//**********************************************************************************************************************
-SummarySharedCommand::SummarySharedCommand(string option){
+SummarySharedCommand::SummarySharedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
else {
//valid paramters for this command
- string Array[] = {"label","calc","groups"};
+ string Array[] = {"label","calc","groups","all","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
//make sure the user has already run the read.otu command
if (globaldata->getSharedFile() == "") {
- mothurOut("You must read a list and a group, or a shared before you can use the summary.shared command."); mothurOutEndLine(); abort = true;
+ m->mothurOut("You must read a list and a group, or a shared before you can use the summary.shared 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->getSharedFile()); //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") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
else {
if (calc == "default") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
}
- splitAtDash(calc, Estimators);
+ m->splitAtDash(calc, Estimators);
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
- splitAtDash(groups, Groups);
+ m->splitAtDash(groups, Groups);
globaldata->Groups = Groups;
}
+ string temp = validParameter.validFile(parameters, "all", false); if (temp == "not found") { temp = "false"; }
+ all = m->isTrue(temp);
+
if (abort == false) {
validCalculator = new ValidCalculators();
}
}
- outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
- openOutputFile(outputFileName, outputFileHandle);
+ outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "shared.summary";
+ m->openOutputFile(outputFileName, outputFileHandle);
+ outputNames.push_back(outputFileName);
+
mult = false;
}
}
}
catch(exception& e) {
- errorOut(e, "SummarySharedCommand", "SummarySharedCommand");
+ m->errorOut(e, "SummarySharedCommand", "SummarySharedCommand");
exit(1);
}
}
void SummarySharedCommand::help(){
try {
- mothurOut("The summary.shared command can only be executed after a successful read.otu command.\n");
- mothurOut("The summary.shared command parameters are label and calc. No parameters are required.\n");
- mothurOut("The summary.shared command should be in the following format: \n");
- mothurOut("summary.shared(label=yourLabel, calc=yourEstimators, groups=yourGroups).\n");
- mothurOut("Example summary.shared(label=unique-.01-.03, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
+ m->mothurOut("The summary.shared command can only be executed after a successful read.otu command.\n");
+ m->mothurOut("The summary.shared command parameters are label, calc and all. No parameters are required.\n");
+ m->mothurOut("The summary.shared command should be in the following format: \n");
+ m->mothurOut("summary.shared(label=yourLabel, calc=yourEstimators, groups=yourGroups).\n");
+ m->mothurOut("Example summary.shared(label=unique-.01-.03, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
validCalculator->printCalc("sharedsummary", cout);
- mothurOut("The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n");
- mothurOut("The default value for groups is all the groups in your groupfile.\n");
- mothurOut("The label parameter is used to analyze specific labels in your input.\n");
- mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups.\n");
- mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
+ m->mothurOut("The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n");
+ m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
+ m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
+ m->mothurOut("The all parameter is used to specify if you want the estimate of all your groups together. This estimate can only be made for sharedsobs and sharedchao calculators. The default is false.\n");
+ m->mothurOut("If you use sharedchao and run into memory issues, set all to false. \n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups.\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
}
catch(exception& e) {
- errorOut(e, "SummarySharedCommand", "help");
+ m->errorOut(e, "SummarySharedCommand", "help");
exit(1);
}
}
try {
if (abort == true) { return 0; }
-
+
//if the users entered no valid calculators don't execute command
if (sumCalculators.size() == 0) { return 0; }
//check if any calcs can do multiples
else{
- for (int i = 0; i < sumCalculators.size(); i++) {
- if (sumCalculators[i]->getMultiple() == true) { mult = true; }
+ if (all){
+ for (int i = 0; i < sumCalculators.size(); i++) {
+ if (sumCalculators[i]->getMultiple() == true) { mult = true; }
+ }
}
}
outputFileHandle << "label" <<'\t' << "comparison" << '\t';
for(int i=0;i<sumCalculators.size();i++){
outputFileHandle << '\t' << sumCalculators[i]->getName();
+ if (sumCalculators[i]->getCols() == 3) { outputFileHandle << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci"; }
}
outputFileHandle << endl;
//create file and put column headers for multiple groups file
if (mult == true) {
- outAllFileName = ((getRootName(globaldata->inputFileName)) + "sharedmultiple.summary");
- openOutputFile(outAllFileName, outAll);
+ outAllFileName = ((m->getRootName(globaldata->inputFileName)) + "sharedmultiple.summary");
+ m->openOutputFile(outAllFileName, outAll);
+ outputNames.push_back(outAllFileName);
outAll << "label" <<'\t' << "comparison" << '\t';
for(int i=0;i<sumCalculators.size();i++){
}
if (lookup.size() < 2) {
- mothurOut("I cannot run the command without at least 2 valid groups.");
+ m->mothurOut("I cannot run the command without at least 2 valid groups.");
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
//close files and clean up
mult = false;
outAll.close();
remove(outAllFileName.c_str());
+ outputNames.pop_back();
}
-
+
+ if (m->control_pressed) {
+ if (mult) { outAll.close(); remove(outAllFileName.c_str()); }
+ outputFileHandle.close(); remove(outputFileName.c_str());
+ delete input; globaldata->ginput = NULL;
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
+ globaldata->Groups.clear();
+ return 0;
+ }
+
+
//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;
//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))) {
+ if (m->control_pressed) {
+ if (mult) { outAll.close(); remove(outAllFileName.c_str()); }
+ outputFileHandle.close(); remove(outputFileName.c_str());
+ delete input; globaldata->ginput = NULL;
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
+ globaldata->Groups.clear();
+ return 0;
+ }
+
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
process(lookup);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ 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);
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
process(lookup);
processedLabels.insert(lookup[0]->getLabel());
lookup = input->getSharedRAbundVectors();
}
+ if (m->control_pressed) {
+ if (mult) { outAll.close(); remove(outAllFileName.c_str()); }
+ outputFileHandle.close(); remove(outputFileName.c_str());
+ delete input; globaldata->ginput = NULL;
+ for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
+ globaldata->Groups.clear();
+ 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++) {
- mothurOut("Your file does not include the label " + *it);
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
lookup = input->getSharedRAbundVectors(lastLabel);
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
process(lookup);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
-
+
//reset groups parameter
globaldata->Groups.clear();
if (mult == true) { outAll.close(); }
for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
-
delete input; globaldata->ginput = NULL;
+
+ if (m->control_pressed) {
+ remove(outAllFileName.c_str());
+ remove(outputFileName.c_str());
+ return 0;
+ }
+
+ 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) {
- errorOut(e, "SummarySharedCommand", "execute");
+ m->errorOut(e, "SummarySharedCommand", "execute");
exit(1);
}
}
/***********************************************************/
-void SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup) {
+int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup) {
try {
//loop through calculators and add to file all for all calcs that can do mutiple groups
if (mult == true) {
for(int i=0;i<sumCalculators.size();i++){
if (sumCalculators[i]->getMultiple() == true) {
sumCalculators[i]->getValues(thisLookup);
+
+ if (m->control_pressed) { return 1; }
+
outAll << '\t';
sumCalculators[i]->print(outAll);
}
int n = 1;
vector<SharedRAbundVector*> subset;
- for (int k = 0; k < (thisLookup.size() - 1); k++) { // pass cdd each set of groups to commpare
+ for (int k = 0; k < (thisLookup.size() - 1); k++) { // pass cdd each set of groups to compare
+
for (int l = n; l < thisLookup.size(); l++) {
outputFileHandle << thisLookup[0]->getLabel() << '\t';
for(int i=0;i<sumCalculators.size();i++) {
sumCalculators[i]->getValues(subset); //saves the calculator outputs
+
+ if (m->control_pressed) { return 1; }
+
outputFileHandle << '\t';
sumCalculators[i]->print(outputFileHandle);
}
}
n++;
}
-
+ return 0;
}
catch(exception& e) {
- errorOut(e, "SummarySharedCommand", "process");
+ m->errorOut(e, "SummarySharedCommand", "process");
exit(1);
}
}
projects / mothur.git / blobdiff