X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtreecommand.cpp;h=89efc9abcf0057f68189ddad6975b5e1464fca09;hb=7588ff51d365aad66f455694afb90b6fd3e6639a;hp=2a3c5d0cdf264ce0c4ecf614b4c3fd46d0ffe51c;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;p=mothur.git diff --git a/readtreecommand.cpp b/readtreecommand.cpp index 2a3c5d0..89efc9a 100644 --- a/readtreecommand.cpp +++ b/readtreecommand.cpp @@ -10,41 +10,86 @@ #include "readtreecommand.h" //********************************************************************************************************************** -ReadTreeCommand::ReadTreeCommand(string option){ +ReadTreeCommand::ReadTreeCommand(string option) { try { globaldata = GlobalData::getInstance(); abort = false; - + //allow user to run help if(option == "help") { help(); abort = true; } else { //valid paramters for this command - string Array[] = {"tree","group"}; + 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 (map::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; } } 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 = ""; mothurOut("tree is a required parameter for the read.tree command."); mothurOutEndLine(); 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 = ""; mothurOut("group is a required parameter for the read.tree command."); mothurOutEndLine(); abort = true; } - else { + else if (groupfile == "not found") { + groupfile = ""; + + m->mothurOut("You have not provided a group file. I am assumming all sequence are from the same group."); m->mothurOutEndLine(); + + if (treefile != "") { Tree* tree = new Tree(treefile); delete tree; } //extracts names from tree to make faked out groupmap + + globaldata->setGroupFile(groupfile); + //read in group map info. + treeMap = new TreeMap(); + for (int i = 0; i < globaldata->Treenames.size(); i++) { treeMap->addSeq(globaldata->Treenames[i], "Group1"); } + globaldata->gTreemap = treeMap; + + }else { globaldata->setGroupFile(groupfile); //read in group map info. treeMap = new TreeMap(groupfile); @@ -52,6 +97,11 @@ ReadTreeCommand::ReadTreeCommand(string option){ 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); @@ -60,7 +110,7 @@ ReadTreeCommand::ReadTreeCommand(string option){ } } catch(exception& e) { - errorOut(e, "ReadTreeCommand", "ReadTreeCommand"); + m->errorOut(e, "ReadTreeCommand", "ReadTreeCommand"); exit(1); } } @@ -68,14 +118,16 @@ ReadTreeCommand::ReadTreeCommand(string option){ void ReadTreeCommand::help(){ try { - mothurOut("The read.tree command must be run before you execute a unifrac.weighted, unifrac.unweighted. \n"); - mothurOut("It also must be run before using the parsimony command, unless you are using the randomtree parameter.\n"); - mothurOut("The read.tree command should be in the following format: read.tree(tree=yourTreeFile, group=yourGroupFile).\n"); - mothurOut("The tree and group parameters are both required.\n"); - mothurOut("Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n\n"); + 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) { - errorOut(e, "ReadTreeCommand", "help"); + m->errorOut(e, "ReadTreeCommand", "help"); exit(1); } } @@ -97,17 +149,33 @@ int ReadTreeCommand::execute(){ readOk = read->read(); - if (readOk != 0) { mothurOut("Read Terminated."); mothurOutEndLine(); globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; } + 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(); } - //output any names that are in names file but not in tree - if (globaldata->Treenames.size() < treeMap->getNumSeqs()) { + + //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; @@ -116,17 +184,70 @@ int ReadTreeCommand::execute(){ 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()) { - mothurOut(treeMap->namesOfSeqs[i] + " is in your namefile and not in your tree. It will be disregarded."); mothurOutEndLine(); + //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) { + m->errorOut(e, "ReadTreeCommand", "execute"); + exit(1); + } +} +/*****************************************************************/ +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]; if ((groupfile == "") && (i != 0)) { globaldata->gTreemap->addSeq(dupNames[i], "Group1"); } } + }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) { - errorOut(e, "ReadTreeCommand", "execute"); + m->errorOut(e, "ReadTreeCommand", "readNamesFile"); exit(1); } }