X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=61b39514e43b79bc146eb3e37ed4dc8d41017a62;hb=ccf2fedbb600a362777a11501bb56c9c7746068e;hp=d5f1534f7535052c75888b04d28211fd522a0410;hpb=eb4bb52af987ff4df7354d95d60cd763aec537e1;p=mothur.git

diff --git a/mothurout.cpp b/mothurout.cpp
index d5f1534..61b3951 100644
--- 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) {
@@ -1014,7 +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++;} }
 			}
@@ -1444,7 +1448,8 @@ map<string, int> MothurOut::readNames(string namefile) {
 			if (control_pressed) { break; }
 			
 			string firstCol, secondCol;
-			in >> firstCol >> secondCol; gobble(in);
+			in >> firstCol;  gobble(in);
+            in >> secondCol; gobble(in);
 			
 			int num = getNumNames(secondCol);
 			
@@ -1924,6 +1929,26 @@ void MothurOut::splitAtDash(string& estim, set<int>& container) {
 		exit(1);
 	}	
 }
+/***********************************************************************/
+string MothurOut::makeList(vector<string>& names) {
+	try {
+		string list = "";
+        
+        if (names.size() == 0) { return list; }
+		
+        for (int i = 0; i < names.size()-1; i++) { list += names[i] + ",";  }
+        
+        //get last name
+        list += names[names.size()-1];
+        
+        return list;
+    }
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "makeList");
+		exit(1);
+	}	
+}
+
 /***********************************************************************/
 //This function parses the a string and puts peices in a vector
 void MothurOut::splitAtComma(string& estim, vector<string>& container) {
@@ -1961,6 +1986,25 @@ 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