added unix to ifdefs. minor changes while testing 1.24.0.

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 001e8c48a8932374d7266b4e6097036c5b2ed9ac..c89d580d64f6c69a6afedada448143ae114453a3 100644 (file)
--- 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 
                                        }
                                }