X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtreecommand.cpp;h=fdfdb050f22c4ccc281646d1d56c8a5aa6b33806;hb=afcbef163b4f32d0ff25a834cb9af8eef8d06ffa;hp=a540c7444a4b2b67a03ca3be29120138faf43ef5;hpb=d037597badc8d18e235c59f0c1114180edb7f98f;p=mothur.git diff --git a/readtreecommand.cpp b/readtreecommand.cpp index a540c74..fdfdb05 100644 --- a/readtreecommand.cpp +++ b/readtreecommand.cpp @@ -10,25 +10,112 @@ #include "readtreecommand.h" //********************************************************************************************************************** -ReadTreeCommand::ReadTreeCommand(){ +ReadTreeCommand::ReadTreeCommand(string option) { try { globaldata = GlobalData::getInstance(); - filename = globaldata->inputFileName; + abort = false; + + //allow user to run help + if(option == "help") { help(); abort = true; } - //read in group map info. - treeMap = new TreeMap(globaldata->getGroupFile()); - treeMap->readMap(); - globaldata->gTreemap = treeMap; - - read = new ReadNewickTree(filename); + else { + //valid paramters for this command + string Array[] = {"tree","group","name","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + map::iterator it; + //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; } + } + + globaldata->newRead(); + + //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; } + } + + } + + + //check for required parameters + treefile = validParameter.validFile(parameters, "tree", true); + if (treefile == "not open") { abort = true; } + else if (treefile == "not found") { treefile = ""; m->mothurOut("tree is a required parameter for the read.tree command."); m->mothurOutEndLine(); abort = true; } + else { globaldata->setTreeFile(treefile); globaldata->setFormat("tree"); } + + groupfile = validParameter.validFile(parameters, "group", true); + if (groupfile == "not open") { abort = true; } + else if (groupfile == "not found") { groupfile = ""; m->mothurOut("group is a required parameter for the read.tree command."); m->mothurOutEndLine(); abort = true; } + else { + globaldata->setGroupFile(groupfile); + //read in group map info. + treeMap = new TreeMap(groupfile); + treeMap->readMap(); + globaldata->gTreemap = treeMap; + } + + namefile = validParameter.validFile(parameters, "name", true); + if (namefile == "not open") { abort = true; } + else if (namefile == "not found") { namefile = ""; } + else { readNamesFile(); } + + if (abort == false) { + filename = treefile; + read = new ReadNewickTree(filename); + } + + } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ReadTreeCommand class Function ReadTreeCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ReadTreeCommand", "ReadTreeCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the ReadTreeCommand class function ReadTreeCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +//********************************************************************************************************************** + +void ReadTreeCommand::help(){ + try { + m->mothurOut("The read.tree command must be run before you execute a unifrac.weighted, unifrac.unweighted. \n"); + m->mothurOut("It also must be run before using the parsimony command, unless you are using the randomtree parameter.\n"); + m->mothurOut("The read.tree command parameters are tree, group and name.\n"); + m->mothurOut("The read.tree command should be in the following format: read.tree(tree=yourTreeFile, group=yourGroupFile).\n"); + m->mothurOut("The tree and group parameters are both required.\n"); + m->mothurOut("The name parameter allows you to enter a namefile.\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n\n"); + } + catch(exception& e) { + m->errorOut(e, "ReadTreeCommand", "help"); exit(1); } } @@ -36,7 +123,7 @@ ReadTreeCommand::ReadTreeCommand(){ //********************************************************************************************************************** ReadTreeCommand::~ReadTreeCommand(){ - delete read; + if (abort == false) { delete read; } } //********************************************************************************************************************** @@ -44,23 +131,111 @@ ReadTreeCommand::~ReadTreeCommand(){ int ReadTreeCommand::execute(){ try { - read->read(); + if (abort == true) { return 0; } - vector T = globaldata->gTree; + int readOk; + + readOk = read->read(); + if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; } + + vector T = globaldata->gTree; + //assemble users trees for (int i = 0; i < T.size(); i++) { + if (m->control_pressed) { + for (int i = 0; i < T.size(); i++) { delete T[i]; } + globaldata->gTree.clear(); + delete globaldata->gTreemap; + return 0; + } + T[i]->assembleTree(); } + + + //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 == globaldata->Treenames.size()) { numNamesInTree = nameMap.size(); } + else { numNamesInTree = globaldata->Treenames.size(); } + }else { numNamesInTree = globaldata->Treenames.size(); } + + //output any names that are in group file but not in tree + if (numNamesInTree < treeMap->getNumSeqs()) { + for (int i = 0; i < treeMap->namesOfSeqs.size(); i++) { + //is that name in the tree? + int count = 0; + for (int j = 0; j < globaldata->Treenames.size(); j++) { + if (treeMap->namesOfSeqs[i] == globaldata->Treenames[j]) { break; } //found it + count++; + } + + if (m->control_pressed) { + for (int i = 0; i < T.size(); i++) { delete T[i]; } + globaldata->gTree.clear(); + delete globaldata->gTreemap; + return 0; + } + + //then you did not find it so report it + if (count == globaldata->Treenames.size()) { + //if it is in your namefile then don't remove + map::iterator it = nameMap.find(treeMap->namesOfSeqs[i]); + + if (it == nameMap.end()) { + m->mothurOut(treeMap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine(); + treeMap->removeSeq(treeMap->namesOfSeqs[i]); + i--; //need this because removeSeq removes name from namesOfSeqs + } + } + } + + globaldata->gTreemap = treeMap; + } + return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ReadTreeCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ReadTreeCommand", "execute"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the ReadTreeCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +/*****************************************************************/ +int ReadTreeCommand::readNamesFile() { + try { + globaldata->names.clear(); + numUniquesInName = 0; + + ifstream in; + m->openInputFile(namefile, in); + + string first, second; + map::iterator itNames; + + while(!in.eof()) { + in >> first >> second; m->gobble(in); + + numUniquesInName++; + + itNames = globaldata->names.find(first); + if (itNames == globaldata->names.end()) { + globaldata->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 dupNames; + m->splitAtComma(second, dupNames); + + for (int i = 0; i < dupNames.size(); i++) { nameMap[dupNames[i]] = dupNames[i]; } + }else { m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); globaldata->names.clear(); namefile = ""; return 1; } + } + in.close(); + + return 0; + } + catch(exception& e) { + m->errorOut(e, "ReadTreeCommand", "readNamesFile"); exit(1); } }