adding more error checking for list and group files. outputs missing.names or missin...

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 717d3aaba162daad61bfcd053f672a3f5f685382..aba07b2a8d97503913cff85fedde5d8562ca4f5c 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -67,6 +67,8 @@ int SharedCommand::execute(){
                if (SharedList->getNumSeqs() != groupMap->getNumSeqs()) {  
                        mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); mothurOutEndLine(); 
                        
+                       createMisMatchFile();
+                       
                        //delete memory
                        for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
                                delete it3->second;
@@ -74,7 +76,7 @@ int SharedCommand::execute(){
                        delete SharedList;
                        globaldata->gSharedList = NULL;
                        
-                       return(0); 
+                       return 1; 
                }
                
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
@@ -181,6 +183,89 @@ void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
                exit(1);
        }
 }
+//**********************************************************************************************************************
+void SharedCommand::createMisMatchFile() {
+       try {
+               ofstream outMisMatch;
+               string outputMisMatchName = getRootName(globaldata->inputFileName);
+               
+               //you have sequences in your list file that are not in your group file
+               if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) { 
+                       outputMisMatchName += "missing.group";
+                       mothurOut("For a list of names that are in your list file and not in your group file, please refer to " + outputMisMatchName + "."); mothurOutEndLine();
+                       
+                       openOutputFile(outputMisMatchName, outMisMatch);
+                       
+                       //go through list and if group returns "not found" output it
+                       for (int i = 0; i < SharedList->getNumBins(); i++) {
+                       
+                               string names = SharedList->get(i); 
+                               
+                               while (names.find_first_of(',') != -1) { 
+                                       string name = names.substr(0,names.find_first_of(','));
+                                       names = names.substr(names.find_first_of(',')+1, names.length());
+                                       string group = groupMap->getGroup(name);
+                                       
+                                       if(group == "not found") {      outMisMatch << name << endl;  }
+                               }
+                               
+                               //get last name
+                               string group = groupMap->getGroup(names);
+                               if(group == "not found") {      outMisMatch << names << endl;  }                                
+                       }
+                       
+                       outMisMatch.close();
+                       
+               
+               }else {//you have sequences in your group file that are not in you list file
+                       
+                       outputMisMatchName += "missing.name";
+                       mothurOut("For a list of names that are in your group file and not in your list file, please refer to " + outputMisMatchName + "."); mothurOutEndLine();
+                       
+                       map<string, string> namesInList;
+                       
+                       //go through listfile and get names
+                       for (int i = 0; i < SharedList->getNumSeqs(); i++) {
+                               
+                               string names = SharedList->get(i); 
+                               
+                               while (names.find_first_of(',') != -1) { 
+                                       string name = names.substr(0,names.find_first_of(','));
+                                       names = names.substr(names.find_first_of(',')+1, names.length());
+                                       
+                                       namesInList[name] = name;
+                               }
+                               
+                               //get last name
+                               namesInList[names] = names;                             
+                       }
+                       
+                       //get names of sequences in groupfile
+                       vector<string> seqNames = groupMap->getNamesSeqs();
+               
+                       map<string, string>::iterator itMatch;
+                       
+                       openOutputFile(outputMisMatchName, outMisMatch);
+                       
+                       //loop through names in seqNames and if they aren't in namesIn list output them
+                       for (int i = 0; i < seqNames.size(); i++) {
+                               
+                               itMatch = namesInList.find(seqNames[i]);
+                               
+                               if (itMatch == namesInList.end()) {
+                               
+                                       outMisMatch << seqNames[i] << endl; 
+                               }
+                       }               
+                       outMisMatch.close();
+               }
+ 
+       }
+       catch(exception& e) {
+               errorOut(e, "SharedCommand", "createMisMatchFile");
+               exit(1);
+       }
+}
 
 //**********************************************************************************************************************