added compile time default path

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 2a210b01ad3a8fb0812c1877595028a851bdbee7..a20a383b6125e135fc1aefeec47e2bc6b892f1e9 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -107,7 +107,17 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                                        #endif
                                        
                                        ifstream in;
-                                       ableToOpen = openInputFile(fastaFileNames[i], in);
+                                       ableToOpen = openInputFile(fastaFileNames[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(fastaFileNames[i]);
+                                                       m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = openInputFile(tryPath, in, "noerror");
+                                                       fastaFileNames[i] = tryPath;
+                                               }
+                                       }
                                        in.close();
                                        
                                        #ifdef USE_MPI  
@@ -122,7 +132,7 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                                        #endif
                                        
                                        if (ableToOpen == 1) { 
-                                               m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine(); 
+                                               m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); 
                                                //erase from file list
                                                fastaFileNames.erase(fastaFileNames.begin()+i);
                                                i--;
@@ -168,7 +178,17 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                                        #endif
 
                                        ifstream in;
-                                       ableToOpen = openInputFile(namefileNames[i], in);
+                                       ableToOpen = openInputFile(namefileNames[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(namefileNames[i]);
+                                                       m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = openInputFile(tryPath, in, "noerror");
+                                                       namefileNames[i] = tryPath;
+                                               }
+                                       }
                                        in.close();
                                        
                                        #ifdef USE_MPI  
@@ -181,8 +201,14 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                                                }
                                                
                                        #endif
-                                       if (ableToOpen == 1) {  m->mothurOut("Unable to match name file with fasta file."); m->mothurOutEndLine(); abort = true;        }
                                        
+                                       if (ableToOpen == 1) { 
+                                               m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();  abort = true;
+                                               //erase from file list
+                                               namefileNames.erase(namefileNames.begin()+i);
+                                               i--;
+                                       }
+
                                }
                        }
 
@@ -213,7 +239,17 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                                        #endif
 
                                        ifstream in;
-                                       ableToOpen = openInputFile(groupfileNames[i], in);
+                                       ableToOpen = openInputFile(groupfileNames[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(groupfileNames[i]);
+                                                       m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = openInputFile(tryPath, in, "noerror");
+                                                       groupfileNames[i] = tryPath;
+                                               }
+                                       }
                                        in.close();
                                        
                                        #ifdef USE_MPI  
@@ -226,8 +262,13 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                                                }
                                                
                                        #endif
-                                       if (ableToOpen == 1) {  m->mothurOut("Unable to match group file with fasta file, not using " + groupfileNames[i] + "."); m->mothurOutEndLine(); groupfileNames[i] = "";        }
                                        
+                                       if (ableToOpen == 1) { 
+                                               m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); groupfileNames[i] = "";
+                                               //erase from file list
+                                               groupfileNames.erase(groupfileNames.begin()+i);
+                                               i--;
+                                       }
                                }
                        }