#include "parsimonycommand.h"
//**********************************************************************************************************************
-vector<string> ParsimonyCommand::getValidParameters(){
+vector<string> ParsimonyCommand::setParameters(){
try {
- string Array[] = {"random","groups","iters","processors","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ 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", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-ParsimonyCommand::ParsimonyCommand(){
- try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["parsimony"] = tempOutNames;
- outputTypes["psummary"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand");
+ m->errorOut(e, "ParsimonyCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> ParsimonyCommand::getRequiredParameters(){
+string ParsimonyCommand::getHelpString(){
try {
- vector<string> myArray;
- return myArray;
+ 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\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "ParsimonyCommand", "getRequiredParameters");
+ m->errorOut(e, "ParsimonyCommand", "getHelpString");
exit(1);
}
}
+
//**********************************************************************************************************************
-vector<string> ParsimonyCommand::getRequiredFiles(){
+ParsimonyCommand::ParsimonyCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["parsimony"] = tempOutNames;
+ outputTypes["psummary"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "ParsimonyCommand", "getRequiredFiles");
+ m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand");
exit(1);
}
}
/***********************************************************/
ParsimonyCommand::ParsimonyCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
abort = false; calledHelp = false;
Groups.clear();
if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = {"random","groups","processors","iters","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
ValidParameters validParameter;
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
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; }
+ }
+ }
+
+ m->runParse = true;
+
+ 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 == "") {
- if (globaldata->gTree.size() == 0) {
- m->mothurOut("You must read a treefile and a groupfile or set the randomtree parameter to the output filename you wish, before you may execute the parsimony command."); m->mothurOutEndLine(); abort = true; }
+ //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; }
+ }
+
+ //check for required parameters
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { 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(globaldata->inputFileName); } }
+ 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 = ""; globaldata->Groups.clear(); }
+ if (groups == "not found") { groups = ""; m->Groups.clear(); }
else {
m->splitAtDash(groups, Groups);
- globaldata->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 = "1"; }
- convert(temp, processors);
-
- if (abort == false) {
- //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 == "") {
- T = globaldata->gTree;
- tmap = globaldata->gTreemap;
-
- if(outputDir == "") { outputDir += m->hasPath(globaldata->getTreeFile()); }
- output = new ColumnFile(outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".parsimony", itersString);
- outputNames.push_back(outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".parsimony");
- outputTypes["parsimony"].push_back(outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".parsimony");
-
- sumFile = outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".psummary";
- m->openOutputFile(sumFile, outSum);
- outputNames.push_back(sumFile);
- outputTypes["psummary"].push_back(sumFile);
- }else { //user wants random distribution
- savetmap = globaldata->gTreemap;
- 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(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "parsimony"); //sets the groups the user wants to analyze
- util->getCombos(groupComb, globaldata->Groups, numComp);
-
- if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
-
- pars = new Parsimony(tmap);
- counter = 0;
-
- }
+ string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ convert(temp, processors);
}
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-void ParsimonyCommand::help(){
- try {
- m->mothurOut("The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter.\n");
- m->mothurOut("The parsimony command parameters are random, groups, processors and iters. 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 parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters).\n");
- m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
- m->mothurOut("Example parsimony(random=out, iters=500).\n");
- m->mothurOut("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");
- m->mothurOut("and iters is 1000. The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual.\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "ParsimonyCommand", "help");
- exit(1);
- }
-}
-
-
/***********************************************************/
int ParsimonyCommand::execute() {
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+
+ //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 == "") {
+ 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++) { remove(outputNames[i].c_str()); } 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 util; delete output;
+ 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++) { remove(outputNames[i].c_str()); } outputTypes.clear();
- globaldata->Groups.clear();
+ m->Groups.clear();
return 0;
}
userData = pars->getValues(T[i], processors, outputDir); //data = AB, AC, BC, ABC.
if (m->control_pressed) {
- delete reading; delete pars; delete util; delete output;
+ 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++) { remove(outputNames[i].c_str()); } outputTypes.clear();
- globaldata->Groups.clear();
+ m->Groups.clear();
return 0;
}
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();
randomData = pars->getValues(randT, processors, outputDir);
if (m->control_pressed) {
- delete reading; delete pars; delete util; delete output; delete randT;
+ delete reading; delete pars; delete output; delete randT;
if (randomtree == "") { outSum.close(); }
for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
- globaldata->Groups.clear();
+ delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ m->Groups.clear();
return 0;
}
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 util; delete output; delete randT;
- globaldata->gTreemap = savetmap;
+ delete reading; delete pars; delete output; delete randT;
+ delete tmap;
for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
- globaldata->Groups.clear();
+ m->Groups.clear();
return 0;
}
randomData = pars->getValues(randT, processors, outputDir);
if (m->control_pressed) {
- delete reading; delete pars; delete util; delete output; delete randT;
- globaldata->gTreemap = savetmap;
+ delete reading; delete pars; delete output; delete randT;
+ delete tmap;
for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
- globaldata->Groups.clear();
+ m->Groups.clear();
return 0;
}
}
if (m->control_pressed) {
- delete reading; delete pars; delete util; delete output;
+ delete reading; delete pars; delete output;
+ delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
if (randomtree == "") { outSum.close(); }
- else { globaldata->gTreemap = savetmap; }
for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
- globaldata->Groups.clear();
+ m->Groups.clear();
return 0;
}
printParsimonyFile();
if (randomtree == "") { printUSummaryFile(); }
- //reset globaldata's treemap if you just did random distrib
- if (randomtree != "") {
- //memory leak prevention
- //if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap; }
- globaldata->gTreemap = savetmap;
- }
-
//reset groups parameter
- globaldata->Groups.clear();
+ m->Groups.clear();
- if (m->control_pressed) {
- delete pars; delete util; delete output;
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
- return 0;
- }
+ 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++) { remove(outputNames[i].c_str()); } outputTypes.clear(); return 0;}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
string s;
getline(cin, s);
- //save tmap for later
- //memory leak prevention
- //if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap; }
- globaldata->gTreemap = tmap;
- globaldata->Treenames = tmap->namesOfSeqs;
+ m->Treenames = tmap->namesOfSeqs;
}
catch(exception& e) {
exit(1);
}
}
-
+/*****************************************************************/
+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);
+ }
+}
/***********************************************************/
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