X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=a56a6217a8c136e1fcb9f3f3078c5418547220fa;hb=f06fdb807822f8e06db003ed809c87250905cfc8;hp=7309c174c83027437e67026869f53161101e11bc;hpb=10c8178dc5e3f96ef8e92a986f1eddd13e622173;p=mothur.git

diff --git a/mothurout.cpp b/mothurout.cpp
index 7309c17..a56a621 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -39,6 +39,8 @@ void MothurOut::printCurrentFiles()  {
 		if (sharedfile != "")		{  mothurOut("shared=" + sharedfile); mothurOutEndLine();			}
 		if (taxonomyfile != "")		{  mothurOut("taxonomy=" + taxonomyfile); mothurOutEndLine();		}
 		if (treefile != "")			{  mothurOut("tree=" + treefile); mothurOutEndLine();				}
+		if (flowfile != "")			{  mothurOut("flow=" + flowfile); mothurOutEndLine();				}
+		if (processors != "1")		{  mothurOut("processors=" + processors); mothurOutEndLine();		}
 		
 	}
 	catch(exception& e) {
@@ -46,6 +48,42 @@ 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;			}
+		if (flowfile != "")			{  return true;			}
+		if (processors != "1")		{  return true;			}
+		
+		return hasCurrent;
+		
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "hasCurrentFiles");
+		exit(1);
+	}
+}
+
 /*********************************************************************************************/
 void MothurOut::clearCurrentFiles()  {
 	try {
@@ -67,7 +105,9 @@ void MothurOut::clearCurrentFiles()  {
 		sfffile = "";
 		oligosfile = "";
 		accnosfile = "";
-		taxonomyfile = "";		
+		taxonomyfile = "";	
+		flowfile = "";
+		processors = "1";
 	}
 	catch(exception& e) {
 		errorOut(e, "MothurOut", "clearCurrentFiles");
@@ -207,6 +247,53 @@ void MothurOut::mothurOutEndLine() {
 	}
 }
 /*********************************************************************************************/
+void MothurOut::mothurOut(string output, ofstream& outputFile) {
+	try {
+		
+#ifdef USE_MPI
+		int pid;
+		MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+		
+		if (pid == 0) { //only one process should output to screen
+#endif
+			
+			cout << output;
+			out << output;
+			outputFile << output;
+			
+#ifdef USE_MPI
+		}
+#endif
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "MothurOut");
+		exit(1);
+	}
+}
+/*********************************************************************************************/
+void MothurOut::mothurOutEndLine(ofstream& outputFile) {
+	try {
+#ifdef USE_MPI
+		int pid;
+		MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+		
+		if (pid == 0) { //only one process should output to screen
+#endif
+			
+			cout << endl;
+			out << endl;
+			outputFile << endl;
+			
+#ifdef USE_MPI
+		}
+#endif
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "MothurOutEndLine");
+		exit(1);
+	}
+}
+/*********************************************************************************************/
 void MothurOut::mothurOutJustToLog(string output) {
 	try {
 		#ifdef USE_MPI
@@ -398,12 +485,12 @@ string MothurOut::getline(ifstream& fileHandle) {
 	
 		string line = "";
 		
-		while (!fileHandle.eof())	{
+		while (fileHandle)	{
 			//get next character
 			char c = fileHandle.get(); 
 			
 			//are you at the end of the line
-			if ((c == '\n') || (c == '\r') || (c == '\f')){  break;	}	
+			if ((c == '\n') || (c == '\r') || (c == '\f') || (c == EOF)){  break;	}	
 			else {		line += c;		}
 		}
 		
@@ -1114,7 +1201,43 @@ vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
 		exit(1);
 	}
 }
-
+/**************************************************************************************************/
+int MothurOut::divideFile(string filename, int& proc, vector<string>& files) {
+	try{
+		
+		vector<unsigned long int> filePos = divideFile(filename, proc);
+		
+		for (int i = 0; i < (filePos.size()-1); i++) {
+			
+			//read file chunk
+			ifstream in;
+			openInputFile(filename, in);
+			in.seekg(filePos[i]);
+			unsigned long int size = filePos[(i+1)] - filePos[i];
+			char* chunk = new char[size];
+			in.read(chunk, size);
+			in.close();
+			
+			//open new file
+			string fileChunkName = filename + "." + toString(i) + ".tmp";
+			ofstream out; 
+			openOutputFile(fileChunkName, out);
+			
+			out << chunk << endl;
+			out.close();
+			delete[] chunk;
+			
+			//save name
+			files.push_back(fileChunkName);
+		}
+				
+		return 0;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "divideFile");
+		exit(1);
+	}
+}
 /***********************************************************************/
 
 bool MothurOut::isTrue(string f){
@@ -1153,6 +1276,33 @@ float MothurOut::ceilDist(float dist, int precision){
 		exit(1);
 	}
 }
+/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, map<string, string>& nameMap) { 
+	try {
+		
+		//open input file
+		ifstream in;
+		openInputFile(namefile, in);
+		
+		while (!in.eof()) {
+			if (control_pressed) { break; }
+			
+			string firstCol, secondCol;
+			in >> firstCol >> secondCol; gobble(in);
+			
+			nameMap[firstCol] = secondCol;
+		}
+		in.close();
+		
+		return 0;
+		
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "readNames");
+		exit(1);
+	}
+}
+
 /**********************************************************************************************************************/
 map<string, int> MothurOut::readNames(string namefile) { 
 	try {
@@ -1183,6 +1333,42 @@ 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);
+	}
+}
 
 /***********************************************************************/