*/
#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;
+ lines.clear();
+ labels.clear();
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string AlignArray[] = {"groups","line","label","calc", "abund"};
+ 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() == "")) {
+ cout << "You must read a list, or a list and a group, or a shared before you can use the venn command." << endl; abort = true;
+ }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ line = validParameter.validFile(parameters, "line", false);
+ if (line == "not found") { line = ""; }
+ else {
+ if(line != "all") { splitAtDash(line, lines); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ //make sure user did not use both the line and label parameters
+ if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
+ //if the user has not specified any line or labels use the ones from read.otu
+ else if ((line == "") && (label == "")) {
+ allLines = globaldata->allLines;
+ labels = globaldata->labels;
+ lines = globaldata->lines;
+ }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ 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"; }
+ }
+ }
+ 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());
+ }
+ }
+ }
+ }
+
+ venn = new Venn();
+ }
+ }
+
+
+
}
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";
exit(1);
}
}
+
+//**********************************************************************************************************************
+
+void VennCommand::help(){
+ try {
+ cout << "The venn command can only be executed after a successful read.otu command." << "\n";
+ cout << "The venn command parameters are groups, calc, abund, line and label. No parameters are required, but you may not use line and label at the same time." << "\n";
+ cout << "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";
+ cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like a venn diagram created for, and are also separated by dashes." << "\n";
+ cout << "The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, abund=yourAbund)." << "\n";
+ cout << "Example venn(groups=A-B-C, line=1-3-5, calc=sharedsobs-sharedchao, abund=20)." << "\n";
+ cout << "The default value for groups is all the groups in your groupfile up to 4, and all lines in your inputfile will be used." << "\n";
+ cout << "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";
+ cout << "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";
+ cout << "The only estmiator available four 4 groups is sharedsobs." << "\n";
+ cout << "The venn command outputs a .svg file for each calculator you specify at each distance you choose." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VennCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ 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;
+ }
+
}
//**********************************************************************************************************************
int VennCommand::execute(){
try {
- int count = 1;
+
+ if (abort == true) { return 0; }
+
+ int count = 1;
+ SAbundVector* lastSAbund;
+ vector<SharedRAbundVector*> lastLookup;
+
+ //if the users entered no valid calculators don't execute command
+ if (vennCalculators.size() == 0) { return 0; }
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();
+ lastLookup = lookup;
}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;
+ lastSAbund = globaldata->sabund;
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;
+ set<int> userLines = lines;
if (format != "list") {
- setGroups();
-
- 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);
+ //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) || (userLines.size() != 0))) {
+
+ if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ userLines.erase(count);
+
+ if (lookup.size() > 4) {
+ cout << "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." << endl;
+ for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
+ }
+ venn->getPic(lookup, vennCalculators);
+ }
+
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
+ cout << lastLookup[0]->getLabel() << '\t' << count << endl;
+ processedLabels.insert(lastLookup[0]->getLabel());
+ userLabels.erase(lastLookup[0]->getLabel());
+ if (lastLookup.size() > 4) {
+ cout << "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." << endl;
+ for (int i = lastLookup.size(); i > 4; i--) { lastLookup.pop_back(); } //no memmory leak because pop_back calls destructor
+ }
+ venn->getPic(lastLookup, vennCalculators);
}
+
+ //prevent memory leak
+ if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
+ lastLookup = lookup;
//get next line to process
- if (format == "sharedfile") {
- order = input->getSharedOrderVector();
- }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;
- }
- }
+ lookup = input->getSharedRAbundVectors();
count++;
}
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ cout << "Your file does not include the label "<< *it;
+ if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
+ cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ needToRun = true;
+ }else {
+ cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ cout << lastLookup[0]->getLabel() << '\t' << count << endl;
+ if (lastLookup.size() > 4) {
+ cout << "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." << endl;
+ for (int i = lastLookup.size(); i > 3; i--) { delete lastLookup[i]; lastLookup.pop_back(); }
+ }
+ venn->getPic(lastLookup, vennCalculators);
+ }
+
+ for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
+
//reset groups parameter
- globaldata->Groups.clear(); globaldata->setGroups("");
+ globaldata->Groups.clear();
}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) || (userLines.size() != 0))) {
+
+ if(allLines == 1 || lines.count(count) == 1 || labels.count(sabund->getLabel()) == 1){
- cout << ordersingle->getLabel() << '\t' << count << endl;
- venn->getPic(ordersingle);
+ cout << sabund->getLabel() << '\t' << count << endl;
+ venn->getPic(sabund, vennCalculators);
+ processedLabels.insert(sabund->getLabel());
+ userLabels.erase(sabund->getLabel());
+ userLines.erase(count);
}
- ordersingle = (input->getOrderVector());
+ if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastSAbund->getLabel()) != 1)) {
+
+ cout << lastSAbund->getLabel() << '\t' << count << endl;
+ venn->getPic(lastSAbund, vennCalculators);
+
+ processedLabels.insert(lastSAbund->getLabel());
+ userLabels.erase(lastSAbund->getLabel());
+ }
+
+ if (count != 1) { delete lastSAbund; }
+ lastSAbund = sabund;
+
+ sabund = input->getSAbundVector();
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);
- }
-}
-
-//**********************************************************************************************************************
-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);
- }
- }
- //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]);
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ cout << "Your file does not include the label "<< *it;
+ if (processedLabels.count(lastSAbund->getLabel()) != 1) {
+ cout << ". I will use " << lastSAbund->getLabel() << "." << endl;
+ needToRun = true;
+ }else {
+ cout << ". Please refer to " << lastSAbund->getLabel() << "." << endl;
}
- globaldata->setGroups("");
- }
- }else {
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[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);
+ //run last line if you need to
+ if (needToRun == true) {
+ cout << lastSAbund->getLabel() << '\t' << count << endl;
+ venn->getPic(lastSAbund, vennCalculators);
}
+ delete lastSAbund;
}
+ for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
+ 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";
+ 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 setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the VennCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
-
}
-/***********************************************************/
+//**********************************************************************************************************************
\ No newline at end of file
projects / mothur.git / blobdiff