#include "unifracunweightedcommand.h"
+//**********************************************************************************************************************
+vector<string> UnifracUnweightedCommand::getValidParameters(){
+ try {
+ string Array[] = {"groups","iters","distance","random", "processors","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracUnweightedCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+UnifracUnweightedCommand::UnifracUnweightedCommand(){
+ try {
+ globaldata = GlobalData::getInstance();
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["unweighted"] = tempOutNames;
+ outputTypes["uwsummary"] = tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ outputTypes["column"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracUnweightedCommand", "UnifracUnweightedCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> UnifracUnweightedCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracUnweightedCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> UnifracUnweightedCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"tree","group"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracUnweightedCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
/***********************************************************/
-UnifracUnweightedCommand::UnifracUnweightedCommand() {
+UnifracUnweightedCommand::UnifracUnweightedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
+ abort = false; calledHelp = false;
+ Groups.clear();
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"groups","iters","distance","random", "processors","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["unweighted"] = tempOutNames;
+ outputTypes["uwsummary"] = tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ outputTypes["column"] = tempOutNames;
+
+ if (globaldata->gTree.size() == 0) {//no trees were read
+ m->mothurOut("You must execute the read.tree command, before you may execute the unifrac.unweighted command."); m->mothurOutEndLine(); abort = true; }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
+
+ itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
+ convert(itersString, iters);
+
+ string temp = validParameter.validFile(parameters, "distance", false);
+ if (temp == "not found") { phylip = false; outputForm = ""; }
+ else{
+ if ((temp == "lt") || (temp == "column") || (temp == "square")) { phylip = true; outputForm = temp; }
+ else { m->mothurOut("Options for distance are: lt, square, or column. Using lt."); m->mothurOutEndLine(); phylip = true; outputForm = "lt"; }
+ }
+
+ temp = validParameter.validFile(parameters, "random", false); if (temp == "not found") { temp = "f"; }
+ random = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
+ convert(temp, processors);
+
+ if (!random) { iters = 0; } //turn off random calcs
+
+ //if user selects distance = true and no groups it won't calc the pairwise
+ if ((phylip) && (Groups.size() == 0)) {
+ groups = "all";
+ m->splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
+
+ if (abort == false) {
+ T = globaldata->gTree;
+ tmap = globaldata->gTreemap;
+ sumFile = outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".uwsummary";
+ outputNames.push_back(sumFile); outputTypes["uwsummary"].push_back(sumFile);
+ m->openOutputFile(sumFile, outSum);
+
+ util = new SharedUtil();
+ util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "unweighted"); //sets the groups the user wants to analyze
+ util->getCombos(groupComb, globaldata->Groups, numComp);
+
+ if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
+
+ unweighted = new Unweighted(tmap);
+
+ }
+
+ }
- T = globaldata->gTree;
- tmap = globaldata->gTreemap;
- sumFile = globaldata->getTreeFile() + ".uwsummary";
- openOutputFile(sumFile, outSum);
-
- setGroups(); //sets users groups to analyze
- 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";
+ m->errorOut(e, "UnifracUnweightedCommand", "UnifracUnweightedCommand");
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";
+}
+
+//**********************************************************************************************************************
+
+void UnifracUnweightedCommand::help(){
+ try {
+ m->mothurOut("The unifrac.unweighted command can only be executed after a successful read.tree command.\n");
+ m->mothurOut("The unifrac.unweighted command parameters are groups, iters, distance, processors and random. No parameters are required.\n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 1 valid group.\n");
+ m->mothurOut("The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree.\n");
+ m->mothurOut("The distance parameter allows you to create a distance file from the results. The default is false. You may set distance to lt, square or column.\n");
+ m->mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is false, meaning compare don't your trees with randomly generated trees.\n");
+ m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
+ m->mothurOut("The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters).\n");
+ m->mothurOut("Example unifrac.unweighted(groups=A-B-C, iters=500).\n");
+ m->mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n");
+ m->mothurOut("The unifrac.unweighted command output two files: .unweighted and .uwsummary their descriptions are in the manual.\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracUnweightedCommand", "help");
exit(1);
}
}
+
+
/***********************************************************/
int UnifracUnweightedCommand::execute() {
try {
-
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ int start = time(NULL);
+
userData.resize(numComp,0); //data[0] = unweightedscore
randomData.resize(numComp,0); //data[0] = unweightedscore
//create new tree with same num nodes and leaves as users
-
+
+ if (numComp < processors) { processors = numComp; }
+
+ outSum << "Tree#" << '\t' << "Groups" << '\t' << "UWScore" <<'\t' << "UWSig" << endl;
+ m->mothurOut("Tree#\tGroups\tUWScore\tUWSig"); m->mothurOutEndLine();
+
//get pscores for users trees
for (int i = 0; i < T.size(); i++) {
+ if (m->control_pressed) {
+ outSum.close();
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
counter = 0;
- unweightedFile = globaldata->getTreeFile() + toString(i+1) + ".unweighted";
- unweightedFileout = globaldata->getTreeFile() + "temp." + toString(i+1) + ".unweighted";
- //column headers
- outSum << "Tree# " << i+1 << endl;
- outSum << "Comb" << '\t' << "UWScore" << '\t' << '\t' << "UWSig" << endl;
-
+
+ if (random) {
+ output = new ColumnFile(outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".unweighted", itersString);
+ outputNames.push_back(outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".unweighted");
+ outputTypes["unweighted"].push_back(outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".unweighted");
+ }
+
+
//get unweighted for users tree
rscoreFreq.resize(numComp);
rCumul.resize(numComp);
utreeScores.resize(numComp);
UWScoreSig.resize(numComp);
- cout << "Processing tree " << i+1 << endl;
- userData = unweighted->getValues(T[i]); //userData[0] = unweightedscore
+ userData = unweighted->getValues(T[i], processors, outputDir); //userData[0] = unweightedscore
+
+ if (m->control_pressed) { if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }return 0; }
//output scores for each combination
for(int k = 0; k < numComp; k++) {
//saves users score
utreeScores[k].push_back(userData[k]);
+
+ //add users score to validscores
+ validScores[userData[k]] = userData[k];
}
-
- //get unweighted scores for random trees
+
+ //get unweighted scores for random trees - if random is false iters = 0
for (int j = 0; j < iters; j++) {
- //we need a different getValues because when we swap the labels we only want to swap those in each parwise comparison
- randomData = unweighted->getValues(T[i], "", "");
+
+ //we need a different getValues because when we swap the labels we only want to swap those in each pairwise comparison
+ randomData = unweighted->getValues(T[i], "", "", processors, outputDir);
+ if (m->control_pressed) { if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
for(int k = 0; k < numComp; k++) {
-//cout << "iter " << j << " comp " << k << " = " << randomData[k] << endl;
//add trees unweighted score to map of scores
- it2 = rscoreFreq[k].find(randomData[k]);
- if (it2 != rscoreFreq[k].end()) {//already have that score
+ map<float,float>::iterator it = rscoreFreq[k].find(randomData[k]);
+ if (it != rscoreFreq[k].end()) {//already have that score
rscoreFreq[k][randomData[k]]++;
}else{//first time we have seen this score
rscoreFreq[k][randomData[k]] = 1;
//add randoms score to validscores
validScores[randomData[k]] = randomData[k];
}
+
+ //report progress
+// m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();
}
-
- for(int a = 0; a < numComp; a++) {
- float rcumul = 1.0000;
- //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++) {
- //make rscoreFreq map and rCumul
- it2 = rscoreFreq[a].find(it->first);
- rCumul[a][it->first] = rcumul;
- //get percentage of random trees with that info
- if (it2 != rscoreFreq[a].end()) { rscoreFreq[a][it->first] /= iters; rcumul-= it2->second; }
- else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
+
+ for(int a = 0; a < numComp; a++) {
+ float rcumul = 1.0000;
+
+ if (random) {
+ //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
+ for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
+ //make rscoreFreq map and rCumul
+ map<float,float>::iterator it2 = rscoreFreq[a].find(it->first);
+ rCumul[a][it->first] = rcumul;
+ //get percentage of random trees with that info
+ if (it2 != rscoreFreq[a].end()) { rscoreFreq[a][it->first] /= iters; rcumul-= it2->second; }
+ else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
+ }
+ UWScoreSig[a].push_back(rCumul[a][userData[a]]);
+ }else { UWScoreSig[a].push_back(0.0); }
+
}
- UWScoreSig[a].push_back(rCumul[a][userData[a]]);
+
+ if (m->control_pressed) { if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ //print output files
+ printUWSummaryFile(i);
+ if (random) { printUnweightedFile(); delete output; }
+ if (phylip) { createPhylipFile(i); }
+
+ rscoreFreq.clear();
+ rCumul.clear();
+ validScores.clear();
+ utreeScores.clear();
+ UWScoreSig.clear();
}
- printUnweightedFile();
- printUWSummaryFile();
-
- rscoreFreq.clear();
- rCumul.clear();
- validScores.clear();
- utreeScores.clear();
- UWScoreSig.clear();
- }
- //reset groups parameter
- globaldata->Groups.clear(); globaldata->setGroups("");
+
outSum.close();
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run unifrac.unweighted."); m->mothurOutEndLine();
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
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";
+ m->errorOut(e, "UnifracUnweightedCommand", "execute");
exit(1);
}
}
void UnifracUnweightedCommand::printUnweightedFile() {
try {
vector<double> data;
+ vector<string> tags;
+ tags.push_back("Score");
+ tags.push_back("RandFreq"); tags.push_back("RandCumul");
+
for(int a = 0; a < numComp; a++) {
- initFile(groupComb[a]);
+ output->initFile(groupComb[a], tags);
//print each line
- for (it = validScores.begin(); it != validScores.end(); it++) {
- data.push_back(it->first); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
- output(data);
+ for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
+ data.push_back(it->first); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
+ output->output(data);
data.clear();
}
- resetFile();
+ output->resetFile();
}
-
- out.close();
- inFile.close();
- remove(unweightedFileout.c_str());
-
}
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";
+ m->errorOut(e, "UnifracUnweightedCommand", "printUnweightedFile");
exit(1);
}
}
/***********************************************************/
-void UnifracUnweightedCommand::printUWSummaryFile() {
+void UnifracUnweightedCommand::printUWSummaryFile(int i) {
try {
//format output
outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
-
+
//print each line
+
for(int a = 0; a < numComp; a++) {
- outSum << setprecision(6) << groupComb[a] << '\t' << '\t' << utreeScores[a][0] << '\t' << UWScoreSig[a][0] << endl;
- cout << setprecision(6) << groupComb[a] << '\t' << '\t' << utreeScores[a][0] << '\t' << UWScoreSig[a][0] << endl;
+ outSum << i+1 << '\t';
+ m->mothurOut(toString(i+1) + "\t");
+
+ if (random) {
+ if (UWScoreSig[a][0] > (1/(float)iters)) {
+ outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
+ cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
+ m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t" + toString(UWScoreSig[a][0])+ "\n");
+ }else {
+ outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
+ cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
+ m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t<" + toString((1/float(iters))) + "\n");
+ }
+ }else{
+ outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl;
+ cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl;
+ m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t0.00\n");
+ }
}
}
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";
+ m->errorOut(e, "UnifracUnweightedCommand", "printUWSummaryFile");
exit(1);
}
}
/***********************************************************/
-
-void UnifracUnweightedCommand::setGroups() {
+void UnifracUnweightedCommand::createPhylipFile(int i) {
try {
- string allGroups = "";
- numGroups = 0;
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() != 0) {
- if (globaldata->Groups[0] != "all") {
- //check that groups are valid
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
- cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
- // erase the invalid group from globaldata->Groups
- globaldata->Groups.erase(globaldata->Groups.begin()+i);
- }
- }
-
- //if the user only entered invalid groups
- if (globaldata->Groups.size() == 0) {
- cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- numGroups++;
- allGroups += tmap->namesOfGroups[i];
- }
- }else {
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- allGroups += globaldata->Groups[i];
- numGroups++;
- }
- }
- }else{//user has enter "all" and wants the default groups
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- numGroups++;
- allGroups += tmap->namesOfGroups[i];
- }
- globaldata->setGroups("");
- }
- }else {
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- allGroups += tmap->namesOfGroups[i];
- }
- numGroups = 1;
+ string phylipFileName;
+ if ((outputForm == "lt") || (outputForm == "square")) {
+ phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".unweighted.phylip.dist";
+ outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName);
+ }else { //column
+ phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".unweighted.column.dist";
+ outputNames.push_back(phylipFileName); outputTypes["column"].push_back(phylipFileName);
}
- //calculate number of comparsions
- numComp = 0;
- for (int r=0; r<numGroups; r++) {
- for (int l = r+1; l < numGroups; l++) {
- groupComb.push_back(globaldata->Groups[r]+globaldata->Groups[l]);
- numComp++;
- }
- }
+ ofstream out;
+ m->openOutputFile(phylipFileName, out);
- //ABC
- if (numComp != 1) {
- groupComb.push_back(allGroups);
- numComp++;
+ if ((outputForm == "lt") || (outputForm == "square")) {
+ //output numSeqs
+ out << globaldata->Groups.size() << endl;
}
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
-}
-/*****************************************************************/
-
-void UnifracUnweightedCommand::initFile(string label){
- try {
- if(counter != 0){
- openOutputFile(unweightedFileout, out);
- openInputFile(unweightedFile, inFile);
-
- string inputBuffer;
- getline(inFile, inputBuffer);
- out << inputBuffer << '\t' << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
- }else{
- openOutputFile(unweightedFileout, out);
- out << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
+ //make matrix with scores in it
+ vector< vector<float> > dists; dists.resize(globaldata->Groups.size());
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ dists[i].resize(globaldata->Groups.size(), 0.0);
}
-
- out.setf(ios::fixed, ios::floatfield);
- out.setf(ios::showpoint);
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-void UnifracUnweightedCommand::output(vector<double> data){
- try {
- if(counter != 0){
- string inputBuffer;
- getline(inFile, inputBuffer);
- out << inputBuffer << setprecision(6) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+ //flip it so you can print it
+ int count = 0;
+ for (int r=0; r<globaldata->Groups.size(); r++) {
+ for (int l = 0; l < r; l++) {
+ dists[r][l] = utreeScores[count][0];
+ dists[l][r] = utreeScores[count][0];
+ count++;
+ }
}
- else{
- out << setprecision(6) << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+
+ //output to file
+ for (int r=0; r<globaldata->Groups.size(); r++) {
+ //output name
+ string name = globaldata->Groups[r];
+ if (name.length() < 10) { //pad with spaces to make compatible
+ while (name.length() < 10) { name += " "; }
+ }
+
+ if (outputForm == "lt") {
+ out << name << '\t';
+
+ //output distances
+ for (int l = 0; l < r; l++) { out << dists[r][l] << '\t'; }
+ out << endl;
+ }else if (outputForm == "square") {
+ out << name << '\t';
+
+ //output distances
+ for (int l = 0; l < globaldata->Groups.size(); l++) { out << setprecision(11) << dists[r][l] << '\t'; }
+ out << endl;
+ }else{
+ //output distances
+ for (int l = 0; l < r; l++) {
+ string otherName = globaldata->Groups[l];
+ if (otherName.length() < 10) { //pad with spaces to make compatible
+ while (otherName.length() < 10) { otherName += " "; }
+ }
+
+ out << name << '\t' << otherName << dists[r][l] << endl;
+ }
+ }
}
-
+ out.close();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "UnifracUnweightedCommand", "createPhylipFile");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-};
+}
+/***********************************************************/
-/***********************************************************************/
-void UnifracUnweightedCommand::resetFile(){
- try {
- if(counter != 0){
- out.close();
- inFile.close();
- }
- else{
- out.close();
- }
- counter = 1;
-
- remove(unweightedFile.c_str());
- rename(unweightedFileout.c_str(), unweightedFile.c_str());
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
projects / mothur.git / blobdiff