added compile time default path

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 885aadc9c05eb34ba16d0dca6e48322dc452e5af..37ab0ba8fe01887c026311b7f03838b67dba563f 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -54,11 +54,21 @@ SffInfoCommand::SffInfoCommand(string option)  {
                                        }
        
                                        ifstream in;
-                                       int ableToOpen = openInputFile(filenames[i], in);
+                                       int ableToOpen = openInputFile(filenames[i], 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(filenames[i]);
+                                                       m->mothurOut("Unable to open " + filenames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = openInputFile(tryPath, in, "noerror");
+                                                       filenames[i] = tryPath;
+                                               }
+                                       }
                                        in.close();
                                        
                                        if (ableToOpen == 1) { 
-                                               m->mothurOut(filenames[i] + " will be disregarded."); m->mothurOutEndLine(); 
+                                               m->mothurOut("Unable to open " + filenames[i] + ". It will be disregarded."); m->mothurOutEndLine();
                                                //erase from file list
                                                filenames.erase(filenames.begin()+i);
                                                i--;
@@ -84,11 +94,21 @@ SffInfoCommand::SffInfoCommand(string option)  {
                                        }
        
                                        ifstream in;
-                                       int ableToOpen = openInputFile(accnosFileNames[i], in);
+                                       int ableToOpen = openInputFile(accnosFileNames[i], 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(accnosFileNames[i]);
+                                                       m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = openInputFile(tryPath, in, "noerror");
+                                                       accnosFileNames[i] = tryPath;
+                                               }
+                                       }
                                        in.close();
                                        
                                        if (ableToOpen == 1) { 
-                                               m->mothurOut(accnosFileNames[i] + " will be disregarded."); m->mothurOutEndLine(); 
+                                               m->mothurOut("Unable to open " + accnosFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
                                                //erase from file list
                                                accnosFileNames.erase(accnosFileNames.begin()+i);
                                                i--;