working on unifrac parallelization

[mothur.git] / makegroupcommand.cpp

diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp
index f567fbda600cecf76338c9081e10d51a872ecbc3..1a2ffe65fd17c79cc28c6a1e7106012ad2e987c7 100644 (file)
--- a/makegroupcommand.cpp
+++ b/makegroupcommand.cpp
@@ -50,28 +50,36 @@ MakeGroupCommand::MakeGroupCommand(string option)  {
                        fastaFileName = validParameter.validFile(parameters, "fasta", false);
                        if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true;  }
                        else { 
-                               splitAtDash(fastaFileName, fastaFileNames);
+                               m->splitAtDash(fastaFileName, fastaFileNames);
                                
                                //go through files and make sure they are good, if not, then disregard them
                                for (int i = 0; i < fastaFileNames.size(); i++) {
                                        if (inputDir != "") {
-                                               string path = hasPath(fastaFileNames[i]);
+                                               string path = m->hasPath(fastaFileNames[i]);
                                                //if the user has not given a path then, add inputdir. else leave path alone.
                                                if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
                                        }
        
-                                       int ableToOpen;
                                        ifstream in;
-                                       
-                                       ableToOpen = openInputFile(fastaFileNames[i], in);
+                                       int ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
+                               
+                                       //if you can't open it, try default location
+                                       if (ableToOpen == 1) {
+                                               if (m->getDefaultPath() != "") { //default path is set
+                                                       string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
+                                                       m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
+                                                       fastaFileNames[i] = tryPath;
+                                               }
+                                       }
                                        in.close();
-
+                                       
                                        if (ableToOpen == 1) { 
+                                               m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
                                                //erase from file list
                                                fastaFileNames.erase(fastaFileNames.begin()+i);
                                                i--;
-                                       }else{  filename += getRootName(getSimpleName(fastaFileNames[i]));  }
-                                       
+                                       }else{  filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));  }
                                }
                                
                                filename += "groups";
@@ -82,7 +90,7 @@ MakeGroupCommand::MakeGroupCommand(string option)  {
                        
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { m->mothurOut("groups is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true;  }
-                       else { splitAtDash(groups, groupsNames);        }
+                       else { m->splitAtDash(groups, groupsNames);     }
 
                        if (groupsNames.size() != fastaFileNames.size()) { m->mothurOut("You do not have the same number of valid fastfile files as groups.  This could be because we could not open a fastafile."); m->mothurOutEndLine(); abort = true;  }
                }
@@ -123,16 +131,20 @@ int MakeGroupCommand::execute(){
                if (abort == true) {    return 0;       }
                
                ofstream out;
-               openOutputFile(filename, out);
+               m->openOutputFile(filename, out);
                
                for (int i = 0; i < fastaFileNames.size(); i++) {
                
+                       if (m->control_pressed) {  out.close(); remove(filename.c_str()); return 0; }
+                       
                        ifstream in;
-                       openInputFile(fastaFileNames[i], in);
+                       m->openInputFile(fastaFileNames[i], in);
                        
                        while (!in.eof()) {
                                
-                               Sequence seq(in); gobble(in);
+                               Sequence seq(in, "no align"); m->gobble(in);
+                               
+                               if (m->control_pressed) {  in.close(); out.close(); remove(filename.c_str()); return 0; }
                                
                                if (seq.getName() != "") {      out << seq.getName() << '\t' << groupsNames[i] << endl;         }
                        }