X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=9704464bf80326c87d4afa556e3353b95fcbf37e;hb=5a4ac4f954c4b4445bcee272f1f8220ddcc9c1e4;hp=eacad376e1e91a519feff3c8e57727662042599b;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96;p=mothur.git

diff --git a/mothurout.cpp b/mothurout.cpp
index eacad37..9704464 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -43,6 +43,7 @@ set<string> MothurOut::getCurrentTypes()  {
         types.insert("tree");
         types.insert("flow");
         types.insert("biom");
+        types.insert("count");
         types.insert("processors");
 
 		return types;
@@ -78,6 +79,7 @@ void MothurOut::printCurrentFiles()  {
 		if (treefile != "")			{  mothurOut("tree=" + treefile); mothurOutEndLine();				}
 		if (flowfile != "")			{  mothurOut("flow=" + flowfile); mothurOutEndLine();				}
         if (biomfile != "")			{  mothurOut("biom=" + biomfile); mothurOutEndLine();				}
+        if (counttablefile != "")	{  mothurOut("count=" + counttablefile); mothurOutEndLine();	}
 		if (processors != "1")		{  mothurOut("processors=" + processors); mothurOutEndLine();		}
 		
 	}
@@ -112,6 +114,7 @@ bool MothurOut::hasCurrentFiles()  {
 		if (treefile != "")			{  return true;			}
 		if (flowfile != "")			{  return true;			}
         if (biomfile != "")			{  return true;			}
+        if (counttablefile != "")	{  return true;			}
 		if (processors != "1")		{  return true;			}
 		
 		return hasCurrent;
@@ -147,6 +150,7 @@ void MothurOut::clearCurrentFiles()  {
 		taxonomyfile = "";	
 		flowfile = "";
         biomfile = "";
+        counttablefile = "";
 		processors = "1";
 	}
 	catch(exception& e) {
@@ -1048,6 +1052,9 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
 
 int MothurOut::renameFile(string oldName, string newName){
 	try {
+        
+        if (oldName == newName) { return 0; }
+        
 		ifstream inTest;
 		int exist = openInputFile(newName, inTest, "");
 		inTest.close();
@@ -1291,16 +1298,6 @@ vector<unsigned long long> MothurOut::setFilePosEachLine(string filename, int& n
 			positions.push_back(0);
 		
 			while(!in.eof()){
-				//unsigned long long lastpos = in.tellg();
-				//input = getline(in); 
-				//if (input.length() != 0) {
-					//unsigned long long pos = in.tellg(); 
-					//if (pos != -1) { positions.push_back(pos - input.length() - 1);	}
-					//else {  positions.push_back(lastpos);  }
-				//}
-				//gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
-				
-				
 				//getline counting reads
 				char d = in.get(); count++;
 				while ((d != '\n') && (d != '\r') && (d != '\f') && (d != in.eof()))	{
@@ -1503,7 +1500,7 @@ vector<string> MothurOut::splitWhiteSpace(string& rest, char buffer[], int size)
         for (int i = 0; i < size; i++) {
             if (!isspace(buffer[i]))  { rest += buffer[i];  }
             else {
-                pieces.push_back(rest);  rest = "";
+                if (rest != "") { pieces.push_back(rest);  rest = ""; }
                 while (i < size) {  //gobble white space
                     if (isspace(buffer[i])) { i++; }
                     else { rest = buffer[i];  break; } //cout << "next piece buffer = " << nextPiece << endl;
@@ -1527,7 +1524,7 @@ vector<string> MothurOut::splitWhiteSpace(string input){
         for (int i = 0; i < input.length(); i++) {
             if (!isspace(input[i]))  { rest += input[i];  }
             else {
-                pieces.push_back(rest);  rest = "";
+                if (rest != "") { pieces.push_back(rest);  rest = ""; }
                 while (i < input.length()) {  //gobble white space
                     if (isspace(input[i])) { i++; }
                     else { rest = input[i];  break; } //cout << "next piece buffer = " << nextPiece << endl;
@@ -1631,6 +1628,46 @@ int MothurOut::readNames(string namefile, map<string, string>& nameMap, bool red
 	}
 }
 /**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, map<string, string>& nameMap, int flip) { 
+	try {
+		
+		//open input file
+		ifstream in;
+		openInputFile(namefile, in);
+        
+        string rest = "";
+        char buffer[4096];
+        bool pairDone = false;
+        bool columnOne = true;
+        string firstCol, secondCol;
+        
+		while (!in.eof()) {
+			if (control_pressed) { break; }
+			
+            in.read(buffer, 4096);
+            vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
+                else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    nameMap[secondCol] = firstCol;
+                    pairDone = false; 
+                }
+            }
+		}
+		in.close();
+		
+		return nameMap.size();
+		
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "readNames");
+		exit(1);
+	}
+}
+/**********************************************************************************************************************/
 int MothurOut::readNames(string namefile, map<string, string>& nameMap, map<string, int>& nameCount) { 
 	try {
 		nameMap.clear(); nameCount.clear();
@@ -1983,6 +2020,28 @@ bool MothurOut::mothurConvert(string item, int& num){
 		exit(1);
 	}
 }
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, intDist& 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 {