X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=3205ae794165a5b8c045c473403d8a66b1b54f90;hb=a150db3c2bfd7b76420048a1e94ebe397f2c6045;hp=65296221759fa879e591bb0967b0f20872106adc;hpb=64581f6d0e63e67d4e119601bea695ebb3f52a13;p=mothur.git

diff --git a/mothurout.cpp b/mothurout.cpp
index 6529622..3205ae7 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) {
@@ -70,6 +72,8 @@ bool MothurOut::hasCurrentFiles()  {
 		if (sharedfile != "")		{  return true;			}
 		if (taxonomyfile != "")		{  return true;			}
 		if (treefile != "")			{  return true;			}
+		if (flowfile != "")			{  return true;			}
+		if (processors != "1")		{  return true;			}
 		
 		return hasCurrent;
 		
@@ -101,7 +105,9 @@ void MothurOut::clearCurrentFiles()  {
 		sfffile = "";
 		oligosfile = "";
 		accnosfile = "";
-		taxonomyfile = "";		
+		taxonomyfile = "";	
+		flowfile = "";
+		processors = "1";
 	}
 	catch(exception& e) {
 		errorOut(e, "MothurOut", "clearCurrentFiles");
@@ -432,12 +438,12 @@ 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;		}
 		}
 		
@@ -1148,7 +1154,43 @@ 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){