fixed bug with aligner and longest base. added deunique.seqs command.

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 1faa651cd85dea92784a7dcc20cfc1fd3a2a1a9d..cfe9d509112e921aef92c0cf914e10f6ca885079 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -69,7 +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);
@@ -233,14 +233,24 @@ string ValidParameters::validFile(map<string, string>& container, string paramet
                                if (pid == 0) {
                        #endif
 
-                               ableToOpen = openInputFile(it->second, in, "noerror");
+                               ableToOpen = m->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);
+                                               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");
+                                               ableToOpen = m->openInputFile(tryPath, in, "noerror");
+                                               container[parameter] = tryPath;
+                                       }
+                               }
+                               
+                               //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();
+                                               ableToOpen = m->openInputFile(tryPath, in, "noerror");
                                                container[parameter] = tryPath;
                                        }
                                }
@@ -309,7 +319,7 @@ 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"};