X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtreecommand.cpp;h=05a65b736f93c376525b1cf64e2ed8275fc9c486;hb=b663591fb57c9508f017fd0891911fd959530125;hp=a11465d669a55de0c5555f616c36f51caef74ea2;hpb=5a1e62397b91f57d0d3aff635891df04b8999a88;p=mothur.git diff --git a/readtreecommand.cpp b/readtreecommand.cpp index a11465d..05a65b7 100644 --- a/readtreecommand.cpp +++ b/readtreecommand.cpp @@ -10,13 +10,48 @@ #include "readtreecommand.h" //********************************************************************************************************************** -ReadTreeCommand::ReadTreeCommand(string option){ +vector ReadTreeCommand::getValidParameters(){ + try { + string Array[] = {"tree","group","name","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ReadTreeCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector ReadTreeCommand::getRequiredParameters(){ + try { + string Array[] = {"tree"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ReadTreeCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector ReadTreeCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ReadTreeCommand", "getRequiredFiles"); + exit(1); + } +} +//********************************************************************************************************************** +ReadTreeCommand::ReadTreeCommand(string option) { try { globaldata = GlobalData::getInstance(); - abort = false; - + abort = false; calledHelp = false; + //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } else { //valid paramters for this command @@ -44,7 +79,7 @@ ReadTreeCommand::ReadTreeCommand(string option){ it = parameters.find("tree"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + 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; } } @@ -52,7 +87,7 @@ ReadTreeCommand::ReadTreeCommand(string option){ it = parameters.find("group"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + 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; } } @@ -60,7 +95,7 @@ ReadTreeCommand::ReadTreeCommand(string option){ it = parameters.find("name"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + 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; } } @@ -71,13 +106,25 @@ ReadTreeCommand::ReadTreeCommand(string option){ //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); @@ -98,7 +145,7 @@ ReadTreeCommand::ReadTreeCommand(string option){ } } catch(exception& e) { - errorOut(e, "ReadTreeCommand", "ReadTreeCommand"); + m->errorOut(e, "ReadTreeCommand", "ReadTreeCommand"); exit(1); } } @@ -106,14 +153,16 @@ 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, if no group file is given then one group is assumed.\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); } } @@ -129,23 +178,39 @@ ReadTreeCommand::~ReadTreeCommand(){ int ReadTreeCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } int readOk; 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(); } + + //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 (globaldata->Treenames.size() < treeMap->getNumSeqs()) { + if (numNamesInTree < treeMap->getNumSeqs()) { for (int i = 0; i < treeMap->namesOfSeqs.size(); i++) { //is that name in the tree? int count = 0; @@ -154,24 +219,33 @@ 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()) { //if it is in your namefile then don't remove map::iterator it = nameMap.find(treeMap->namesOfSeqs[i]); if (it == nameMap.end()) { - mothurOut(treeMap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); mothurOutEndLine(); + 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) { - errorOut(e, "ReadTreeCommand", "execute"); + m->errorOut(e, "ReadTreeCommand", "execute"); exit(1); } } @@ -179,33 +253,36 @@ int ReadTreeCommand::execute(){ int ReadTreeCommand::readNamesFile() { try { globaldata->names.clear(); + numUniquesInName = 0; ifstream in; - openInputFile(namefile, in); + m->openInputFile(namefile, in); string first, second; map::iterator itNames; while(!in.eof()) { - in >> first >> second; gobble(in); + 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; - splitAtComma(second, dupNames); + m->splitAtComma(second, dupNames); - for (int i = 0; i < dupNames.size(); i++) { nameMap[dupNames[i]] = dupNames[i]; } - }else { mothurOut(first + " has already been seen in namefile, disregarding names file."); mothurOutEndLine(); in.close(); globaldata->names.clear(); return 1; } + 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", "readNamesFile"); + m->errorOut(e, "ReadTreeCommand", "readNamesFile"); exit(1); } }