X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=65296221759fa879e591bb0967b0f20872106adc;hb=64581f6d0e63e67d4e119601bea695ebb3f52a13;hp=59e4fdcc080fe91e946dbc7d3b2a66d9e1dc02a0;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/mothurout.cpp b/mothurout.cpp
index 59e4fdc..6529622 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -46,6 +46,40 @@ void 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 {
@@ -1183,6 +1217,42 @@ map<string, int> MothurOut::readNames(string namefile) {
 		exit(1);
 	}
 }
+/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, vector<seqPriorityNode>& nameVector, map<string, string>& fastamap) { 
+	try {
+		int error = 0;
+		
+		//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);
+			
+			map<string, string>::iterator it = fastamap.find(firstCol);
+			if (it == fastamap.end()) {
+				error = 1;
+				mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
+			}else {
+				seqPriorityNode temp(num, it->second, firstCol);
+				nameVector.push_back(temp);
+			}
+		}
+		in.close();
+		
+		return error;
+		
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "readNames");
+		exit(1);
+	}
+}
 
 /***********************************************************************/
 
@@ -1731,6 +1801,23 @@ bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
 	}
 }
 /**************************************************************************************************/
+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);
+	}
+}
+/**************************************************************************************************/