chimeras, fix to sabundvector and sharedsabundvector that caused getRabundVector...

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 89f57eb5ca1aa80bf0d72d5aa47fcdabca6d8ef2..1fe2300387a96e81500a0b41c76190df02aba935 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -11,14 +11,17 @@
 
 //**********************************************************************************************************************
 
-SharedCommand::SharedCommand(){
+SharedCommand::SharedCommand(string o) : outputDir(o) {
        try {
                globaldata = GlobalData::getInstance();
                
                //getting output filename
                filename = globaldata->inputFileName;
-               filename = getRootName(filename);
+               if (outputDir == "") { outputDir += hasPath(filename); }
+               
+               filename = outputDir + getRootName(getSimpleName(filename));
                filename = filename + "shared";
+               
                openOutputFile(filename, out);
                pickedGroups = false;
                
@@ -41,7 +44,7 @@ SharedCommand::SharedCommand(){
                }
                
                //set fileroot
-               fileroot = getRootName(globaldata->getListFile());
+               fileroot = outputDir + getRootName(getSimpleName(globaldata->getListFile()));
                
                //clears file before we start to write to it below
                for (int i=0; i<groups.size(); i++) {
@@ -62,7 +65,7 @@ int SharedCommand::execute(){
                //lookup.clear();
                string errorOff = "no error";
                //errorOff = "";
-                       
+               
                //read in listfile
                read = new ReadOTUFile(globaldata->inputFileName);      
                read->read(&*globaldata); 
@@ -98,7 +101,7 @@ int SharedCommand::execute(){
                                groups += globaldata->Groups[i] + ".";
                        }
                
-                       string newGroupFile = getRootName(globaldata->inputFileName) + groups + "groups";
+                       string newGroupFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + groups + "groups";
                        ofstream outGroups;
                        openOutputFile(newGroupFile, outGroups);
                
@@ -197,6 +200,13 @@ int SharedCommand::execute(){
                }
 
                
+               //change format to shared  to speed up commands
+               globaldata->setFormat("sharedfile");
+               globaldata->setListFile("");
+               globaldata->setGroupFile("");
+               globaldata->setSharedFile(filename);
+
+               
                return 0;
        }
        catch(exception& e) {
@@ -270,7 +280,7 @@ void SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
 void SharedCommand::createMisMatchFile() {
        try {
                ofstream outMisMatch;
-               string outputMisMatchName = getRootName(globaldata->inputFileName);
+               string outputMisMatchName = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
                
                //you have sequences in your list file that are not in your group file
                if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) { 
@@ -288,10 +298,10 @@ void SharedCommand::createMisMatchFile() {
                                        string name = names.substr(0,names.find_first_of(','));
                                        names = names.substr(names.find_first_of(',')+1, names.length());
                                        string group = groupMap->getGroup(name);
-       cout << name << endl;                           
+                               
                                        if(group == "not found") {      outMisMatch << name << endl;  }
                                }
-       cout << names << endl;                  
+                       
                                //get last name
                                string group = groupMap->getGroup(names);
                                if(group == "not found") {      outMisMatch << names << endl;  }