X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=c89d580d64f6c69a6afedada448143ae114453a3;hb=43ed0accfbc2852849e104ff7eccdd2c42acd4ec;hp=001e8c48a8932374d7266b4e6097036c5b2ed9ac;hpb=7f0cae4f4853cc3f12bc751ee06ea31c7c97496e;p=mothur.git

diff --git a/mothurout.cpp b/mothurout.cpp
index 001e8c4..c89d580 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -143,7 +143,7 @@ void MothurOut::setDefaultPath(string pathname)  {
 	
 		//add / to name if needed
 		string lastChar = pathname.substr(pathname.length()-1);
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			if (lastChar != "/") { pathname += "/"; }
 		#else
 			if (lastChar != "\\") { pathname += "\\"; }	
@@ -212,8 +212,8 @@ void MothurOut::mothurOut(string output) {
 			if (pid == 0) { //only one process should output to screen
 		#endif
 		
-		cout << output;
 		out << output;
+        logger() << output;
 		
 		#ifdef USE_MPI
 			}
@@ -234,8 +234,8 @@ void MothurOut::mothurOutEndLine() {
 			if (pid == 0) { //only one process should output to screen
 		#endif
 		
-		cout << endl;
 		out << endl;
+        logger() << endl;
 		
 		#ifdef USE_MPI
 			}
@@ -257,13 +257,15 @@ void MothurOut::mothurOut(string output, ofstream& outputFile) {
 		if (pid == 0) { //only one process should output to screen
 #endif
 			
-			cout << output;
+			
 			out << output;
 			outputFile << output;
+            logger() << output;
 			
 #ifdef USE_MPI
 		}
 #endif
+        
 	}
 	catch(exception& e) {
 		errorOut(e, "MothurOut", "MothurOut");
@@ -280,9 +282,9 @@ void MothurOut::mothurOutEndLine(ofstream& outputFile) {
 		if (pid == 0) { //only one process should output to screen
 #endif
 			
-			cout << endl;
 			out << endl;
 			outputFile << endl;
+            logger() << endl;
 			
 #ifdef USE_MPI
 		}
@@ -332,7 +334,7 @@ void MothurOut::errorOut(exception& e, string object, string function) {
 //
 // On failure, returns 0.0, 0.0
 int MothurOut::mem_usage(double& vm_usage, double& resident_set) {
-  #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+  #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
   
 	   vm_usage     = 0.0;
 	   resident_set = 0.0;
@@ -504,7 +506,7 @@ string MothurOut::getline(ifstream& fileHandle) {
 }
 /***********************************************************************/
 
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #ifdef USE_COMPRESSION
 inline bool endsWith(string s, const char * suffix){
   size_t suffixLength = strlen(suffix);
@@ -518,7 +520,7 @@ string MothurOut::getRootName(string longName){
 	
 		string rootName = longName;
 
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #ifdef USE_COMPRESSION
     if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) {
       int pos = rootName.find_last_of('.');
@@ -673,7 +675,7 @@ string MothurOut::getFullPathName(string fileName){
 				
 		string cwd;
 		//get current working directory 
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)	
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)	
 			
 			if (path.find("~") != -1) { //go to home directory
 				string homeDir;
@@ -726,7 +728,7 @@ string MothurOut::getFullPathName(string fileName){
 					}else if (path[(pos-1)] == '/') { //you want the current working dir ./
 						path = path.substr(0, pos);
 					}else if (pos == 1) { break;  //you are at the end
-					}else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
+					}else { mothurOut("cannot resolve path for " +  fileName + "\n"); return fileName; }
 				}
 			
 				for (int i = index; i >= 0; i--) {
@@ -772,7 +774,7 @@ string MothurOut::getFullPathName(string fileName){
 					}else if (path[(pos-1)] == '\\') { //you want the current working dir ./
 						path = path.substr(0, pos);
 					}else if (pos == 1) { break;  //you are at the end
-					}else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
+					}else { mothurOut("cannot resolve path for " +  fileName + "\n"); return fileName; }
 				}
 			
 				for (int i = index; i >= 0; i--) {
@@ -796,7 +798,7 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
 	try {
 			//get full path name
 			string completeFileName = getFullPathName(fileName);
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #ifdef USE_COMPRESSION
       // check for gzipped or bzipped file
       if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
@@ -842,7 +844,7 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
 
 		//get full path name
 		string completeFileName = getFullPathName(fileName);
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #ifdef USE_COMPRESSION
   // check for gzipped or bzipped file
   if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
@@ -893,7 +895,7 @@ int MothurOut::renameFile(string oldName, string newName){
 		int exist = openInputFile(newName, inTest, "");
 		inTest.close();
 		
-	#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)		
+	#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)		
 		if (exist == 0) { //you could open it so you want to delete it
 			string command = "rm " + newName;
 			system(command.c_str());
@@ -920,7 +922,7 @@ int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
 	try { 
 	
 		string completeFileName = getFullPathName(fileName);
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #ifdef USE_COMPRESSION
     // check for gzipped file
     if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
@@ -996,7 +998,7 @@ string MothurOut::sortFile(string distFile, string outputDir){
 
 		
 		//if you can, use the unix sort since its been optimized for years
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			string command = "sort -n -k +3 " + distFile + " -o " + outfile;
 			system(command.c_str());
 		#else //you are stuck with my best attempt...
@@ -1151,7 +1153,7 @@ vector<unsigned long long> MothurOut::setFilePosEachLine(string filename, int& n
 					while(isspace(d) && (d != in.eof()))		{ d=in.get(); count++;}
 				}
 				positions.push_back(count-1);
-				cout << count-1 << endl;
+				//cout << count-1 << endl;
 			}
 			in.close();
 		
@@ -1199,7 +1201,7 @@ vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
 			fclose (pFile);
 		}
 		
-	#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+	#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				
 		//estimate file breaks
 		unsigned long long chunkSize = 0;
@@ -1477,6 +1479,26 @@ int MothurOut::getNumNames(string names){
 }
 /***********************************************************************/
 
+int MothurOut::getNumChar(string line, char c){
+	try {
+		int count = 0;
+		
+		if(line != ""){
+			for(int i=0;i<line.size();i++){
+				if(line[i] == c){
+					count++;
+				}
+			}
+		}
+		
+		return count;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "getNumChar");
+		exit(1);
+	}
+}
+/***********************************************************************/
 int MothurOut::mothurRemove(string filename){
 	try {
 		filename = getFullPathName(filename);
@@ -1494,6 +1516,84 @@ int MothurOut::mothurRemove(string filename){
 		exit(1);
 	}
 }
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, int& num){
+	try {
+		bool error = false;
+		
+		if (isNumeric1(item)) {
+			convert(item, num);
+		}else {
+			num = 0;
+			error = true;
+			mothurOut("[ERROR]: cannot convert " + item + " to an integer."); mothurOutEndLine();
+			commandInputsConvertError = true;
+		}
+		
+		return error;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "mothurConvert");
+		exit(1);
+	}
+}
+/***********************************************************************/
+bool MothurOut::isNumeric1(string stringToCheck){
+	try {
+		bool numeric = false;
+		
+		if(stringToCheck.find_first_not_of("0123456789.-") == string::npos) { numeric = true; }
+			
+		return numeric;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "isNumeric1");
+		exit(1);
+	}
+	
+}
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, float& num){
+	try {
+		bool error = false;
+		
+		if (isNumeric1(item)) {
+			convert(item, num);
+		}else {
+			num = 0;
+			error = true;
+			mothurOut("[ERROR]: cannot convert " + item + " to a float."); mothurOutEndLine();
+			commandInputsConvertError = true;
+		}
+		
+		return error;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "mothurConvert");
+		exit(1);
+	}
+}
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, double& num){
+	try {
+		bool error = false;
+		
+		if (isNumeric1(item)) {
+			convert(item, num);
+		}else {
+			num = 0;
+			error = true;
+			mothurOut("[ERROR]: cannot convert " + item + " to a double."); mothurOutEndLine();
+			commandInputsConvertError = true;
+		}
+		
+		return error;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "mothurConvert");
+		exit(1);
+	}
+}
 /**************************************************************************************************/
 
 vector<vector<double> > MothurOut::binomial(int maxOrder){
@@ -2054,7 +2154,7 @@ int MothurOut::removeConfidences(string& tax) {
 				int pos2 = taxon.find_last_of(')');
 				if (pos2 != -1) {
 					string confidenceScore = taxon.substr(pos+1, (pos2-(pos+1)));
-					if (isContainingOnlyDigits(confidenceScore)) {
+					if (isNumeric1(confidenceScore)) {
 						taxon = taxon.substr(0, pos); //rip off confidence 
 					}
 				}