added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / catchallcommand.cpp

diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index 329b56a2c24dcf024ca66cab0f160b76438c0922..1cfd4154686cd4884e275f4c3ea8c8ca3d5624d3 100644 (file)
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -49,6 +49,27 @@ string CatchAllCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+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;
@@ -236,7 +257,7 @@ int CatchAllCommand::execute() {
                        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"); } 
@@ -283,10 +304,10 @@ int CatchAllCommand::execute() {
                                                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"); }
                     
@@ -336,10 +357,10 @@ int CatchAllCommand::execute() {
                                                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"); }
@@ -410,11 +431,10 @@ int CatchAllCommand::execute() {
                                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);
                 
@@ -491,7 +511,7 @@ string CatchAllCommand::combineSummmary(vector<string>& outputNames) {
        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);