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

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 8f05cfcc567a8f0e5d9cbdc867bf15bebd887f11..f3330f7672e1fbaef8300f70b88c625ac9857b1c 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -52,6 +52,29 @@ string SharedCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string SharedCommand::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 == "shared")            {   outputFileName =  "shared";   }
+            else if (type == "rabund")    {   outputFileName =  "rabund";   }
+            else if (type == "group")        {   outputFileName =  "groups";   }
+            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, "SharedCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+
 //**********************************************************************************************************************
 SharedCommand::SharedCommand(){        
        try {
@@ -131,6 +154,10 @@ SharedCommand::SharedCommand(string option)  {
                                 }
                         }
                         
+             vector<string> tempOutNames;
+             outputTypes["rabund"] = tempOutNames;
+             outputTypes["shared"] = tempOutNames;
+             outputTypes["group"] = tempOutNames;
                         
                         //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 = ""; }
@@ -221,7 +248,7 @@ int SharedCommand::execute(){
                if (outputDir == "") { outputDir += m->hasPath(filename); }
                
                filename = outputDir + m->getRootName(m->getSimpleName(filename));
-               filename = filename + "shared";
+               filename = filename + getOutputFileNameTag("shared");
                outputNames.push_back(filename); outputTypes["shared"].push_back(filename);
                
         if (listfile != "") {  createSharedFromListGroup(filename);  }
@@ -762,9 +789,9 @@ int SharedCommand::createSharedFromListGroup(string filename) {
         
         //clears file before we start to write to it below
         for (int i=0; i<Groups.size(); i++) {
-            m->mothurRemove((fileroot + Groups[i] + ".rabund"));
-            outputNames.push_back((fileroot + Groups[i] + ".rabund"));
-            outputTypes["rabund"].push_back((fileroot + Groups[i] + ".rabund"));
+            m->mothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund")));
+            outputNames.push_back((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund")));
+            outputTypes["rabund"].push_back((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund")));
         }
         
         string errorOff = "no error";
@@ -781,7 +808,7 @@ int SharedCommand::createSharedFromListGroup(string filename) {
             delete SharedList; delete groupMap; 
             for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
             out.close(); m->mothurRemove(filename); 
-            for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + ".rabund"));                }
+            for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund")));             }
             return 0; 
         }
         
@@ -818,7 +845,7 @@ int SharedCommand::createSharedFromListGroup(string filename) {
                 }
             }else { groups = "merge"; }
             
-            string newGroupFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + groups + "groups";
+            string newGroupFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + groups + getOutputFileNameTag("group");
             outputTypes["group"].push_back(newGroupFile); 
             outputNames.push_back(newGroupFile);
             ofstream outGroups;
@@ -844,7 +871,7 @@ int SharedCommand::createSharedFromListGroup(string filename) {
                 delete SharedList; delete groupMap;
                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
                 out.close(); m->mothurRemove(filename); 
-                for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + ".rabund"));            }
+                for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund")));         }
                 return 0; 
             }
             
@@ -862,7 +889,7 @@ int SharedCommand::createSharedFromListGroup(string filename) {
                     for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
                     for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
                     out.close(); m->mothurRemove(filename); 
-                    for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + ".rabund"));                }
+                    for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund")));             }
                     return 0; 
                 }
                 
@@ -892,7 +919,7 @@ int SharedCommand::createSharedFromListGroup(string filename) {
                     for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
                     for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
                     out.close(); m->mothurRemove(filename); 
-                    for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + ".rabund"));                }
+                    for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund")));             }
                     return 0; 
                 }
                 
@@ -938,7 +965,7 @@ int SharedCommand::createSharedFromListGroup(string filename) {
                 delete groupMap;
                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;   }
                 out.close(); m->mothurRemove(filename); 
-                for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + ".rabund"));            }
+                for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund")));         }
                 return 0; 
             }
             
@@ -958,7 +985,7 @@ int SharedCommand::createSharedFromListGroup(string filename) {
                
         if (m->control_pressed) { 
             m->mothurRemove(filename); 
-            for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + ".rabund"));                }
+            for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund")));             }
             return 0; 
         }
 
@@ -987,7 +1014,7 @@ void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup, ofst
                                Groups.push_back(thislookup[i]->getGroup());
                                
                                RAbundVector rav = thislookup[i]->getRAbundVector();
-                               m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
+                               m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + "." + getOutputFileNameTag("rabund"), *(filehandles[thislookup[i]->getGroup()]));
                                rav.print(*(filehandles[thislookup[i]->getGroup()]));
                                (*(filehandles[thislookup[i]->getGroup()])).close();
                        }
@@ -1015,7 +1042,7 @@ void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup, ofst
                                        Groups.push_back((myIt->second)->getGroup());
                                
                                        RAbundVector rav = (myIt->second)->getRAbundVector();
-                                       m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));
+                                       m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + "." + getOutputFileNameTag("rabund"), *(filehandles[(myIt->second)->getGroup()]));
                                        rav.print(*(filehandles[(myIt->second)->getGroup()]));
                                        (*(filehandles[(myIt->second)->getGroup()])).close();
                                }else{