X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validparameter.cpp;h=7855ddedd11f05b8e8c628e2d5c49c82be646a9b;hb=ec1b5bc7460ac8ad40f54f0729900d9ed98e7292;hp=50cd4e316186847b350a13b465f6d032ed91fcb8;hpb=dd173a49e37f6bae73a63c32dd7c98d317bb4a79;p=mothur.git

diff --git a/validparameter.cpp b/validparameter.cpp
index 50cd4e3..7855dde 100644
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -214,7 +214,7 @@ 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);
@@ -232,20 +232,35 @@ string ValidParameters::validFile(map<string, string>& container, string paramet
 				
 				if (pid == 0) {
 			#endif
-
+				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() + m->getSimpleName(it->second);
 						m->mothurOut("Unable to open " + it->second + ". Trying default " + tryPath); m->mothurOutEndLine();
-						ableToOpen = m->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++) { 
@@ -276,6 +291,18 @@ string ValidParameters::validFile(map<string, string>& container, string paramet
 					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"; }
+				}
 			}
 		}else { return "not found"; }