X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=validparameter.cpp;h=7d1af2551c7a6717c1d3ea807af0e56de0fc218e;hp=e82a9e8d4446430d125c168d66e0ababc8651655;hb=615301e57c25e241356a9c2380648d117709458d;hpb=80c3fe03a8fd1635d3ad7918ff00beb973449f50

diff --git a/validparameter.cpp b/validparameter.cpp
index e82a9e8..7d1af25 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");
@@ -55,7 +69,7 @@ bool ValidParameters::isValidParameter(string parameter, vector<string> cParams,
 		vector<string> range = parameterRanges[parameter];
 		
 		vector<string> values;
-		splitAtDash(value, values);
+		m->splitAtDash(value, values);
 		
 		for(int i = 0; i < values.size(); i++) {
 			value = values.at(i);
@@ -200,13 +214,17 @@ bool ValidParameters::isValidParameter(string parameter, vector<string> cParams,
 string ValidParameters::validFile(map<string, string>& container, string parameter, bool isFile) {
 	try {
 		int ableToOpen;
-		ifstream in;
+		
 		map<string, string>::iterator it;
 		
 		it = container.find(parameter);
 		if(it != container.end()){ //no parameter given
 
 			if(isFile == true) {
+				
+				int pos = (it->second).find(".tx.");
+				if (pos != string::npos) { m->sharedHeaderMode = "tax"; }
+				else { m->sharedHeaderMode = "otu"; }
 			
 			#ifdef USE_MPI	
 				int pid, processors;
@@ -214,38 +232,89 @@ string ValidParameters::validFile(map<string, string>& container, string paramet
 				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, "noerror");
+				ifstream in;
+				ableToOpen = m->openInputFile(it->second, in, "noerror");
+				in.close();
 				
 				//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);
+						string tryPath = m->getDefaultPath() + m->getSimpleName(it->second);
 						m->mothurOut("Unable to open " + it->second + ". Trying default " + tryPath); m->mothurOutEndLine();
-						ableToOpen = openInputFile(tryPath, in, "noerror");
+						ifstream in2;
+						ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+						in2.close();
 						container[parameter] = tryPath;
 					}
 				}
 				
-				in.close();
+				//if you can't open it, try default location
+				if (ableToOpen == 1) {
+					if (m->getOutputDir() != "") { //default path is set
+						string tryPath = m->getOutputDir() + m->getSimpleName(it->second);
+						m->mothurOut("Unable to open " + it->second + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+						ifstream in2;
+						ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+						container[parameter] = tryPath;
+						in2.close();
+					}
+				}
+				
+				
 
 			#ifdef USE_MPI	
 					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_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;	
 				}
 				
-				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"; 
 				}
+				
+				//check phylip file to make sure its really phylip and not column
+				if ((it->first == "phylip") && (ableToOpen != 1)) {
+					ifstream inPhylip;
+					m->openInputFile(it->second, inPhylip);
+										
+					string numTest, name;
+					inPhylip >> numTest >> name;
+					inPhylip.close();
+					
+					if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ". I suspect you entered a column formatted file as a phylip file, aborting."); m->mothurOutEndLine(); return "not found"; }
+				}
+                
+                //check for blank file
+                if (ableToOpen != 1) {
+                    if (m->isBlank(container[parameter])) {
+                        m->mothurOut("[ERROR]: " + container[parameter] + " is blank, aborting."); m->mothurOutEndLine(); return "not found"; 
+                    }
+                }
+                    
 			}
 		}else { return "not found"; }
 		
@@ -279,7 +348,7 @@ void ValidParameters::initParameterRanges() {
 		string precisionArray[] = {">=","10", "<","NA", "between"};
 		parameterRanges["precision"] = addParameters(precisionArray, rangeSize);
 		
-		string itersArray[] = {">=","10", "<","NA", "between"};
+		string itersArray[] = {">=","1", "<","NA", "between"};
 		parameterRanges["iters"] = addParameters(itersArray, rangeSize);
 
 		string abundArray[] = {">=","5", "<","NA", "between"};