*/
#include "venncommand.h"
+#include "ace.h"
+#include "sobs.h"
+#include "chao1.h"
+//#include "jackknife.h"
+#include "sharedsobscollectsummary.h"
+#include "sharedchao1.h"
+#include "sharedace.h"
+
//**********************************************************************************************************************
-VennCommand::VennCommand(){
+VennCommand::VennCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- venn = new Venn();
- format = globaldata->getFormat();
+ abort = false;
+ allLines = 1;
+ labels.clear();
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string AlignArray[] = {"groups","label","calc", "abund","outputdir","inputdir"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //make sure the user has already run the read.otu command
+ if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
+ m->mothurOut("You must read a list, or a list and a group, or a shared before you can use the venn command."); m->mothurOutEndLine(); abort = true;
+ }
+
+ //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 = "";
+ outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ //if the user has not specified any labels use the ones from read.otu
+ if (label == "") {
+ allLines = globaldata->allLines;
+ labels = globaldata->labels;
+ }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
+
+ format = globaldata->getFormat();
+ calc = validParameter.validFile(parameters, "calc", false);
+ if (calc == "not found") {
+ if(format == "list") { calc = "sobs"; }
+ else { calc = "sharedsobs"; }
+ }
+ else {
+ if (calc == "default") {
+ if(format == "list") { calc = "sobs"; }
+ else { calc = "sharedsobs"; }
+ }
+ }
+ m->splitAtDash(calc, Estimators);
+
+ string temp;
+ temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
+ convert(temp, abund);
+
+ if (abort == false) {
+ validCalculator = new ValidCalculators();
+
+ int i;
+
+ if (format == "list") {
+ for (i=0; i<Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("vennsingle", Estimators[i]) == true) {
+ if (Estimators[i] == "sobs") {
+ vennCalculators.push_back(new Sobs());
+ }else if (Estimators[i] == "chao") {
+ vennCalculators.push_back(new Chao1());
+ }else if (Estimators[i] == "ace") {
+ if(abund < 5)
+ abund = 10;
+ vennCalculators.push_back(new Ace(abund));
+ }
+ }
+ }
+ }else {
+ for (i=0; i<Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("vennshared", Estimators[i]) == true) {
+ if (Estimators[i] == "sharedsobs") {
+ vennCalculators.push_back(new SharedSobsCS());
+ }else if (Estimators[i] == "sharedchao") {
+ vennCalculators.push_back(new SharedChao1());
+ }else if (Estimators[i] == "sharedace") {
+ vennCalculators.push_back(new SharedAce());
+ }
+ }
+ }
+ }
+
+ //if the users entered no valid calculators don't execute command
+ if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); abort = true; }
+ else { venn = new Venn(outputDir); }
+ }
+
+ }
+
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function VennCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "VennCommand", "VennCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the VennCommand class function VennCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+//**********************************************************************************************************************
+
+void VennCommand::help(){
+ try {
+ m->mothurOut("The venn command can only be executed after a successful read.otu command.\n");
+ m->mothurOut("The venn command parameters are groups, calc, abund and label. No parameters are required.\n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups.\n");
+ m->mothurOut("The group names are separated by dashes. The label allows you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n");
+ m->mothurOut("The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n");
+ m->mothurOut("Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n");
+ m->mothurOut("The default value for groups is all the groups in your groupfile up to 4, and all labels in your inputfile will be used.\n");
+ m->mothurOut("The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups.\n");
+ m->mothurOut("The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a list and group file or a shared file.\n");
+ m->mothurOut("The only estmiator available four 4 groups is sharedsobs.\n");
+ m->mothurOut("The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "VennCommand", "help");
exit(1);
- }
+ }
}
+
+
//**********************************************************************************************************************
VennCommand::~VennCommand(){
- delete input;
- delete read;
- delete venn;
+ if (abort == false) {
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete venn;
+ globaldata->sabund = NULL;
+ delete validCalculator;
+ }
+
}
//**********************************************************************************************************************
int VennCommand::execute(){
try {
- int count = 1;
+
+ if (abort == true) { return 0; }
+
+ string lastLabel;
+ vector<string> outputNames;
if (format == "sharedfile") {
//you have groups
- read = new ReadPhilFile(globaldata->inputFileName);
+ read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
input = globaldata->ginput;
- order = input->getSharedOrderVector();
- }else if (format == "shared") {
- //you are using a list and a groupfile
- read = new ReadPhilFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
- SharedList = globaldata->gSharedList;
- order = SharedList->getSharedOrderVector();
+ lookup = input->getSharedRAbundVectors();
+ lastLabel = lookup[0]->getLabel();
}else if (format == "list") {
//you are using just a list file and have only one group
- read = new ReadPhilFile(globaldata->inputFileName);
+ read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
- ordersingle = globaldata->gorder;
+ sabund = globaldata->sabund;
+ lastLabel = sabund->getLabel();
input = globaldata->ginput;
}
-
+
+ //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 = labels;
if (format != "list") {
- setGroups();
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- while(order != NULL){
-
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
-
- cout << order->getLabel() << '\t' << count << endl;
- venn->getPic(order);
+ if (m->control_pressed) {
+ for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ globaldata->Groups.clear();
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ if (lookup.size() > 4) {
+ m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile."); m->mothurOutEndLine();
+ for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
+ }
+
+ vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); } }
+ }
+
+ if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookup[0]->getLabel();
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ if (lookup.size() > 4) {
+ m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile."); m->mothurOutEndLine();
+ for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
+ }
+ vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); } }
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
}
+
+
+ lastLabel = lookup[0]->getLabel();
//get next line to process
- if (format == "sharedfile") {
- order = input->getSharedOrderVector();
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors();
+ }
+
+ if (m->control_pressed) {
+ for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
+ globaldata->Groups.clear();
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
}else {
- //you are using a list and a groupfile
- SharedList = input->getSharedListVector(); //get new list vector to process
- if (SharedList != NULL) {
- order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
- }else {
- break;
- }
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
- count++;
}
-
+
+ //run last label if you need to
+ if (needToRun == true) {
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ if (lookup.size() > 4) {
+ m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile."); m->mothurOutEndLine();
+ for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
+ }
+ vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); } }
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ }
+
+
//reset groups parameter
- globaldata->Groups.clear(); globaldata->setGroups("");
+ globaldata->Groups.clear();
+
+ if (m->control_pressed) {
+ for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
}else{
- while(ordersingle != NULL){
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(ordersingle->getLabel()) == 1){
+ while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) {
+ for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
+ delete sabund;
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
+ if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
- cout << ordersingle->getLabel() << '\t' << count << endl;
- venn->getPic(ordersingle);
+ m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
+ vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); } }
+
+ processedLabels.insert(sabund->getLabel());
+ userLabels.erase(sabund->getLabel());
}
- ordersingle = (input->getOrderVector());
- count++;
- }
- }
-
- return 0;
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the VennCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
+ if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = sabund->getLabel();
+
+ delete sabund;
+ sabund = input->getSAbundVector(lastLabel);
+
+ m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
+ vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); } }
-//**********************************************************************************************************************
-void VennCommand::setGroups() {
- try {
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() != 0) {
- if (globaldata->Groups[0] != "all") {
- //check that groups are valid
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
- cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
- // erase the invalid group from globaldata->Groups
- globaldata->Groups.erase(globaldata->Groups.begin()+i);
- }
- }
+
+ processedLabels.insert(sabund->getLabel());
+ userLabels.erase(sabund->getLabel());
+
+ //restore real lastlabel to save below
+ sabund->setLabel(saveLabel);
+ }
+
+ lastLabel = sabund->getLabel();
+
+ delete sabund;
+ sabund = input->getSAbundVector();
+ }
- //if the user only entered invalid groups
- if (globaldata->Groups.size() == 0) {
- cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using the first three groups in your groupfile." << endl;
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
- }
- }
- }else{//user has enter "all" and wants the default groups
- globaldata->Groups.clear();
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+ if (m->control_pressed) {
+ for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
- globaldata->setGroups("");
}
- }else {
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+
+ //run last label if you need to
+ if (needToRun == true) {
+ if (sabund != NULL) { delete sabund; }
+ sabund = input->getSAbundVector(lastLabel);
+
+ m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
+ vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); } }
+
+ delete sabund;
+
+ }
+
+ if (m->control_pressed) {
+ for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
}
}
+ for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
- //check to make sure their are only 3 groups
- if (globaldata->Groups.size() > 3) {
- cout << "You may only use 3 groups at a time with this command. I will choose the first three and disregard the rest." << endl;
- for (int i = 3; i < globaldata->Groups.size(); i++) {
- globaldata->Groups.erase(globaldata->Groups.begin()+i);
- }
- }
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "VennCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the VennCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
-/***********************************************************/
+//**********************************************************************************************************************
projects / mothur.git / blobdiff