added uchime_src folder. added biom parameter to make.shared. added biom as a current...

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 4df5f96eb6086e8d2e8e96e3f448948540a1c8b4..ae4cb524cba877f5a9ec843e1686569032c6528d 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -40,6 +40,7 @@ void MothurOut::printCurrentFiles()  {
                if (taxonomyfile != "")         {  mothurOut("taxonomy=" + taxonomyfile); mothurOutEndLine();           }
                if (treefile != "")                     {  mothurOut("tree=" + treefile); mothurOutEndLine();                           }
                if (flowfile != "")                     {  mothurOut("flow=" + flowfile); mothurOutEndLine();                           }
+        if (biomfile != "")                    {  mothurOut("biom=" + biomfile); mothurOutEndLine();                           }
                if (processors != "1")          {  mothurOut("processors=" + processors); mothurOutEndLine();           }
                
        }
@@ -73,6 +74,7 @@ bool MothurOut::hasCurrentFiles()  {
                if (taxonomyfile != "")         {  return true;                 }
                if (treefile != "")                     {  return true;                 }
                if (flowfile != "")                     {  return true;                 }
+        if (biomfile != "")                    {  return true;                 }
                if (processors != "1")          {  return true;                 }
                
                return hasCurrent;
@@ -107,6 +109,7 @@ void MothurOut::clearCurrentFiles()  {
                accnosfile = "";
                taxonomyfile = "";      
                flowfile = "";
+        biomfile = "";
                processors = "1";
        }
        catch(exception& e) {
@@ -598,6 +601,48 @@ 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 = "";
@@ -621,7 +666,7 @@ string MothurOut::hasPath(string longName){
 
 string MothurOut::getExtension(string longName){
        try {
-               string extension = longName;
+               string extension = "";
                
                if(longName.find_last_of('.') != longName.npos){
                        int pos = longName.find_last_of('.');
@@ -972,7 +1017,8 @@ int MothurOut::appendFiles(string temp, string filename) {
                
                int numLines = 0;
                if (ableToOpen == 0) { //you opened it
-                       while(char c = input.get()){
+                       while(!input.eof()){
+                char c = input.get();
                                if(input.eof())         {       break;                  }
                                else                            {       output << c;    if (c == '\n') {numLines++;} }
                        }
@@ -1919,6 +1965,25 @@ void MothurOut::splitAtComma(string& estim, vector<string>& container) {
                exit(1);
        }       
 }
+/***********************************************************************/
+//This function splits up the various option parameters
+void MothurOut::splitAtChar(string& prefix, string& suffix, char c){
+       try {
+               prefix = suffix.substr(0,suffix.find_first_of(c));
+               if ((suffix.find_first_of(c)+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
+                       suffix = suffix.substr(suffix.find_first_of(c)+1, suffix.length());
+                       string space = " ";
+                       while(suffix.at(0) == ' ')
+                               suffix = suffix.substr(1, suffix.length());
+               }
+        
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "splitAtComma");
+               exit(1);
+       }       
+}
+
 /***********************************************************************/
 
 //This function splits up the various option parameters