Minor edits

mothur · 5562475076351a4df206eb7310db085cf041aa33 · mothur-westcott committed Feb 16, 2017 · Feb 16, 2017 · 5562475
1 parent 58430e4
commit 5562475076351a4df206eb7310db085cf041aa33
Unified Split

Showing with 33 additions and 28 deletions.

+9 −4 source/commands/makecontigscommand.cpp

+2 −4 source/commands/pcrseqscommand.cpp

+2 −1 source/commands/renamefilecommand.cpp

+4 −6 source/engine.cpp

+16 −13 source/mothurout.cpp
diff --git a/source/commands/makecontigscommand.cpp b/source/commands/makecontigscommand.cpp
@@ -825,6 +825,10 @@ unsigned long long MakeContigsCommand::processSingleFileOption(map<string, int>&
 //**********************************************************************************************************************
 unsigned long long MakeContigsCommand::processMultipleFileOption(map<string, int>& totalGroupCounts, vector<string>& theseOutputFileNames, map<string, string>& theseAllFileNames) {
     try {
+        
+        //read file
+        vector< vector<string> > fileInputs = readFileNames(file);  if (m->control_pressed) { return 0; }
+        
         unsigned long long numReads = 0;
         
         map<string, string> cvars;
@@ -861,10 +865,6 @@ unsigned long long MakeContigsCommand::processMultipleFileOption(map<string, int
         theseOutputFileNames.push_back(compositeQualFile);
         theseOutputFileNames.push_back(compositeMisMatchFile);
         
-        
-        //read file
-        vector< vector<string> > fileInputs = readFileNames(file);
-        
         if (gz) {
             numReads = createProcessesGroups(fileInputs, compositeGroupFile, compositeFastaFile, compositeScrapFastaFile, compositeQualFile, compositeScrapQualFile, compositeMisMatchFile, totalGroupCounts, theseAllFileNames); theseOutputFileNames.push_back(compositeGroupFile);
         }else {
@@ -2976,6 +2976,9 @@ vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
             
             bool skip = false;
             string line = m->getline(in);  m->gobble(in);
+            
+            if (m->debug) {  m->mothurOut("[DEBUG]: " + line +"\n");  }
+            
             vector<string> pieces = m->splitWhiteSpace(line);
             
             string group = "";
@@ -3267,6 +3270,8 @@ vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
             gz = true;
         }else { gz = false; }
         
+        if (files.size() == 0) { m->control_pressed = true; }
+        
         return files;
     }
     catch(exception& e) {
diff --git a/source/commands/pcrseqscommand.cpp b/source/commands/pcrseqscommand.cpp
@@ -1161,16 +1161,14 @@ int PcrSeqsCommand::readGroup(set<string> names){
 		while(!in.eof()){
 			if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 			
-			in >> name;				//read from first column
-			in >> group;			//read from second column
+			in >> name;		m->gobble(in);		//read from first column
+			in >> group;	m->gobble(in);		//read from second column
 			
 			//if this name is in the accnos file
 			if (names.count(name) == 0) {
 				wroteSomething = true;
 				out << name << '\t' << group << endl;
 			}else {  removedCount++;  }
-            
-			m->gobble(in);
 		}
 		in.close();
 		out.close();
diff --git a/source/commands/renamefilecommand.cpp b/source/commands/renamefilecommand.cpp
@@ -469,7 +469,8 @@ RenameFileCommand::RenameFileCommand(string option)  {
             if (outputfile == "not found") {
                 if (!mothurGenerated) { m->mothurOut("[ERROR]: you must enter an output file name"); m->mothurOutEndLine();  abort=true; }
                 outputfile = "";
-            }else { mothurGenerated=false; }
+            }else { mothurGenerated=false; if (outputDir != "") { outputfile = outputDir + m->getSimpleName(outputfile);  } }
+            
             
             if ((!mothurGenerated) && (numFiles > 1)) {
                 m->mothurOut("[ERROR]: You cannot use more than one file parameter unless mothur is generating the output filenames for you.\n"); abort= true;
diff --git a/source/engine.cpp b/source/engine.cpp
@@ -45,8 +45,8 @@ InteractEngine::InteractEngine(string path){
     #ifdef MOTHUR_FILES
     #else
         //set default location to search for files to mothur's executable location.  This will resolve issue of double-clicking on the executable which opens mothur and sets pwd to your home directory instead of the mothur directory and leads to "unable to find file" errors.
-        string tempDefault = path.substr(0, (path.find_last_of('m')));
-        if (tempDefault != "") { mout->setDefaultPath(tempDefault); }
+        //string tempDefault = path.substr(0, (path.find_last_of('m')));
+        mout->setDefaultPath(mout->mothurProgramPath);
     #endif
 }
 
@@ -184,8 +184,7 @@ BatchEngine::BatchEngine(string path, string batchFileName){
 #ifdef MOTHUR_FILES
 #else
         //set default location to search for files to mothur's executable location.  This will resolve issue of double-clicking on the executable which opens mothur and sets pwd to your home directory instead of the mothur directory and leads to "unable to find file" errors.
-        string tempDefault = path.substr(0, (path.find_last_of('m')));
-        if (tempDefault != "") { mout->setDefaultPath(tempDefault); }
+        mout->setDefaultPath(mout->mothurProgramPath);
 #endif
 
 				
@@ -321,8 +320,7 @@ ScriptEngine::ScriptEngine(string path, string commandString){
 #ifdef MOTHUR_FILES
 #else
         //set default location to search for files to mothur's executable location.  This will resolve issue of double-clicking on the executable which opens mothur and sets pwd to your home directory instead of the mothur directory and leads to "unable to find file" errors.
-        string tempDefault = path.substr(0, (path.find_last_of('m')));
-        if (tempDefault != "") { mout->setDefaultPath(tempDefault); }
+        mout->setDefaultPath(mout->mothurProgramPath);
 #endif
 
 				
diff --git a/source/mothurout.cpp b/source/mothurout.cpp
@@ -309,14 +309,16 @@ void MothurOut::setFileName(string filename)  {
 void MothurOut::setDefaultPath(string pathname)  {
 	try {
 	
-		//add / to name if needed
-		string lastChar = pathname.substr(pathname.length()-1);
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-			if (lastChar != "/") { pathname += "/"; }
-		#else
-			if (lastChar != "\\") { pathname += "\\"; }	
-		#endif
-		
+        if (pathname != "") {
+            //add / to name if needed
+            string lastChar = pathname.substr(pathname.length()-1);
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+            if (lastChar != "/") { pathname += "/"; }
+#else
+            if (lastChar != "\\") { pathname += "\\"; }
+#endif
+        }
+        
 		defaultPath = getFullPathName(pathname);
 		
 	}
@@ -329,14 +331,15 @@ void MothurOut::setDefaultPath(string pathname)  {
 void MothurOut::setBlastPath(string pathname)  {
     try {
         
-        //add / to name if needed
-        string lastChar = pathname.substr(pathname.length()-1);
+        if (pathname != "") {
+            //add / to name if needed
+            string lastChar = pathname.substr(pathname.length()-1);
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-        if (lastChar != "/") { pathname += "/"; }
+            if (lastChar != "/") { pathname += "/"; }
 #else
-        if (lastChar != "\\") { pathname += "\\"; }
+            if (lastChar != "\\") { pathname += "\\"; }
 #endif
-        
+        }
         blastPath = getFullPathName(pathname);
         
     }