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

[mothur.git] / rarefactsharedcommand.cpp

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index fecf972c7ec99f80dda6f921706c6916a9d1679f..a312df07ec1508d1d257bc443ac895467be61525 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -62,7 +62,27 @@ string RareFactSharedCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string RareFactSharedCommand::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 == "sharedrarefaction") {  outputFileName =  "shared.rarefaction"; }
+            else if (type == "sharedr_nseqs") {  outputFileName =  "shared.r_nseqs"; }
+            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, "RareFactSharedCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 RareFactSharedCommand::RareFactSharedCommand(){        
        try {
@@ -286,11 +306,11 @@ int RareFactSharedCommand::process(GroupMap& designMap, string thisSet){
                for (int i=0; i<Estimators.size(); i++) {
                        if (validCalculator.isValidCalculator("sharedrarefaction", Estimators[i]) == true) { 
                                if (Estimators[i] == "sharedobserved") { 
-                                       rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
-                                       outputNames.push_back(fileNameRoot+"shared.rarefaction"); outputTypes["sharedrarefaction"].push_back(fileNameRoot+"shared.rarefaction");
+                                       rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+getOutputFileNameTag("sharedrarefaction"), "")));
+                                       outputNames.push_back(fileNameRoot+getOutputFileNameTag("sharedrarefaction")); outputTypes["sharedrarefaction"].push_back(fileNameRoot+getOutputFileNameTag("sharedrarefaction"));
                                }else if (Estimators[i] == "sharednseqs") { 
-                                       rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
-                                       outputNames.push_back(fileNameRoot+"shared.r_nseqs"); outputTypes["sharedr_nseqs"].push_back(fileNameRoot+"shared.r_nseqs");
+                                       rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+getOutputFileNameTag("sharedr_nseqs"), "")));
+                                       outputNames.push_back(fileNameRoot+getOutputFileNameTag("sharedr_nseqs")); outputTypes["sharedr_nseqs"].push_back(fileNameRoot+getOutputFileNameTag("sharedr_nseqs"));
                                }
                        }
             file2Group[outputNames.size()-1] = thisSet;