//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;
+ mothurOut("You must read a list, or a list and a group, or a shared before you can use the venn command."); mothurOutEndLine(); abort = true;
}
//check for optional parameter and set defaults
}
//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 ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); 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;
}
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";
+ 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";
- 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";
+ mothurOut("The venn command can only be executed after a successful read.otu command.\n");
+ mothurOut("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");
+ 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");
+ mothurOut("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");
+ mothurOut("The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, abund=yourAbund).\n");
+ mothurOut("Example venn(groups=A-B-C, line=1-3-5, calc=sharedsobs-sharedchao, abund=20).\n");
+ mothurOut("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");
+ 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");
+ 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");
+ mothurOut("The only estmiator available four 4 groups is sharedsobs.\n");
+ mothurOut("The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n");
+ mothurOut("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";
+ errorOut(e, "VennCommand", "help");
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);
- }
}
if (abort == true) { return 0; }
int count = 1;
- SAbundVector* lastSAbund;
- vector<SharedRAbundVector*> lastLookup;
-
+ string lastLabel;
+
//if the users entered no valid calculators don't execute command
if (vennCalculators.size() == 0) { return 0; }
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
- lastLookup = lookup;
+ lastLabel = lookup[0]->getLabel();
}else if (format == "list") {
//you are using just a list file and have only one group
read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
sabund = globaldata->sabund;
- lastSAbund = globaldata->sabund;
+ lastLabel = sabund->getLabel();
input = globaldata->ginput;
}
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;
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
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;
+ 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."); mothurOutEndLine();
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 ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
- 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
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ if (lookup.size() > 4) {
+ 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."); mothurOutEndLine();
+ for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
}
- venn->getPic(lastLookup, vennCalculators);
+ venn->getPic(lookup, vennCalculators);
}
- //prevent memory leak
- if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
- lastLookup = lookup;
+
+ lastLabel = lookup[0]->getLabel();
//get next line to process
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors();
count++;
}
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;
+ mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
needToRun = true;
}else {
- cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
}
}
//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 < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ if (lookup.size() > 4) {
+ 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."); mothurOutEndLine();
+ for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
+ }
+ venn->getPic(lookup, vennCalculators);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
//reset groups parameter
globaldata->Groups.clear();
if(allLines == 1 || lines.count(count) == 1 || labels.count(sabund->getLabel()) == 1){
- cout << sabund->getLabel() << '\t' << count << endl;
+ mothurOut(sabund->getLabel()); mothurOutEndLine();
venn->getPic(sabund, vennCalculators);
processedLabels.insert(sabund->getLabel());
userLines.erase(count);
}
- if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastSAbund->getLabel()) != 1)) {
-
- cout << lastSAbund->getLabel() << '\t' << count << endl;
- venn->getPic(lastSAbund, vennCalculators);
+ if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete sabund;
+ sabund = input->getSAbundVector(lastLabel);
+
+ mothurOut(sabund->getLabel()); mothurOutEndLine();
+ venn->getPic(sabund, vennCalculators);
- processedLabels.insert(lastSAbund->getLabel());
- userLabels.erase(lastSAbund->getLabel());
+ processedLabels.insert(sabund->getLabel());
+ userLabels.erase(sabund->getLabel());
}
- if (count != 1) { delete lastSAbund; }
- lastSAbund = sabund;
-
+ lastLabel = sabund->getLabel();
+
+ delete sabund;
sabund = input->getSAbundVector();
count++;
}
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;
+ mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
needToRun = true;
}else {
- cout << ". Please refer to " << lastSAbund->getLabel() << "." << endl;
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
}
}
//run last line if you need to
if (needToRun == true) {
- cout << lastSAbund->getLabel() << '\t' << count << endl;
- venn->getPic(lastSAbund, vennCalculators);
+ if (sabund != NULL) { delete sabund; }
+ sabund = input->getSAbundVector(lastLabel);
+
+ mothurOut(sabund->getLabel()); mothurOutEndLine();
+ venn->getPic(sabund, vennCalculators);
+ delete sabund;
+
}
- 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 execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "VennCommand", "execute");
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);
- }
}
//**********************************************************************************************************************
projects / mothur.git / blobdiff