X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=8fde2fd105d2b100715cc244a6d9a16bbd9eb353;hb=82bf18e3ef0a52345519f91a682e64cc385b56bb;hp=eb452b19a681e5ebe83d71ca7975a4140f703a55;hpb=3e2465c16d187247ce3befd29811c2d5dfc15ee8;p=mothur.git

diff --git a/mothurout.cpp b/mothurout.cpp
index eb452b1..8fde2fd 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -18,6 +18,97 @@ MothurOut* MothurOut::getInstance() {
 	return _uniqueInstance;
 }
 /*********************************************************************************************/
+void MothurOut::printCurrentFiles()  {
+	try {
+		if (accnosfile != "")		{  mothurOut("accnos=" + accnosfile); mothurOutEndLine();			}
+		if (columnfile != "")		{  mothurOut("column=" + columnfile); mothurOutEndLine();			}
+		if (designfile != "")		{  mothurOut("design=" + designfile); mothurOutEndLine();			}
+		if (fastafile != "")		{  mothurOut("fasta=" + fastafile); mothurOutEndLine();				}
+		if (groupfile != "")		{  mothurOut("group=" + groupfile); mothurOutEndLine();				}
+		if (listfile != "")			{  mothurOut("list=" + listfile); mothurOutEndLine();				}
+		if (namefile != "")			{  mothurOut("name=" + namefile); mothurOutEndLine();				}
+		if (oligosfile != "")		{  mothurOut("oligos=" + oligosfile); mothurOutEndLine();			}
+		if (orderfile != "")		{  mothurOut("order=" + orderfile); mothurOutEndLine();				}
+		if (ordergroupfile != "")	{  mothurOut("ordergroup=" + ordergroupfile); mothurOutEndLine();	}
+		if (phylipfile != "")		{  mothurOut("phylip=" + phylipfile); mothurOutEndLine();			}
+		if (qualfile != "")			{  mothurOut("qfile=" + qualfile); mothurOutEndLine();				}
+		if (rabundfile != "")		{  mothurOut("rabund=" + rabundfile); mothurOutEndLine();			}
+		if (relabundfile != "")		{  mothurOut("relabund=" + relabundfile); mothurOutEndLine();		}
+		if (sabundfile != "")		{  mothurOut("sabund=" + sabundfile); mothurOutEndLine();			}
+		if (sfffile != "")			{  mothurOut("sff=" + sfffile); mothurOutEndLine();					}
+		if (sharedfile != "")		{  mothurOut("shared=" + sharedfile); mothurOutEndLine();			}
+		if (taxonomyfile != "")		{  mothurOut("taxonomy=" + taxonomyfile); mothurOutEndLine();		}
+		if (treefile != "")			{  mothurOut("tree=" + treefile); mothurOutEndLine();				}
+		
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "printCurrentFiles");
+		exit(1);
+	}
+}
+/*********************************************************************************************/
+bool MothurOut::hasCurrentFiles()  {
+	try {
+		bool hasCurrent = false;
+		
+		if (accnosfile != "")		{  return true;			}
+		if (columnfile != "")		{  return true;			}
+		if (designfile != "")		{  return true;			}
+		if (fastafile != "")		{  return true;			}
+		if (groupfile != "")		{  return true;			}
+		if (listfile != "")			{  return true;			}
+		if (namefile != "")			{  return true;			}
+		if (oligosfile != "")		{  return true;			}
+		if (orderfile != "")		{  return true;			}
+		if (ordergroupfile != "")	{  return true;			}
+		if (phylipfile != "")		{  return true;			}
+		if (qualfile != "")			{  return true;			}
+		if (rabundfile != "")		{  return true;			}
+		if (relabundfile != "")		{  return true;			}
+		if (sabundfile != "")		{  return true;			}
+		if (sfffile != "")			{  return true;			}
+		if (sharedfile != "")		{  return true;			}
+		if (taxonomyfile != "")		{  return true;			}
+		if (treefile != "")			{  return true;			}
+		
+		return hasCurrent;
+		
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "hasCurrentFiles");
+		exit(1);
+	}
+}
+
+/*********************************************************************************************/
+void MothurOut::clearCurrentFiles()  {
+	try {
+		phylipfile = "";
+		columnfile = "";
+		listfile = "";
+		rabundfile = "";
+		sabundfile = "";
+		namefile = "";
+		groupfile = "";
+		designfile = "";
+		orderfile = "";
+		treefile = "";
+		sharedfile = "";
+		ordergroupfile = "";
+		relabundfile = "";
+		fastafile = "";
+		qualfile = "";
+		sfffile = "";
+		oligosfile = "";
+		accnosfile = "";
+		taxonomyfile = "";		
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "clearCurrentFiles");
+		exit(1);
+	}
+}
+/*********************************************************************************************/
 void MothurOut::setFileName(string filename)  {
 	try {
 		logFileName = filename;
@@ -489,6 +580,7 @@ bool MothurOut::isBlank(string fileName){
 			//check for blank file
 			gobble(fileHandle);
 			if (fileHandle.eof()) { fileHandle.close(); return true;  }
+			fileHandle.close();
 		}
 		return false;
 	}
@@ -926,7 +1018,7 @@ vector<unsigned long int> MothurOut::setFilePosFasta(string filename, int& num)
 			
 			in.seekg(size);
 		
-			while(char c = in.get()){
+			while(in.get()){
 				if(in.eof())		{	break;	}
 				else				{	size++;	}
 			}
@@ -1095,6 +1187,36 @@ float MothurOut::ceilDist(float dist, int precision){
 		exit(1);
 	}
 }
+/**********************************************************************************************************************/
+map<string, int> MothurOut::readNames(string namefile) { 
+	try {
+		
+		map<string, int> nameMap;
+		
+		//open input file
+		ifstream in;
+		openInputFile(namefile, in);
+		
+		while (!in.eof()) {
+			if (control_pressed) { break; }
+			
+			string firstCol, secondCol;
+			in >> firstCol >> secondCol; gobble(in);
+			
+			int num = getNumNames(secondCol);
+			
+			nameMap[firstCol] = num;
+		}
+		in.close();
+		
+		return nameMap;
+		
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "readNames");
+		exit(1);
+	}
+}
 
 /***********************************************************************/
 
@@ -1642,7 +1764,23 @@ bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
 		exit(1);
 	}
 }
-
+/**************************************************************************************************/
+bool MothurOut::isContainingOnlyDigits(string input) {
+	try{
+		
+		//are you a digit in ascii code
+		for (int i = 0;i < input.length(); i++){
+			if( input[i]>47 && input[i]<58){}
+			else { return false; }
+		}
+		
+		return true;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "isContainingOnlyDigits");		
+		exit(1);
+	}
+}
 /**************************************************************************************************/