X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validparameter.cpp;h=1faa651cd85dea92784a7dcc20cfc1fd3a2a1a9d;hb=8f7164a88df624fd0a8d1eddbb3d744463cc9ecb;hp=d693bcb721184c251896c917328f9d9d07b3fc18;hpb=e189982e0a9b7352ad57cc38ccee675f128be22e;p=mothur.git

diff --git a/validparameter.cpp b/validparameter.cpp
index d693bcb..1faa651 100644
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -15,6 +15,20 @@ ValidParameters::ValidParameters() {
 	try {
 		m = MothurOut::getInstance();
 		initParameterRanges();
+		commandName = "";
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ValidParameters", "ValidParameters");
+		exit(1);
+	}
+}
+/***********************************************************************/
+
+ValidParameters::ValidParameters(string c) {
+	try {
+		m = MothurOut::getInstance();
+		initParameterRanges();
+		commandName = c;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ValidParameters", "ValidParameters");
@@ -197,7 +211,7 @@ 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;
@@ -209,23 +223,59 @@ 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 (commandName == "") { processors = 1; }
 				
 				if (pid == 0) {
 			#endif
 
-				ableToOpen = openInputFile(it->second, in);
+				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	
-					MPI_Bcast(&ableToOpen, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send ableToOPen
+					for(int i = 1; i < processors; i++) { 
+						MPI_Send(&ableToOpen, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+						
+						int length = container[parameter].length();
+						MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+						MPI_Send(&(container[parameter][0]), length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
+	
+					}
 				}else {
-					MPI_Bcast(&ableToOpen, 1, MPI_INT, 0, MPI_COMM_WORLD); //get ableToOPen
+					MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+					
+					int length;
+					MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+					//recieve container
+					char* tempBuf = new char[length];
+					MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
+					
+					container[parameter] = tempBuf;
+					if (container[parameter].length() > length) { container[parameter] = container[parameter].substr(0, length);  }
+					delete tempBuf;	
 				}
+				
 			#endif
 			
-				if (ableToOpen == 1) { return "not open"; }
+				if (ableToOpen == 1) { 
+					m->mothurOut("Unable to open " + container[parameter]); m->mothurOutEndLine();
+					return "not open"; 
+				}
 			}
 		}else { return "not found"; }
 		
@@ -262,12 +312,6 @@ 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);