From: Sarah Westcott <mothur.westcott@gmail.com>
Date: Wed, 11 Apr 2012 15:35:07 +0000 (-0400)
Subject: fixed bug with windows version of trim.seqs when run with 1 processor. fixed file... 
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=eb4bb52af987ff4df7354d95d60cd763aec537e1

fixed bug with windows version of trim.seqs when run with 1 processor. fixed file output redirect for shhh.slows command.  modified mothur so that you can set input and output directories using the parameters in the command.
---

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 0c9504d..d81045e 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -304,7 +304,49 @@ CommandFactory::~CommandFactory(){
 	delete shellcommand;
 	delete pipecommand;
 }
+/***********************************************************/
 
+/***********************************************************/
+int CommandFactory::checkForRedirects(string optionString) {
+    try {
+        
+        int pos = optionString.find("outputdir");
+        if (pos != string::npos) { //user has set outputdir in command option string
+            string outputOption = "";
+            bool foundEquals = false;
+            for(int i=pos;i<optionString.length();i++){
+                if(optionString[i] == ',')       { break;               }		
+                else if(optionString[i] == '=')  { foundEquals = true;	}
+                if (foundEquals)       {   outputOption += optionString[i]; }
+            }
+            if(m->dirCheck(outputOption)){ 
+                setOutputDirectory(outputOption); 
+                m->mothurOut("Setting output directory to: " + outputOption); m->mothurOutEndLine();
+            }
+        }
+        
+        pos = optionString.find("inputdir");
+        if (pos != string::npos) { //user has set inputdir in command option string
+            string intputOption = "";
+            bool foundEquals = false;
+            for(int i=pos;i<optionString.length();i++){
+                if(optionString[i] == ',')       { break;               }		
+                else if(optionString[i] == '=')  { foundEquals = true;	}
+                if (foundEquals)       {   intputOption += optionString[i]; }
+            }
+            if(m->dirCheck(intputOption)){ 
+                setInputDirectory(intputOption); 
+                m->mothurOut("Setting input directory to: " + intputOption); m->mothurOutEndLine();
+            }
+        }
+        
+        return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "CommandFactory", "getCommand");
+		exit(1);
+	}
+}
 /***********************************************************/
 
 /***********************************************************/
@@ -313,7 +355,9 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 	try {
         
 		delete command;   //delete the old command
-		
+        
+        checkForRedirects(optionString);
+        		
 		//user has opted to redirect output from dir where input files are located to some other place
 		if (outputDir != "") { 
 			if (optionString != "") { optionString += ", outputdir=" + outputDir; }
@@ -463,6 +507,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 	try {
 		delete pipecommand;   //delete the old command
 		
+        checkForRedirects(optionString);
+        
 		//user has opted to redirect output from dir where input files are located to some other place
 		if (outputDir != "") { 
 			if (optionString != "") { optionString += ", outputdir=" + outputDir; }
diff --git a/commandfactory.hpp b/commandfactory.hpp
index 3c19e87..e95db80 100644
--- a/commandfactory.hpp
+++ b/commandfactory.hpp
@@ -48,6 +48,8 @@ private:
 	string outputDir, inputDir, logFileName;
 	bool append;
 	
+    int checkForRedirects(string);
+    
 	static CommandFactory* _uniqueInstance;
 	CommandFactory( const CommandFactory& ); // Disable copy constructor
 	void operator=( const CommandFactory& ); // Disable assignment operator
diff --git a/mothurout.cpp b/mothurout.cpp
index 98f5ce0..d5f1534 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -598,6 +598,48 @@ string MothurOut::getPathName(string longName){
 }
 /***********************************************************************/
 
+bool MothurOut::dirCheck(string& dirName){
+	try {
+        
+        string tag = "";
+        #ifdef USE_MPI
+            int pid; 
+            MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+		
+            tag = toString(pid);
+        #endif
+
+        //add / to name if needed
+        string lastChar = dirName.substr(dirName.length()-1);
+        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+        if (lastChar != "/") { dirName += "/"; }
+        #else
+        if (lastChar != "\\") { dirName += "\\"; }	
+        #endif
+
+        //test to make sure directory exists
+        dirName = getFullPathName(dirName);
+        string outTemp = dirName + tag + "temp";
+        ofstream out;
+        out.open(outTemp.c_str(), ios::trunc);
+        if(!out) {
+            mothurOut(dirName + " directory does not exist or is not writable."); mothurOutEndLine(); 
+        }else{
+            out.close();
+            mothurRemove(outTemp);
+            return true;
+        }
+        
+        return false;
+    }
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "dirCheck");
+		exit(1);
+	}	
+    
+}
+/***********************************************************************/
+
 string MothurOut::hasPath(string longName){
 	try {
 		string path = "";
diff --git a/mothurout.h b/mothurout.h
index e1c8222..0659e4e 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -73,6 +73,7 @@ class MothurOut {
 		
 		//functions from mothur.h
 		//file operations
+        bool dirCheck(string&); //completes path, appends appropriate / or \, makes sure dir is writable.
 		vector<unsigned long long> divideFile(string, int&);
 		int divideFile(string, int&, vector<string>&);
 		vector<unsigned long long> setFilePosEachLine(string, int&);
diff --git a/setdircommand.cpp b/setdircommand.cpp
index 081a306..55b752d 100644
--- a/setdircommand.cpp
+++ b/setdircommand.cpp
@@ -101,14 +101,6 @@ int SetDirectoryCommand::execute(){
 		
 		commandFactory = CommandFactory::getInstance();
 		
-		string tag = "";
-#ifdef USE_MPI
-		int pid; 
-		MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-		
-		tag = toString(pid);
-#endif
-		
 		m->mothurOut("Mothur's directories:"); m->mothurOutEndLine();
 		
 		//redirect output
@@ -120,27 +112,10 @@ int SetDirectoryCommand::execute(){
 			m->mothurOut("outputDir=" + output); m->mothurOutEndLine();  
 			commandFactory->setOutputDirectory(output);
 		}else {
-			//add / to name if needed
-			string lastChar = output.substr(output.length()-1);
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-				if (lastChar != "/") { output += "/"; }
-			#else
-				if (lastChar != "\\") { output += "\\"; }	
-			#endif
-			
-			//test to make sure directory exists
-			output = m->getFullPathName(output);
-			string outTemp = output + tag + "temp";
-			ofstream out;
-			out.open(outTemp.c_str(), ios::trunc);
-			if(!out) {
-				m->mothurOut(output + " directory does not exist or is not writable."); m->mothurOutEndLine(); 
-			}else{
-				out.close();
-				m->mothurRemove(outTemp);
-				m->mothurOut("outputDir=" + output); m->mothurOutEndLine();  
+            if (m->dirCheck(output)) {
+                m->mothurOut("outputDir=" + output); m->mothurOutEndLine();  
 				commandFactory->setOutputDirectory(output);
-			}
+            }
 		}
 		
 		//redirect input
@@ -152,28 +127,11 @@ int SetDirectoryCommand::execute(){
 			m->mothurOut("inputDir=" + input); m->mothurOutEndLine();  
 			commandFactory->setInputDirectory(input);
 		}else {
-			//add / to name if needed
-			string lastChar = input.substr(input.length()-1);
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-				if (lastChar != "/") { input += "/"; }
-			#else
-				if (lastChar != "\\") { input += "\\"; }	
-			#endif
-			
-			//test to make sure directory exists
-			input = m->getFullPathName(input);
-			string inTemp = input + tag + "temp";
-			ofstream in;
-			in.open(inTemp.c_str(), ios::trunc);
-			if(!in) {
-				m->mothurOut(input + " directory does not exist or is not writable."); m->mothurOutEndLine(); 
-			}else{
-				in.close();
-				m->mothurRemove(inTemp);
-				m->mothurOut("inputDir=" + input); m->mothurOutEndLine();  
+            if (m->dirCheck(input)) {
+                m->mothurOut("inputDir=" + input); m->mothurOutEndLine();  
 				commandFactory->setInputDirectory(input); 
-			}
-		}
+            }
+        }
 		
 		//set default
 		if (tempdefault == "clear") {  
@@ -194,28 +152,11 @@ int SetDirectoryCommand::execute(){
 			m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();  
 			m->setDefaultPath(tempdefault);
 		}else {
-			//add / to name if needed
-			string lastChar = tempdefault.substr(tempdefault.length()-1);
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-				if (lastChar != "/") { tempdefault += "/"; }
-			#else
-				if (lastChar != "\\") { tempdefault += "\\"; }	
-			#endif
-			
-			//test to make sure directory exists
-			tempdefault = m->getFullPathName(tempdefault);
-			string inTemp = tempdefault + tag + "temp";
-			ofstream in;
-			in.open(inTemp.c_str(), ios::trunc);
-			if(!in) {
-				m->mothurOut(tempdefault + " directory does not exist or is not writable."); m->mothurOutEndLine(); 
-			}else{
-				in.close();
-				m->mothurRemove(inTemp);
-				m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();  
-				m->setDefaultPath(tempdefault);
-			}
-		}
+            if (m->dirCheck(tempdefault)) {
+                m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();  
+				m->setDefaultPath(tempdefault); 
+            }
+        }
 
 		return 0;
 	}
diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 6ef9532..89d7828 100644
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -128,8 +128,10 @@ ShhherCommand::ShhherCommand(string option) {
 					if (path == "") {	parameters["file"] = inputDir + it->second;		}
 				}
 			}
-			
-			
+            
+            //if the user changes the output directory command factory will send this info to us in the output parameter 
+			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = "";	}
+            
 			//check for required parameters
 			flowFileName = validParameter.validFile(parameters, "flow", true);
 			flowFilesFileName = validParameter.validFile(parameters, "file", true);
@@ -146,13 +148,15 @@ ShhherCommand::ShhherCommand(string option) {
 			}
 			else{
 				ofstream temp;
-
+                
+                string thisoutputDir = m->hasPath(flowFilesFileName); //if user entered a file with a path then preserve it
+                
 				//flow.files = 9 character offset
-				compositeFASTAFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
+				compositeFASTAFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
 				m->openOutputFile(compositeFASTAFileName, temp);
 				temp.close();
 				
-				compositeNamesFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
+				compositeNamesFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
 				m->openOutputFile(compositeNamesFileName, temp);
 				temp.close();
 			}
@@ -214,17 +218,10 @@ ShhherCommand::ShhherCommand(string option) {
                 if (flowFileVector.size() == 0) {  m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
             }
             else{
+                outputDir += m->hasPath(flowFileName);
                 flowFileVector.push_back(flowFileName);
             }
-
-			
-			//if the user changes the output directory command factory will send this info to us in the output parameter 
-			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	
-				outputDir = "";	
-				outputDir += m->hasPath(flowFileName); //if user entered a file with a path then preserve it	
-			}
-			
-			
+		
 			//check for optional parameter and set defaults
 			// ...at some point should added some additional type checking...
 			string temp;
diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index b480702..9f8fafb 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -1190,9 +1190,8 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {
                 cout << fastaFilePos[startIndex] << '\t' << numSeqsPerProcessor << endl;
                 if (qfilename != "") {  qLines.push_back(linePair(qfileFilePos[startIndex], numSeqsPerProcessor)); }
             }
-        
-            if(qfilename == "")	{	qLines = lines;	} //files with duds
         }
+            if(qfilename == "")	{	qLines = lines;	} //files with duds
 			return 1;
 		
 		#endif