added path search for lookup file in shhh.seqs

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index f7c3e59714f4109398f97fb67d8dcb908a1ae9fd..459dca300f525b3d642ac5620f8f9c1c3e07426a 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -31,7 +31,7 @@ vector<string> ShhherCommand::setParameters(){
        try {
                CommandParameter pflow("flow", "InputTypes", "", "", "none", "fileflow", "none",false,false); parameters.push_back(pflow);
                CommandParameter pfile("file", "InputTypes", "", "", "none", "fileflow", "none",false,false); parameters.push_back(pfile);
-               CommandParameter plookup("lookup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plookup);
+               CommandParameter plookup("lookup", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plookup);
                CommandParameter pcutoff("cutoff", "Number", "", "0.01", "", "", "",false,false); parameters.push_back(pcutoff);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
                CommandParameter pmaxiter("maxiter", "Number", "", "1000", "", "", "",false,false); parameters.push_back(pmaxiter);
@@ -187,9 +187,74 @@ ShhherCommand::ShhherCommand(string option) {
                        // ...at some point should added some additional type checking...
                        string temp;
                        temp = validParameter.validFile(parameters, "lookup", true);
-                       if (temp == "not found")        {       lookupFileName = "LookUp_Titanium.pat"; }
-                       else if(temp == "not open")     {       abort = true;                   } 
-                       else                                            {       lookupFileName = temp;  }
+                       if (temp == "not found")        {       
+                               lookupFileName = "LookUp_Titanium.pat"; 
+                               
+                               int ableToOpen;
+                               ifstream in;
+                               ableToOpen = m->openInputFile(lookupFileName, in, "noerror");
+                               in.close();     
+                               
+                               //if you can't open it, try input location
+                               if (ableToOpen == 1) {
+                                       if (inputDir != "") { //default path is set
+                                               string tryPath = inputDir + lookupFileName;
+                                               m->mothurOut("Unable to open " + lookupFileName + ". Trying input directory " + tryPath); m->mothurOutEndLine();
+                                               ifstream in2;
+                                               ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+                                               in2.close();
+                                               lookupFileName = tryPath;
+                                       }
+                               }
+                               
+                               //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(lookupFileName);
+                                               m->mothurOut("Unable to open " + lookupFileName + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                               ifstream in2;
+                                               ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+                                               in2.close();
+                                               lookupFileName = tryPath;
+                                       }
+                               }
+                               
+                               //if you can't open it its not in current working directory or inputDir, try mothur excutable location
+                               if (ableToOpen == 1) {
+                                       string exepath = m->argv;
+                                       string tempPath = exepath;
+                                       for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
+                                       exepath = exepath.substr(0, (tempPath.find_last_of('m')));
+                                       
+                                       string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
+                                       m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
+                                       ifstream in2;
+                                       ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+                                       in2.close();
+                                       lookupFileName = tryPath;
+                               }
+                               
+                               if (ableToOpen == 1) {  m->mothurOut("Unable to open " + lookupFileName + "."); m->mothurOutEndLine(); abort=true;  }
+                       }
+                       else if(temp == "not open")     {       
+                               
+                               lookupFileName = validParameter.validFile(parameters, "lookup", false);
+                               
+                               //if you can't open it its not inputDir, try mothur excutable location
+                               string exepath = m->argv;
+                               string tempPath = exepath;
+                               for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
+                               exepath = exepath.substr(0, (tempPath.find_last_of('m')));
+                                       
+                               string tryPath = m->getFullPathName(exepath) + lookupFileName;
+                               m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
+                               ifstream in2;
+                               int ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+                               in2.close();
+                               lookupFileName = tryPath;
+                               
+                               if (ableToOpen == 1) {  m->mothurOut("Unable to open " + lookupFileName + "."); m->mothurOutEndLine(); abort=true;  }
+                       }else                                           {       lookupFileName = temp;  }
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);