscoreFreq.end()) { uscoreFreq[it->first] /= T.size(); ucumul+= it2->second; }
+ else { uscoreFreq[it->first] = 0.0000; } //no user trees with that score
+ //make uCumul map
+ uCumul[it->first] = ucumul;
+
+ //make rscoreFreq map and rCumul
+ it2 = totalrscoreFreq.find(it->first);
+ //get percentage of random trees with that info
+ if (it2 != totalrscoreFreq.end()) { totalrscoreFreq[it->first] /= (iters*T.size()); rcumul+= it2->second; }
+ else { totalrscoreFreq[it->first] = 0.0000; } //no random trees with that score
+ rCumul[it->first] = rcumul;
+ }
+
+ printUnweightedFile();
+ printUWSummaryFile();
+
+ //reset randomTree parameter to 0
+ globaldata->setRandomTree("0");
+
+ delete randT;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracUnweightedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************/
+void UnifracUnweightedCommand::printUnweightedFile() {
+ try {
+ //column headers
+
+ out << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
+
+ //format output
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ //print each line
+ for (it = validScores.begin(); it != validScores.end(); it++) {
+ out << setprecision(6) << it->first << '\t' << '\t' << uscoreFreq[it->first] << '\t' << uCumul[it->first] << '\t' << totalrscoreFreq[it->first] << '\t' << rCumul[it->first] << endl;
+ }
+
+ out.close();
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUnweightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracUnweightedCommand class function printUnweightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************/
+void UnifracUnweightedCommand::printUWSummaryFile() {
+ try {
+ //column headers
+ outSum << "Tree#" << '\t' << "UWScore" << '\t' << '\t' << "UWSig" << endl;
+
+ //format output
+ outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
+
+ //print each line
+ for (int i = 0; i< T.size(); i++) {
+ outSum << setprecision(6) << i+1 << '\t' << '\t' << utreeScores[i] << '\t' << UWScoreSig[i] << endl;
+ }
+
+ outSum.close();
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracUnweightedCommand class function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************/
+void UnifracUnweightedCommand::saveRandomScores() {
+ try {
+ //update total map with new random scores
+ for (it = rscoreFreq.begin(); it != rscoreFreq.end(); it++) {
+ //does this score already exist in the total map
+ it2 = totalrscoreFreq.find(it->first);
+ //if yes then add them
+ if (it2 != totalrscoreFreq.end()) {
+ it2->second += it->second;
+ }else{ //its a new score
+ totalrscoreFreq[it->first] = 1;
+ }
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function saveRandomScores. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracUnweightedCommand class function saveRandomScores. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************/
\ No newline at end of file
--- /dev/null
+#ifndef UNIFRACUNWEIGHTEDCOMMAND_H
+#define UNIFRACUNWEIGHTEDCOMMAND_H
+
+/*
+ * unifracunweightedcommand.h
+ * Mothur
+ *
+ * Created by Sarah Westcott on 2/9/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include <iostream>
+#include <fstream>
+#include <vector>
+#include <map>
+#include <cmath>
+#include "command.hpp"
+#include "unweighted.h"
+#include "treemap.h"
+
+using namespace std;
+
+class GlobalData;
+
+class UnifracUnweightedCommand : public Command {
+
+ public:
+ UnifracUnweightedCommand();
+ ~UnifracUnweightedCommand() { delete unweighted; }
+ int execute();
+
+ private:
+ GlobalData* globaldata;
+ vector<Tree*> T; //user trees
+ vector<float> utreeScores; //user tree unweighted scores
+ vector<float> UWScoreSig; //tree unweighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
+ Tree* randT; //random tree
+ TreeMap* tmap;
+ Unweighted* unweighted;
+ string sumFile, distFile, unweightedFile;
+ int iters;
+ EstOutput userData; //unweighted score info for user tree
+ EstOutput randomData; //unweighted score info for random trees
+ map<float, float> validScores; //contains scores from both user and random
+ map<float, float> rscoreFreq; //unweighted score, number of random trees with that score.
+ map<float, float> uscoreFreq; //unweighted, number of user trees with that score.
+ map<float, float> totalrscoreFreq; //unweighted score, number of random trees with that score.
+ map<float, float> rCumul; //unweighted score, cumulative percentage of number of random trees with that score or lower.
+ map<float, float> uCumul; //unweighted, cumulative percentage of number of user trees with that score or lower .
+ map<float, float>::iterator it;
+ map<float, float>::iterator it2;
+
+ ofstream outSum, outDist, out;
+
+ void printUWSummaryFile();
+ void printUnweightedFile();
+ void saveRandomScores();
+
+};
+
+
+
+#endif
\ No newline at end of file
--- /dev/null
+/*
+ * unifracweightedcommand.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 2/9/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "unifracweightedcommand.h"
+
+/***********************************************************/
+UnifracWeightedCommand::UnifracWeightedCommand() {
+ try {
+ globaldata = GlobalData::getInstance();
+
+ T = globaldata->gTree;
+ tmap = globaldata->gTreemap;
+ weightedFile = globaldata->getTreeFile() + ".weighted";
+ openOutputFile(weightedFile, out);
+ sumFile = globaldata->getTreeFile() + ".wsummary";
+ openOutputFile(sumFile, outSum);
+ distFile = globaldata->getTreeFile() + ".wdistrib";
+ openOutputFile(distFile, outDist);
+
+ numGroups = tmap->getNumGroups();
+
+ //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
+ numComp = 0;
+ int n = 1;
+ for (int i=1; i<numGroups; i++) {
+ numComp += i;
+ for (int l = n; l < numGroups; l++) {
+ //set group comparison labels
+ groupComb.push_back(tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]);
+ }
+ n++;
+ }
+
+ convert(globaldata->getIters(), iters); //how many random trees to generate
+ weighted = new Weighted(tmap);
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function UnifracWeightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracWeightedCommand class function UnifracWeightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************/
+int UnifracWeightedCommand::execute() {
+ try {
+
+ //get weighted for users tree
+ userData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC...
+ randomData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC...
+ uscoreFreq.resize(numComp);
+ validScores.resize(numComp);
+ totalrscoreFreq.resize(numComp);
+ uCumul.resize(numComp);
+
+ //format output
+ outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
+ outDist << "Tree#" << '\t' << "Iter" << '\t' << "Groups"<< '\t' << "WScore" << endl;
+
+
+ //create new tree with same num nodes and leaves as users
+ randT = new Tree();
+
+ //get pscores for users trees
+ for (int i = 0; i < T.size(); i++) {
+ rscoreFreq.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC...
+ rCumul.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC...
+
+ cout << "Processing tree " << i+1 << endl;
+ userData = weighted->getValues(T[i]); //userData[0] = weightedscore
+
+ //save users score
+ for (int s=0; s<numComp; s++) {
+ //update uscoreFreq
+ it = uscoreFreq[s].find(userData[s]);
+ if (it == uscoreFreq[s].end()) {//new score
+ uscoreFreq[s][userData[s]] = 1;
+ }else{ uscoreFreq[s][userData[s]]++; }
+
+ //add user score to valid scores
+ validScores[s][userData[s]] = userData[s];
+
+ //save users tree score for summary file
+ utreeScores.push_back(userData[s]);
+ }
+
+ //copy T[i]'s info.
+ randT->getCopy(T[i]);
+
+ //get pscores for random trees
+ for (int j = 0; j < iters; j++) {
+ //create a random tree with same topology as T[i], but different labels
+ randT->assembleRandomUnifracTree();
+ //get pscore of random tree
+ randomData = weighted->getValues(randT);
+
+ //save ramdoms score
+ for (int p=0; p<numComp; p++) {
+ //add trees weighted score random score freq
+ it2 = rscoreFreq[p].find(randomData[p]);
+ if (it2 != rscoreFreq[p].end()) {//already have that score
+ rscoreFreq[p][randomData[p]]++;
+ }else{//first time we have seen this score
+ rscoreFreq[p][randomData[p]] = 1;
+ }
+
+ //add random score to valid scores
+ validScores[p][randomData[p]] = randomData[p];
+
+ //output info to uwdistrib file
+ outDist << i+1 << '\t' << '\t'<< j+1 << '\t' << '\t' << groupComb[p] << '\t'<< randomData[p] << endl;
+ }
+ }
+
+ saveRandomScores(); //save all random scores for weighted file
+
+ //find the signifigance of the score for summary file
+ for (int t = 0; t < numComp; t++) {
+ float rcumul = 0.0000;
+ for (it = validScores[t].begin(); it != validScores[t].end(); it++) {
+ //make rscoreFreq map and rCumul
+ it2 = rscoreFreq[t].find(it->first);
+ //get percentage of random trees with that info
+ if (it2 != rscoreFreq[t].end()) { rscoreFreq[t][it->first] /= iters; rcumul+= it2->second; }
+ else { rscoreFreq[t][it->first] = 0.0000; } //no random trees with that score
+ rCumul[t][it->first] = rcumul;
+ }
+ }
+
+ //save the signifigance of the users score for printing later
+ for (int f = 0; f < numComp; f++) {
+ WScoreSig.push_back(rCumul[f][userData[f]]);
+ }
+
+
+ //clear random data
+ rscoreFreq.clear();
+ rCumul.clear();
+ }
+
+ rCumul.resize(numComp);
+ for (int b = 0; b < numComp; b++) {
+ float ucumul = 0.0000;
+ float rcumul = 0.0000;
+ //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
+ for (it = validScores[b].begin(); it != validScores[b].end(); it++) {
+ it2 = uscoreFreq[b].find(it->first);
+ //user data has that score
+ if (it2 != uscoreFreq[b].end()) { uscoreFreq[b][it->first] /= T.size(); ucumul+= it2->second; }
+ else { uscoreFreq[b][it->first] = 0.0000; } //no user trees with that score
+ //make uCumul map
+ uCumul[b][it->first] = ucumul;
+
+ //make rscoreFreq map and rCumul
+ it2 = totalrscoreFreq[b].find(it->first);
+ //get percentage of random trees with that info
+ if (it2 != totalrscoreFreq[b].end()) { totalrscoreFreq[b][it->first] /= (iters * T.size()); rcumul+= it2->second; }
+ else { totalrscoreFreq[b][it->first] = 0.0000; } //no random trees with that score
+ rCumul[b][it->first] = rcumul;
+ }
+ }
+
+ printWeightedFile();
+ printWSummaryFile();
+
+ //reset randomTree parameter to 0
+ globaldata->setRandomTree("0");
+
+ delete randT;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracWeightedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************/
+void UnifracWeightedCommand::printWeightedFile() {
+ try {
+ //column headers
+
+ out << "Group" << '\t' << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
+
+ //format output
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ //for each group
+ for (int e = 0; e < numComp; e++) {
+ //print each line in that group
+ for (it = validScores[e].begin(); it != validScores[e].end(); it++) {
+ out << setprecision(6) << groupComb[e] << '\t' << it->first << '\t' << '\t' << uscoreFreq[e][it->first] << '\t' << uCumul[e][it->first] << '\t' << totalrscoreFreq[e][it->first] << '\t' << rCumul[e][it->first] << endl;
+ }
+ }
+
+ out.close();
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracWeightedCommand class function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+
+/***********************************************************/
+void UnifracWeightedCommand::printWSummaryFile() {
+ try {
+ //column headers
+ outSum << "Tree#" << '\t' << "Groups" << '\t' << '\t' << "WScore" << '\t' << '\t' << "WSig" << endl;
+
+ //format output
+ outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
+
+ //print each line
+ int count = 0;
+ for (int i = 0; i < T.size(); i++) {
+ for (int j = 0; j < numComp; j++) {
+ outSum << setprecision(6) << i+1 << '\t' << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << WScoreSig[count] << endl;
+ count++;
+ }
+ }
+ outSum.close();
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracWeightedCommand class function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************/
+void UnifracWeightedCommand::saveRandomScores() {
+ try {
+ for (int e = 0; e < numComp; e++) {
+ //update total map with new random scores
+ for (it = rscoreFreq[e].begin(); it != rscoreFreq[e].end(); it++) {
+ //does this score already exist in the total map
+ it2 = totalrscoreFreq[e].find(it->first);
+ //if yes then add them
+ if (it2 != totalrscoreFreq[e].end()) {
+ totalrscoreFreq[e][it->first] += rscoreFreq[e][it->first];
+ }else{ //its a new score
+ totalrscoreFreq[e][it->first] = rscoreFreq[e][it->first];
+ }
+ }
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function saveRandomScores. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracWeightedCommand class function saveRandomScores. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************/
--- /dev/null
+#ifndef UNIFRACWEIGHTEDCOMMAND_H
+#define UNIFRACWEIGHTEDCOMMAND_H
+
+/*
+ * unifracweightedcommand.h
+ * Mothur
+ *
+ * Created by Sarah Westcott on 2/9/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include <iostream>
+#include <fstream>
+#include <vector>
+#include <map>
+#include <cmath>
+#include "command.hpp"
+#include "weighted.h"
+#include "treemap.h"
+
+using namespace std;
+
+class GlobalData;
+
+class UnifracWeightedCommand : public Command {
+
+ public:
+ UnifracWeightedCommand();
+ ~UnifracWeightedCommand() { delete weighted; }
+ int execute();
+
+ private:
+ GlobalData* globaldata;
+ vector<Tree*> T; //user trees
+ vector<float> utreeScores; //user tree unweighted scores
+ vector<float> WScoreSig; //tree weighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
+ vector<string> groupComb; // AB. AC, BC...
+ Tree* randT; //random tree
+ TreeMap* tmap;
+ Weighted* weighted;
+ string weightedFile, sumFile, distFile;
+ int iters, numGroups, numComp;
+ EstOutput userData; //weighted score info for user tree
+ EstOutput randomData; //weighted score info for random trees
+ vector< map<float, float> > validScores; //vector<contains scores from both user and random> each group comb has an entry
+ vector< map<float, float> > rscoreFreq; //vector<weighted score, number of random trees with that score.> each group comb has an entry
+ vector< map<float, float> > uscoreFreq; //vector<weighted, number of user trees with that score.> each group comb has an entry
+ vector< map<float, float> > totalrscoreFreq; //vector<weighted score, number of random trees with that score.> each group comb has an entry
+ vector< map<float, float> > rCumul; //vector<weighted score, number of random trees with that score.> each group comb has an entry
+ vector< map<float, float> > uCumul; //vector<weighted, cumulative percentage of number of user trees with that score or lower.> each group comb has an entry
+ map<float, float>::iterator it;
+ map<float, float>::iterator it2;
+
+ ofstream outSum, outDist, out;
+
+ void printWSummaryFile();
+ void printWeightedFile();
+ void saveRandomScores();
+};
+
+
+
+#endif
--- /dev/null
+/*
+ * unweighted.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 2/9/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "unweighted.h"
+
+/**************************************************************************************************/
+
+EstOutput Unweighted::getValues(Tree* t) {
+ try {
+
+ //clear out old values
+ data.resize(1,0);
+ penalty.resize(t->getNumLeaves(), 0);
+
+ map<string,double> unique; //group, total of all branch lengths of nodes with that group.
+ double shared = 0.0000;
+ double UW=0.0000;
+
+ //add up the branch lengths for each group.
+ for(int i=0;i<t->getNumLeaves();i++){
+ if(t->tree[i].pGroups.size() > 0){
+ unique[t->tree[i].pGroups.begin()->first] += t->tree[i].getBranchLength();
+ }
+ }
+
+ //for each non-leaf node
+ for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
+
+ int lc = t->tree[i].getLChild(); //lc = vector index of left child
+ int rc = t->tree[i].getRChild(); //rc = vector index of right child
+
+ //get penalty values
+ if(t->tree[rc].pGroups.size() == 0 || t->tree[lc].pGroups.size() == 0){
+ penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]);
+ }
+ else if(t->tree[i].pGroups.size() > t->tree[rc].pGroups.size() || t->tree[i].pGroups.size() > t->tree[lc].pGroups.size()){
+ penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]+1);
+ }
+ else{
+ penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]);
+ }
+
+ //not sure when this would ever be true??? if your parent is root could be, but pGroups.size() should never be 0.
+ if(t->tree[i].getParent() == -1 && (t->tree[lc].pGroups.size() == 0 || t->tree[rc].pGroups.size() == 0)){
+ shared -= 1;
+ }
+ else if(penalty[i] != 0 && t->tree[i].pGroups.size() != 0){
+ shared += t->tree[i].getBranchLength();
+ }
+ else if( t->tree[i].pGroups.size() != 0){
+ unique[t->tree[i].pGroups.begin()->first] += t->tree[i].getBranchLength();
+ }
+ }
+
+ map<string,double>::iterator pos;
+ for(pos=unique.begin();pos!=unique.end();pos++){
+ if(pos->first!="xxx"){
+ UW += unique[pos->first];
+ }
+ }
+
+ UW /= (UW + shared);
+
+ if (isnan(UW) || isinf(UW)) { UW = 0; }
+
+ data[0] = UW;
+
+ return data;
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Unweighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Unweighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+
+/**************************************************************************************************/
\ No newline at end of file
--- /dev/null
+#ifndef UNWEIGHTED_H
+#define UNWEIGHTED_H
+
+
+/*
+ * unweighted.h
+ * Mothur
+ *
+ * Created by Sarah Westcott on 2/9/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "treecalculator.h"
+#include "treemap.h"
+
+/***********************************************************************/
+
+class Unweighted : public TreeCalculator {
+
+ public:
+ Unweighted(TreeMap* t) : tmap(t) {};
+ ~Unweighted() {};
+ EstOutput getValues(Tree*);
+
+ private:
+ EstOutput data;
+ vector<int> penalty;
+ TreeMap* tmap;
+
+};
+
+/***********************************************************************/
+
+
+
+#endif
\ No newline at end of file
commands["read.dist"] = "read.dist";
commands["read.otu"] = "read.otu";
- // commands["read.tree"] = "read.tree";
+ commands["read.tree"] = "read.tree";
commands["cluster"] = "cluster";
commands["deconvolute"] = "deconvolute";
+ commands["parsimony"] = "parsimony";
commands["help"] = "help";
commands["quit"] = "quit";
commands["collect.single"] = "collect.single";
commands["rarefaction.shared"] = "rarefaction.shared";
commands["summary.single"] = "summary.single";
commands["summary.shared"] = "summary.shared";
+ commands["unifrac.weighted"] = "unifrac.weighted";
+ commands["unifrac.unweighted"] = "unifrac.unweighted";
+
}
catch(exception& e) {
parameters["shared"] = "shared";
parameters["summary"] = "summary";
parameters["sharedsummary"] = "sharedsummary";
-
+ parameters["randomtree"] = "randomtree";
+ parameters["groups"] = "groups";
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
--- /dev/null
+/*
+ * weighted.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 2/9/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "weighted.h"
+
+/**************************************************************************************************/
+
+EstOutput Weighted::getValues(Tree* t) {
+ try {
+
+ int numGroups = tmap->getNumGroups();
+
+ //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
+ int n = 1;
+ for (int i=1; i<numGroups; i++) {
+ for (int l = n; l < numGroups; l++) {
+ //initialize weighted scores
+ WScore[tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]] = 0.0;
+ }
+ }
+
+ data.clear(); //clear out old values
+
+ double D = 0.0000;
+
+ for(int i=0;i<t->getNumLeaves();i++){
+ int index = i;
+ double sum = 0.0000;
+
+ //while you aren't at root
+ while(t->tree[index].getParent() != -1){
+
+ if(t->tree[index].pGroups.size() != 0){
+ sum += t->tree[index].getBranchLength();
+ }
+
+ //old_index = you
+ int old_index = index;
+ //index = your parent
+ index = t->tree[index].getParent();
+
+ //if you grandparent is the root
+ if(t->tree[index].getParent() == -1 && t->tree[old_index].pGroups.size() != 0){
+ int lc = t->tree[t->tree[index].getLChild()].pGroups.size();
+ int rc = t->tree[t->tree[index].getRChild()].pGroups.size();
+
+
+ if(lc == 0 || rc == 0){
+ sum -= t->tree[old_index].getBranchLength();
+ }
+ }
+ }
+
+ if(t->tree[i].getGroup() != ""){
+ sum /= (double)tmap->seqsPerGroup[t->tree[i].getGroup()];
+ D += sum;
+ }
+ }
+
+
+ for(int i=0;i<t->getNumNodes();i++){
+ //calculate weighted score for each of the group comb i.e. with groups A,B,C = AB, AC, BC.
+ n = 1;
+ for (int b=1; b<numGroups; b++) {
+ for (int l = n; l < numGroups; l++) {
+ double u;
+ //does this node have descendants from group b-1
+ it = t->tree[i].pcount.find(tmap->namesOfGroups[b-1]);
+ //if it does u = # of its descendants with a certain group / total number in tree with a certain group
+ if (it != t->tree[i].pcount.end()) {
+ u = (double) t->tree[i].pcount[tmap->namesOfGroups[b-1]] / (double) tmap->seqsPerGroup[tmap->namesOfGroups[b-1]];
+ }else { u = 0.00; }
+
+ //does this node have descendants from group l
+ it = t->tree[i].pcount.find(tmap->namesOfGroups[l]);
+ //if it does subtract their percentage from u
+ if (it != t->tree[i].pcount.end()) {
+ u -= (double) t->tree[i].pcount[tmap->namesOfGroups[l]] / (double) tmap->seqsPerGroup[tmap->namesOfGroups[l]];
+ }
+
+ u = abs(u) * t->tree[i].getBranchLength();
+
+ //save groupcombs u value
+ WScore[tmap->namesOfGroups[b-1]+tmap->namesOfGroups[l]] += u;
+
+ }
+ n++;
+ }
+ }
+
+ //calculate weighted score for each group combination
+ double UN;
+ n = 1;
+ for (int i=1; i<numGroups; i++) {
+ for (int l = n; l < numGroups; l++) {
+ UN = (WScore[tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]] / D);
+ if (isnan(UN) || isinf(UN)) { UN = 0; }
+ data.push_back(UN);
+ }
+ }
+
+ return data;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Weighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Weighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+
+/**************************************************************************************************/
\ No newline at end of file
--- /dev/null
+#ifndef WEIGHTED_H
+#define WEIGHTED_H
+
+
+/*
+ * weighted.h
+ * Mothur
+ *
+ * Created by Sarah Westcott on 2/9/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "treecalculator.h"
+#include "treemap.h"
+
+/***********************************************************************/
+
+class Weighted : public TreeCalculator {
+
+ public:
+ Weighted(TreeMap* t) : tmap(t) {};
+ ~Weighted() {};
+ EstOutput getValues(Tree*);
+
+ private:
+ EstOutput data;
+ TreeMap* tmap;
+ map<string, int>::iterator it;
+ map<string, float> WScore; //a score for each group combination i.e. AB, AC, BC.
+};
+
+/***********************************************************************/
+
+
+#endif
\ No newline at end of file
projects / mothur.git / commitdiff