#include "parsimonycommand.h"
+//**********************************************************************************************************************
+vector<string> ParsimonyCommand::setParameters(){
+ try {
+ CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter prandom("random", "String", "", "", "", "", "",false,false); parameters.push_back(prandom);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParsimonyCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ParsimonyCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The parsimony command parameters are tree, group, name, random, groups, processors and iters. tree parameter is required unless you have valid current tree file or are using random.\n";
+ helpString += "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";
+ helpString += "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";
+ helpString += "The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters).\n";
+ helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
+ helpString += "Example parsimony(random=out, iters=500).\n";
+ helpString += "The default value for random is "" (meaning you want to use the trees in your inputfile, randomtree=out means you just want the random distribution of trees outputted to out.rd_parsimony),\n";
+ helpString += "and iters is 1000. The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParsimonyCommand", "getHelpString");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+ParsimonyCommand::ParsimonyCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["parsimony"] = tempOutNames;
+ outputTypes["psummary"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand");
+ exit(1);
+ }
+}
/***********************************************************/
-ParsimonyCommand::ParsimonyCommand() {
+ParsimonyCommand::ParsimonyCommand(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 if(option == "citation") { citation(); abort = true; calledHelp = true;}
- //randomtree will tell us if user had their own treefile or if they just want the random distribution
- randomtree = globaldata->getRandomTree();
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
+
+ ValidParameters validParameter;
- //user has entered their own tree
- if (randomtree == "") {
- 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);
-
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() != 0) {
- //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);
- }
- }
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
- //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]);
- }
- }
- }else {
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["parsimony"] = tempOutNames;
+ outputTypes["psummary"] = tempOutNames;
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("tree");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["tree"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["group"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
}
}
-
- }else { //user wants random distribution
- savetmap = globaldata->gTreemap;
- getUserInput();
- parsFile = randomtree + ".rd_parsimony";
- openOutputFile(parsFile, out);
+
+ m->runParse = true;
+ m->Groups.clear();
+ m->namesOfGroups.clear();
+ m->Treenames.clear();
+ m->names.clear();
+
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+
+ randomtree = validParameter.validFile(parameters, "random", false); if (randomtree == "not found") { randomtree = ""; }
+
+ //are you trying to use parsimony without reading a tree or saying you want random distribution
+ if (randomtree == "") {
+ //check for required parameters
+ treefile = validParameter.validFile(parameters, "tree", true);
+ if (treefile == "not open") { abort = true; }
+ else if (treefile == "not found") { //if there is a current design file, use it
+ treefile = m->getTreeFile();
+ if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setTreeFile(treefile); }
+
+ //check for required parameters
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
+ }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; if (randomtree == "") { outputDir += m->hasPath(treefile); } }
+
+ //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 = ""; m->Groups.clear(); }
+ else {
+ m->splitAtDash(groups, Groups);
+ m->Groups = Groups;
+ }
+
+ itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
+ convert(itersString, iters);
+
+ string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ convert(temp, processors);
+
}
-
- 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";
+ m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand");
exit(1);
}
}
/***********************************************************/
int ParsimonyCommand::execute() {
try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
- //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;
+ //randomtree will tell us if user had their own treefile or if they just want the random distribution
+ //user has entered their own tree
+ if (randomtree == "") {
+
+ m->setTreeFile(treefile);
+
+ if (groupfile != "") {
+ //read in group map info.
+ tmap = new TreeMap(groupfile);
+ tmap->readMap();
+ }else{ //fake out by putting everyone in one group
+ Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
+ tmap = new TreeMap();
+
+ for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
+ }
+
+ if (namefile != "") { readNamesFile(); }
+
+ read = new ReadNewickTree(treefile);
+ int readOk = read->read(tmap);
+
+ if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete tmap; delete read; return 0; }
+
+ read->AssembleTrees();
+ T = read->getTrees();
+ delete read;
+
+ //make sure all files match
+ //if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size.
+ int numNamesInTree;
+ if (namefile != "") {
+ if (numUniquesInName == m->Treenames.size()) { numNamesInTree = nameMap.size(); }
+ else { numNamesInTree = m->Treenames.size(); }
+ }else { numNamesInTree = m->Treenames.size(); }
+
+
+ //output any names that are in group file but not in tree
+ if (numNamesInTree < tmap->getNumSeqs()) {
+ for (int i = 0; i < tmap->namesOfSeqs.size(); i++) {
+ //is that name in the tree?
+ int count = 0;
+ for (int j = 0; j < m->Treenames.size(); j++) {
+ if (tmap->namesOfSeqs[i] == m->Treenames[j]) { break; } //found it
+ count++;
+ }
+
+ if (m->control_pressed) {
+ delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ m->Groups.clear();
+ return 0;
+ }
+
+ //then you did not find it so report it
+ if (count == m->Treenames.size()) {
+ //if it is in your namefile then don't remove
+ map<string, string>::iterator it = nameMap.find(tmap->namesOfSeqs[i]);
+
+ if (it == nameMap.end()) {
+ m->mothurOut(tmap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
+ tmap->removeSeq(tmap->namesOfSeqs[i]);
+ i--; //need this because removeSeq removes name from namesOfSeqs
+ }
+ }
+ }
+ }
+
+ if(outputDir == "") { outputDir += m->hasPath(treefile); }
+ output = new ColumnFile(outputDir + m->getSimpleName(treefile) + ".parsimony", itersString);
+ outputNames.push_back(outputDir + m->getSimpleName(treefile) + ".parsimony");
+ outputTypes["parsimony"].push_back(outputDir + m->getSimpleName(treefile) + ".parsimony");
+
+ sumFile = outputDir + m->getSimpleName(treefile) + ".psummary";
+ m->openOutputFile(sumFile, outSum);
+ outputNames.push_back(sumFile);
+ outputTypes["psummary"].push_back(sumFile);
+ }else { //user wants random distribution
+ getUserInput();
+
+ if(outputDir == "") { outputDir += m->hasPath(randomtree); }
+ output = new ColumnFile(outputDir+ m->getSimpleName(randomtree), itersString);
+ outputNames.push_back(outputDir+ m->getSimpleName(randomtree));
+ outputTypes["parsimony"].push_back(outputDir+ m->getSimpleName(randomtree));
+ }
+
+ //set users groups to analyze
+ util = new SharedUtil();
+ util->setGroups(m->Groups, tmap->namesOfGroups, allGroups, numGroups, "parsimony"); //sets the groups the user wants to analyze
+ util->getCombos(groupComb, m->Groups, numComp);
+ delete util;
+
+ if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
+
+ pars = new Parsimony(tmap);
+ counter = 0;
+
+ Progress* reading;
+ reading = new Progress("Comparing to random:", iters);
+
+ if (m->control_pressed) {
+ delete reading; delete pars; delete output;
+ delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ if (randomtree == "") { outSum.close(); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ m->Groups.clear();
+ return 0;
+ }
+
+ //get pscore for users tree
+ userData.resize(numComp,0); //data = AB, AC, BC, ABC.
+ randomData.resize(numComp,0); //data = AB, AC, BC, ABC.
+ rscoreFreq.resize(numComp);
+ uscoreFreq.resize(numComp);
+ rCumul.resize(numComp);
+ uCumul.resize(numComp);
+ userTreeScores.resize(numComp);
+ UScoreSig.resize(numComp);
+
if (randomtree == "") {
//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];
+ userData = pars->getValues(T[i], processors, outputDir); //data = AB, AC, BC, ABC.
- //save score for summary file
- userTreeScores.push_back(userData[0]);
-
+ if (m->control_pressed) {
+ delete reading; delete pars; delete output;
+ delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ if (randomtree == "") { outSum.close(); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ m->Groups.clear();
+ return 0;
+ }
+
+
+ //output scores for each combination
+ for(int k = 0; k < numComp; k++) {
+
+ //update uscoreFreq
+ map<int,double>::iterator it = uscoreFreq[k].find(userData[k]);
+ if (it == uscoreFreq[k].end()) {//new score
+ uscoreFreq[k][userData[k]] = 1;
+ }else{ uscoreFreq[k][userData[k]]++; }
+
+ //add users score to valid scores
+ validScores[userData[k]] = userData[k];
+
+ //save score for summary file
+ userTreeScores[k].push_back(userData[k]);
+ }
}
//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();
+ randT = new Tree(tmap);
+
//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;
+ randomData = pars->getValues(randT, processors, outputDir);
+
+ if (m->control_pressed) {
+ delete reading; delete pars; delete output; delete randT;
+ if (randomtree == "") { outSum.close(); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ m->Groups.clear();
+ return 0;
}
+
+ for(int r = 0; r < numComp; r++) {
+ //add trees pscore to map of scores
+ map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
+ if (it != rscoreFreq[r].end()) {//already have that score
+ rscoreFreq[r][randomData[r]]++;
+ }else{//first time we have seen this score
+ rscoreFreq[r][randomData[r]] = 1;
+ }
- //add randoms score to validscores
- validScores[randomData[0]] = randomData[0];
+ //add randoms score to validscores
+ validScores[randomData[r]] = randomData[r];
+ }
+
+ //update progress bar
+ reading->update(j);
- //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();
+ randT = new Tree(tmap);
//create random relationships between nodes
+
randT->assembleRandomTree();
+
+ if (m->control_pressed) {
+ delete reading; delete pars; delete output; delete randT;
+ delete tmap;
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ m->Groups.clear();
+ return 0;
+ }
+
+
//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;
+ randomData = pars->getValues(randT, processors, outputDir);
+
+ if (m->control_pressed) {
+ delete reading; delete pars; delete output; delete randT;
+ delete tmap;
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ m->Groups.clear();
+ return 0;
}
- //add randoms score to validscores
- validScores[randomData[0]] = randomData[0];
-
+ for(int r = 0; r < numComp; r++) {
+ //add trees pscore to map of scores
+ map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
+ if (it != rscoreFreq[r].end()) {//already have that score
+ rscoreFreq[r][randomData[r]]++;
+ }else{//first time we have seen this score
+ rscoreFreq[r][randomData[r]] = 1;
+ }
+
+ //add randoms score to validscores
+ validScores[randomData[r]] = randomData[r];
+ }
+
+ //update progress bar
+ reading->update(j);
+
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 == "") {
- 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;
+
+ for(int a = 0; a < numComp; a++) {
+ 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 (map<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) {
+ if (randomtree == "") {
+ map<int,double>::iterator it2 = uscoreFreq[a].find(it->first);
+ //user data has that score
+ if (it2 != uscoreFreq[a].end()) { uscoreFreq[a][it->first] /= T.size(); ucumul+= it2->second; }
+ else { uscoreFreq[a][it->first] = 0.0000; } //no user trees with that score
+ //make uCumul map
+ uCumul[a][it->first] = ucumul;
+ }
+
+ //make rscoreFreq map and rCumul
+ map<int,double>::iterator it2 = rscoreFreq[a].find(it->first);
+ //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
+ rCumul[a][it->first] = rcumul;
}
- //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[a].size(); h++) {
+ UScoreSig[a].push_back(rCumul[a][userTreeScores[a][h]]);
+ }
}
- //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]]);
+ if (m->control_pressed) {
+ delete reading; delete pars; delete output;
+ delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ if (randomtree == "") { outSum.close(); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ m->Groups.clear();
+ return 0;
}
+
+ //finish progress bar
+ reading->finish();
+ delete reading;
- printParsimonyFile();
- printUSummaryFile();
- //reset globaldata's treemap if you just did random distrib
- if (randomtree != "") { globaldata->gTreemap = savetmap; }
+ printParsimonyFile();
+ if (randomtree == "") { printUSummaryFile(); }
- //reset randomTree parameter to ""
- globaldata->setRandomTree("");
//reset groups parameter
- globaldata->Groups.clear();
+ m->Groups.clear();
+
+ delete pars; delete output;
+ delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;}
+
+ 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 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";
+ m->errorOut(e, "ParsimonyCommand", "execute");
exit(1);
}
}
/***********************************************************/
void ParsimonyCommand::printParsimonyFile() {
try {
- //column headers
+ vector<double> data;
+ vector<string> tags;
+
if (randomtree == "") {
- out << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
+ tags.push_back("Score"); tags.push_back("UserFreq"); tags.push_back("UserCumul"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
}else {
- out << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
+ tags.push_back("Score"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
+ }
+
+ for(int a = 0; a < numComp; a++) {
+ output->initFile(groupComb[a], tags);
+ //print each line
+ for (map<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) {
+ if (randomtree == "") {
+ data.push_back(it->first); data.push_back(uscoreFreq[a][it->first]); data.push_back(uCumul[a][it->first]); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
+ }else{
+ data.push_back(it->first); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
+ }
+ output->output(data);
+ data.clear();
+ }
+ output->resetFile();
}
-
- //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 == "") {
- 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";
+ m->errorOut(e, "ParsimonyCommand", "printParsimonyFile");
exit(1);
}
}
/***********************************************************/
-void ParsimonyCommand::printUSummaryFile() {
+int ParsimonyCommand::printUSummaryFile() {
try {
//column headers
- outSum << "Tree#" << '\t' << "ParsScore" << '\t' << '\t' << "ParsSig" << endl;
+ outSum << "Tree#" << '\t' << "Groups" << '\t' << "ParsScore" << '\t' << "ParsSig" << endl;
+ m->mothurOut("Tree#\tGroups\tParsScore\tParsSig"); m->mothurOutEndLine();
//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;
+ for(int a = 0; a < numComp; a++) {
+ if (m->control_pressed) { outSum.close(); return 0; }
+ if (UScoreSig[a][i] > (1/(float)iters)) {
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
+ m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString(UScoreSig[a][i])); m->mothurOutEndLine();
+ }else {
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << "<" << (1/float(iters)) << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << "<" << (1/float(iters)) << endl;
+ m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString((1/float(iters)))); m->mothurOutEndLine();
+ }
+ }
}
outSum.close();
+ return 0;
}
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";
+ m->errorOut(e, "ParsimonyCommand", "printUSummaryFile");
exit(1);
}
}
//create treemap
tmap = new TreeMap();
- cout << "Please enter the number of groups you would like to analyze: ";
+ m->mothurOut("Please enter the number of groups you would like to analyze: ");
cin >> numGroups;
-
+ m->mothurOutJustToLog(toString(numGroups)); m->mothurOutEndLine();
+
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 << ": ";
+ m->mothurOut("Please enter the number of sequences in group " + toString(i) + ": ");
cin >> num;
+ m->mothurOutJustToLog(toString(num)); m->mothurOutEndLine();
//set tmaps seqsPerGroup
tmap->seqsPerGroup[toString(i)] = num;
+ tmap->namesOfGroups.push_back(toString(i));
//set tmaps namesOfSeqs
for (int j = 0; j < num; j++) {
string s;
getline(cin, s);
- //save tmap for later
- globaldata->gTreemap = tmap;
+ m->Treenames = tmap->namesOfSeqs;
}
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";
+ m->errorOut(e, "ParsimonyCommand", "getUserInput");
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";
+}
+/*****************************************************************/
+int ParsimonyCommand::readNamesFile() {
+ try {
+ m->names.clear();
+ numUniquesInName = 0;
+
+ ifstream in;
+ m->openInputFile(namefile, in);
+
+ string first, second;
+ map<string, string>::iterator itNames;
+
+ while(!in.eof()) {
+ in >> first >> second; m->gobble(in);
+
+ numUniquesInName++;
+
+ itNames = m->names.find(first);
+ if (itNames == m->names.end()) {
+ m->names[first] = second;
+
+ //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
+ vector<string> dupNames;
+ m->splitAtComma(second, dupNames);
+
+ for (int i = 0; i < dupNames.size(); i++) {
+ nameMap[dupNames[i]] = dupNames[i];
+ if ((groupfile == "") && (i != 0)) { tmap->addSeq(dupNames[i], "Group1"); }
+ }
+ }else { m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); m->names.clear(); namefile = ""; return 1; }
+ }
+ in.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParsimonyCommand", "readNamesFile");
exit(1);
}
}
/***********************************************************/
+
projects / mothur.git / blobdiff