X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=aligncommand.cpp;fp=aligncommand.cpp;h=75466f95b242ae08a71a88a40efec3a8fd230c86;hp=8215de301b646f4d4571944de85dddb40478e7e5;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hpb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 8215de3..75466f9 100644
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -875,7 +875,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
 			if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 			in.close(); m->mothurRemove(tempFile);
 			
-			appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
+			m->appendFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
 			m->mothurRemove((alignFileName + toString(processIDS[i]) + ".temp"));
 			
 			appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
@@ -892,7 +892,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
 			rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
 			
 			for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
-				appendAlignFiles(nonBlankAccnosFiles[h], accnosFName);
+				m->appendFiles(nonBlankAccnosFiles[h], accnosFName);
 				m->mothurRemove(nonBlankAccnosFiles[h]);
 			}
 		}else { //recreate the accnosfile if needed
@@ -957,7 +957,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
 		else { m->mothurRemove(accnosFName); } //remove so other files can be renamed to it
 		
 		for (int i = 1; i < processors; i++) {
-			appendAlignFiles((alignFileName + toString(i) + ".temp"), alignFileName);
+			m->appendFiles((alignFileName + toString(i) + ".temp"), alignFileName);
 			m->mothurRemove((alignFileName + toString(i) + ".temp"));
 			
 			appendReportFiles((reportFileName + toString(i) + ".temp"), reportFileName);
@@ -973,7 +973,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
 			rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
 			
 			for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
-				appendAlignFiles(nonBlankAccnosFiles[h], accnosFName);
+				m->appendFiles(nonBlankAccnosFiles[h], accnosFName);
 				m->mothurRemove(nonBlankAccnosFiles[h]);
 			}
 		}else { //recreate the accnosfile if needed
@@ -990,29 +990,6 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
 		exit(1);
 	}
 }
-/**************************************************************************************************/
-
-void AlignCommand::appendAlignFiles(string temp, string filename) {
-	try{
-		
-		ofstream output;
-		ifstream input;
-		m->openOutputFileAppend(filename, output);
-		m->openInputFile(temp, input);
-		
-		while(char c = input.get()){
-			if(input.eof())		{	break;			}
-			else				{	output << c;	}
-		}
-		
-		input.close();
-		output.close();
-	}
-	catch(exception& e) {
-		m->errorOut(e, "AlignCommand", "appendAlignFiles");
-		exit(1);
-	}
-}
 //**********************************************************************************************************************
 
 void AlignCommand::appendReportFiles(string temp, string filename) {
@@ -1025,10 +1002,11 @@ void AlignCommand::appendReportFiles(string temp, string filename) {
 
 		while (!input.eof())	{	char c = input.get(); if (c == 10 || c == 13){	break;	}	} // get header line
 				
-		while(char c = input.get()){
-			if(input.eof())		{	break;			}
-			else				{	output << c;	}
-		}
+        char buffer[4096];        
+        while (!input.eof()) {
+            input.read(buffer, 4096);
+            output.write(buffer, input.gcount());
+        }
 		
 		input.close();
 		output.close();