pat's slight modifications to trim.seqs

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 2d29ee3f668ee1817cb71c82189c2a8c6f61cf00..e82a9e8d4446430d125c168d66e0ababc8651655 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -197,7 +197,7 @@ bool ValidParameters::isValidParameter(string parameter, vector<string> cParams,
 
 /******************************************************/
 
-string ValidParameters::validFile(map<string, string> container, string parameter, bool isFile) {
+string ValidParameters::validFile(map<string, string>& container, string parameter, bool isFile) {
        try {
                int ableToOpen;
                ifstream in;
@@ -209,21 +209,43 @@ string ValidParameters::validFile(map<string, string> container, string paramete
                        if(isFile == true) {
                        
                        #ifdef USE_MPI  
-                               int pid;
+                               int pid, processors;
+                               MPI_Status status;
                                MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+                               MPI_Comm_size(MPI_COMM_WORLD, &processors);
                                
                                if (pid == 0) {
                        #endif
 
-                               ableToOpen = openInputFile(it->second, in);
-
-                               if (ableToOpen == 1) { return "not open"; }
-                               in.close();
+                               ableToOpen = openInputFile(it->second, 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() + getSimpleName(it->second);
+                                               m->mothurOut("Unable to open " + it->second + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                               ableToOpen = openInputFile(tryPath, in, "noerror");
+                                               container[parameter] = tryPath;
+                                       }
+                               }
+                               
+                               in.close();
+
                        #ifdef USE_MPI  
+                                       for(int i = 1; i < processors; i++) { 
+                                               MPI_Send(&ableToOpen, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+                                       }
+                               }else {
+                                       MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
                                }
+                               
+                               MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
                        #endif
-
+                       
+                               if (ableToOpen == 1) { 
+                                       m->mothurOut("Unable to open " + container[parameter]); m->mothurOutEndLine();
+                                       return "not open"; 
+                               }
                        }
                }else { return "not found"; }
                
@@ -260,12 +282,6 @@ void ValidParameters::initParameterRanges() {
                string itersArray[] = {">=","10", "<","NA", "between"};
                parameterRanges["iters"] = addParameters(itersArray, rangeSize);
 
-               string freqArray[] = {">=","1", "<","NA", "between"};
-               parameterRanges["freq"] = addParameters(freqArray, rangeSize);
-
-               //string lineArray[] = {">=","1", "<","NA", "between"};
-               //parameterRanges["line"] = addParameters(lineArray, rangeSize);
-
                string abundArray[] = {">=","5", "<","NA", "between"};
                parameterRanges["abund"] = addParameters(abundArray, rangeSize);