//sorts lowest to highest
inline bool compareSharedRabunds(SharedRAbundVector* left, SharedRAbundVector* right){
return (left->getGroup() < right->getGroup());
-}
-//**********************************************************************************************************************
-vector<string> SharedCommand::getValidParameters(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "SharedCommand", "getValidParameters");
- exit(1);
- }
}
//**********************************************************************************************************************
-SharedCommand::SharedCommand(){
- try {
+vector<string> SharedCommand::setParameters(){
+ try {
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
+ CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pordergroup);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["rabund"] = tempOutNames;
- outputTypes["shared"] = tempOutNames;
+ 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, "SharedCommand", "SharedCommand");
+ m->errorOut(e, "SharedCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> SharedCommand::getRequiredParameters(){
+string SharedCommand::getHelpString(){
try {
- vector<string> myArray;
- return myArray;
+ string helpString = "";
+ helpString += "The make.shared command reads a list and group file and creates a shared file, as well as a rabund file for each group.\n";
+ helpString += "The make.shared command parameters are list, group, ordergroup, groups and label. list and group are required unless a current file is available.\n";
+ helpString += "The groups parameter allows you to indicate which groups you want to include, group names should be separated by dashes. ex. groups=A-B-C. Default is all groups in your groupfile.\n";
+ helpString += "The label parameter allows you to indicate which labels you want to include, label names should be separated by dashes. Default is all labels in your list file.\n";
+ helpString += "The ordergroup parameter allows you to indicate the order of the groups in the sharedfile, by default the groups are listed alphabetically.\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "SharedCommand", "getRequiredParameters");
+ m->errorOut(e, "SharedCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> SharedCommand::getRequiredFiles(){
+SharedCommand::SharedCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "SharedCommand", "getRequiredFiles");
+ m->errorOut(e, "SharedCommand", "SharedCommand");
exit(1);
}
}
//**********************************************************************************************************************
-
-SharedCommand::SharedCommand(string o) : outputDir(o) {
+SharedCommand::SharedCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["rabund"] = tempOutNames;
- outputTypes["shared"] = tempOutNames;
-
- //getting output filename
- filename = globaldata->inputFileName;
- if (outputDir == "") { outputDir += m->hasPath(filename); }
-
- filename = outputDir + m->getRootName(m->getSimpleName(filename));
- filename = filename + "shared";
- outputTypes["shared"].push_back(filename);
+ abort = false; calledHelp = false;
+ allLines = 1;
- m->openOutputFile(filename, out);
- pickedGroups = false;
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
- groupMap = globaldata->gGroupmap;
-
- //if hte user has not specified any groups then use them all
- if (globaldata->Groups.size() == 0) {
- groups = groupMap->namesOfGroups;
- }else{ //they have specified groups
- groups = globaldata->Groups;
- pickedGroups = true;
- }
-
- //fill filehandles with neccessary ofstreams
- int i;
- ofstream* temp;
- for (i=0; i<groups.size(); i++) {
- temp = new ofstream;
- filehandles[groups[i]] = temp;
+ else {
+
+ //valid paramters for this command
+ string Array[] = {"list","label","group","groups","ordergroup","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string, string>::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; }
+ }
+
+ //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("list");
+ //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["list"] = 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("ordergroup");
+ //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["ordergroup"] = inputDir + it->second; }
+ }
+ }
+
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+
+ //check for required parameters
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { abort = true; }
+ else if (listfile == "not found") {
+ listfile = m->getListFile();
+ if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
+ if (ordergroupfile == "not open") { abort = true; }
+ else if (ordergroupfile == "not found") { ordergroupfile = ""; }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") {
+ groupfile = m->getGroupFile();
+ if (groupfile != "") {
+ m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine();
+ groupMap = new GroupMap(groupfile);
+
+ int error = groupMap->readMap();
+ if (error == 1) { abort = true; }
+ m->namesOfGroups = groupMap->namesOfGroups;
+ }
+ else { m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else {
+ groupMap = new GroupMap(groupfile);
+
+ int error = groupMap->readMap();
+ if (error == 1) { abort = true; }
+ m->namesOfGroups = groupMap->namesOfGroups;
+ m->setGroupFile(groupfile);
+ }
+
+ string groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ m->Groups = Groups;
+ }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ string label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ //getting output filename
+ filename = listfile;
+ if (outputDir == "") { outputDir += m->hasPath(filename); }
+
+ filename = outputDir + m->getRootName(m->getSimpleName(filename));
+ filename = filename + "shared";
+ outputTypes["shared"].push_back(filename);
+
+ m->openOutputFile(filename, out);
+ pickedGroups = false;
+
+ //if hte user has not specified any groups then use them all
+ if (Groups.size() == 0) {
+ Groups = groupMap->namesOfGroups; m->Groups = Groups;
+ }
+
+ //fill filehandles with neccessary ofstreams
+ int i;
+ ofstream* temp;
+ for (i=0; i<Groups.size(); i++) {
+ temp = new ofstream;
+ filehandles[Groups[i]] = temp;
+ }
+
+ //set fileroot
+ fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
+
+ //clears file before we start to write to it below
+ for (int i=0; i<Groups.size(); i++) {
+ remove((fileroot + Groups[i] + ".rabund").c_str());
+ outputNames.push_back((fileroot + Groups[i] + ".rabund"));
+ outputTypes["rabund"].push_back((fileroot + Groups[i] + ".rabund"));
+ }
+
}
- //set fileroot
- fileroot = outputDir + m->getRootName(m->getSimpleName(globaldata->getListFile()));
-
- //clears file before we start to write to it below
- for (int i=0; i<groups.size(); i++) {
- remove((fileroot + groups[i] + ".rabund").c_str());
- outputNames.push_back((fileroot + groups[i] + ".rabund"));
- outputTypes["rabund"].push_back((fileroot + groups[i] + ".rabund"));
- }
-
}
catch(exception& e) {
m->errorOut(e, "SharedCommand", "SharedCommand");
//errorOff = "";
//if user provided an order file containing the order the shared file should be in read it
- if (globaldata->getOrderGroupFile() != "") { readOrderFile(); }
+ if (ordergroupfile != "") { readOrderFile(); }
- //read in listfile
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
- delete read;
-
- input = globaldata->ginput;
- SharedList = globaldata->gSharedList;
+ input = new InputData(listfile, "shared");
+ SharedList = input->getSharedListVector();
string lastLabel = SharedList->getLabel();
vector<SharedRAbundVector*> lookup;
if (m->control_pressed) {
- delete input; delete SharedList; globaldata->ginput = NULL; globaldata->gSharedList = NULL;
+ delete input; delete SharedList; delete groupMap;
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); remove(filename.c_str());
- for (int i=0; i<groups.size(); i++) { remove((fileroot + groups[i] + ".rabund").c_str()); }
- return 1;
+ for (int i=0; i<Groups.size(); i++) { remove((fileroot + Groups[i] + ".rabund").c_str()); }
+ return 0;
}
- if ((globaldata->Groups.size() == 0) && (SharedList->getNumSeqs() != groupMap->getNumSeqs())) { //if the user has not specified any groups and their files don't match exit with error
+ if ((m->Groups.size() == 0) && (SharedList->getNumSeqs() != groupMap->getNumSeqs())) { //if the user has not specified any groups and their files don't match exit with error
m->mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); m->mothurOutEndLine();
out.close();
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
delete it3->second;
}
- delete input;
- globaldata->ginput = NULL;
- delete SharedList;
- globaldata->gSharedList = NULL;
+
+ delete input; delete SharedList; delete groupMap;
- return 1;
+ return 0;
}
//if user has specified groups make new groupfile for them
- if (globaldata->Groups.size() != 0) { //make new group file
+ if (m->Groups.size() != 0) { //make new group file
string groups = "";
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- groups += globaldata->Groups[i] + ".";
- }
+ if (m->Groups.size() < 4) {
+ for (int i = 0; i < m->Groups.size(); i++) {
+ groups += m->Groups[i] + ".";
+ }
+ }else { groups = "merge"; }
- string newGroupFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + groups + "groups";
+ string newGroupFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + groups + "groups";
ofstream outGroups;
m->openOutputFile(newGroupFile, outGroups);
string groupName;
for (int i = 0; i < names.size(); i++) {
groupName = groupMap->getGroup(names[i]);
- if (isValidGroup(groupName, globaldata->Groups)) {
+ if (isValidGroup(groupName, m->Groups)) {
outGroups << names[i] << '\t' << groupName << endl;
}
}
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
- set<string> userLabels = globaldata->labels;
+ set<string> userLabels = labels;
- while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+ while((SharedList != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) {
- delete input; delete SharedList; globaldata->ginput = NULL; globaldata->gSharedList = NULL;
+ delete input; delete SharedList; delete groupMap;
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); remove(filename.c_str());
- for (int i=0; i<groups.size(); i++) { remove((fileroot + groups[i] + ".rabund").c_str()); }
- return 1;
+ for (int i=0; i<Groups.size(); i++) { remove((fileroot + Groups[i] + ".rabund").c_str()); }
+ return 0;
}
- if(globaldata->allLines == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
+ if(allLines == 1 || labels.count(SharedList->getLabel()) == 1){
lookup = SharedList->getSharedRAbundVector();
}
if (m->control_pressed) {
- delete input; delete SharedList; globaldata->ginput = NULL; globaldata->gSharedList = NULL;
+ delete input; delete SharedList; delete groupMap;
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); remove(filename.c_str());
- for (int i=0; i<groups.size(); i++) { remove((fileroot + groups[i] + ".rabund").c_str()); }
- return 1;
+ for (int i=0; i<Groups.size(); i++) { remove((fileroot + Groups[i] + ".rabund").c_str()); }
+ return 0;
}
printSharedData(lookup); //prints info to the .shared file
if (m->control_pressed) {
- delete input; delete SharedList; globaldata->ginput = NULL; globaldata->gSharedList = NULL;
+ delete input; delete SharedList; delete groupMap;
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); remove(filename.c_str());
- for (int i=0; i<groups.size(); i++) { remove((fileroot + groups[i] + ".rabund").c_str()); }
- return 1;
+ for (int i=0; i<Groups.size(); i++) { remove((fileroot + Groups[i] + ".rabund").c_str()); }
+ return 0;
}
printSharedData(lookup); //prints info to the .shared file
}
if (m->control_pressed) {
- delete input; globaldata->ginput = NULL;
+ delete input; delete groupMap;
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); remove(filename.c_str());
- for (int i=0; i<groups.size(); i++) { remove((fileroot + groups[i] + ".rabund").c_str()); }
- return 1;
+ for (int i=0; i<Groups.size(); i++) { remove((fileroot + Groups[i] + ".rabund").c_str()); }
+ return 0;
}
printSharedData(lookup); //prints info to the .shared file
delete SharedList;
}
- globaldata->gSharedList = NULL;
-
out.close();
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
delete it3->second;
}
-
- //change format to shared to speed up commands
- globaldata->setFormat("sharedfile");
- globaldata->setListFile("");
- globaldata->setGroupFile("");
- globaldata->setSharedFile(filename);
-
+ delete input; delete groupMap;
if (m->control_pressed) {
- delete input; globaldata->ginput = NULL;
remove(filename.c_str());
- for (int i=0; i<groups.size(); i++) { remove((fileroot + groups[i] + ".rabund").c_str()); }
- return 1;
+ for (int i=0; i<Groups.size(); i++) { remove((fileroot + Groups[i] + ".rabund").c_str()); }
+ return 0;
}
//set rabund file as new current rabundfile
if (order.size() == 0) { //user has not specified an order so do aplabetically
sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
- globaldata->Groups.clear();
+ m->Groups.clear();
//initialize bin values
for (int i = 0; i < thislookup.size(); i++) {
out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
thislookup[i]->print(out);
- globaldata->Groups.push_back(thislookup[i]->getGroup());
+ m->Groups.push_back(thislookup[i]->getGroup());
RAbundVector rav = thislookup[i]->getRAbundVector();
m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
myMap[thislookup[i]->getGroup()] = thislookup[i];
}
- globaldata->Groups.clear();
+ m->Groups.clear();
//loop through ordered list and print the rabund
for (int i = 0; i < order.size(); i++) {
out << (myIt->second)->getLabel() << '\t' << (myIt->second)->getGroup() << '\t';
(myIt->second)->print(out);
- globaldata->Groups.push_back((myIt->second)->getGroup());
+ m->Groups.push_back((myIt->second)->getGroup());
RAbundVector rav = (myIt->second)->getRAbundVector();
m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));
int SharedCommand::createMisMatchFile() {
try {
ofstream outMisMatch;
- string outputMisMatchName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName));
+ string outputMisMatchName = outputDir + m->getRootName(m->getSimpleName(listfile));
//you have sequences in your list file that are not in your group file
if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) {
order.clear();
ifstream in;
- m->openInputFile(globaldata->getOrderGroupFile(), in);
+ m->openInputFile(ordergroupfile, in);
string thisGroup;
while(!in.eof()){
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