globaldata = GlobalData::getInstance();
abort = false;
allLines = 1;
- lines.clear();
labels.clear();
Estimators.clear();
else {
//valid paramters for this command
- string Array[] = {"line","label","calc","groups"};
+ string Array[] = {"label","calc","groups","all","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
mothurOut("You must read a list and a group, or a shared before you can use the summary.shared command."); 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 += 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...
- 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 {
else { allLines = 1; }
}
- //make sure user did not use both the line and label parameters
- 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 == "")) {
+ //if the user has not specified any labels use the ones from read.otu
+ if(label == "") {
allLines = globaldata->allLines;
labels = globaldata->labels;
- lines = globaldata->lines;
}
calc = validParameter.validFile(parameters, "calc", false);
globaldata->Groups = Groups;
}
+ string temp = validParameter.validFile(parameters, "all", false); if (temp == "not found") { temp = "false"; }
+ all = isTrue(temp);
+
if (abort == false) {
validCalculator = new ValidCalculators();
}
}
- outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
+ outputFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "shared.summary";
openOutputFile(outputFileName, outputFileHandle);
mult = false;
}
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, line and calc. No parameters are required, but you may not use \n");
- mothurOut("both the line and label parameters at the same time. The summary.shared command should be in the following format: \n");
- mothurOut("summary.shared(label=yourLabel, line=yourLines, calc=yourEstimators, groups=yourGroups).\n");
- mothurOut("Example summary.shared(label=unique-.01-.03, line=0,5,10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
+ mothurOut("The summary.shared command parameters are label, calc and all. 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");
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 and line parameters are used to analyze specific lines in your input.\n");
+ mothurOut("The label parameter is used to analyze specific labels in your input.\n");
+ 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");
+ mothurOut("If you use sharedchao and run into memory issues, set all to false. \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. line), '=' and parameters (i.e.yourLines).\n\n");
+ mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
}
catch(exception& e) {
errorOut(e, "SummarySharedCommand", "help");
try {
if (abort == true) { return 0; }
-
- int count = 1;
//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; }
+ }
}
}
//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;
-
+
//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))) {
+ while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
process(lookup);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
- userLines.erase(count);
}
if ((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);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
}
-
-
lastLabel = lookup[0]->getLabel();
//prevent memory leak
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors();
- count++;
}
//output error messages about any remaining user labels
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
lookup = input->getSharedRAbundVectors(lastLabel);
mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
projects / mothur.git / blobdiff