}
}
//**********************************************************************************************************************
+string CatchAllCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "csv") { outputFileName = "csv"; }
+ else if (type == "summary") { outputFileName = "catchall.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CatchAllCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
CatchAllCommand::CatchAllCommand(){
try {
abort = true; calledHelp = true;
set<string> processedLabels;
set<string> userLabels = labels;
- string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "catchall.summary";
+ string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + getOutputFileNameTag("summary");
summaryfilename = m->getFullPathName(summaryfilename);
if (m->debug) { m->mothurOut("[DEBUG]: Input File = " + inputFileNames[p] + ".\n[DEBUG]: inputdata address = " + toString(&input) + ".\n[DEBUG]: sabund address = " + toString(&sabund) + ".\n"); }
filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
- outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
- outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
- outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
- outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
+ outputNames.push_back(filename + "_Analysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_Analysis." + getOutputFileNameTag("csv"));
+ outputNames.push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv"));
+ outputNames.push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv"));
+ outputNames.push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv"));
if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
- outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
- outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
- outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
- outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
+ outputNames.push_back(filename + "_Analysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_Analysis." + getOutputFileNameTag("csv"));
+ outputNames.push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv"));
+ outputNames.push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv"));
+ outputNames.push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv"));
if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
- outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
- outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
- outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
- outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
- if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
+ outputNames.push_back(filename + "_Analysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_Analysis." + getOutputFileNameTag("csv"));
+ outputNames.push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv"));
+ outputNames.push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv"));
+ outputNames.push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
try {
ofstream out;
- string combineFileName = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
+ string combineFileName = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("summary");
//open combined file
m->openOutputFile(combineFileName, out);