X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.cpp;h=a68fbfcba365207d7847c7eeaff12d9e4a4914e2;hb=ce8794490ab1d83adcdb2b92e0302a1e43e17adf;hp=389235a034918aa556d95e40bd05d98e95cc49ed;hpb=e8c014de33edac1fb91d7593e143bf1f5107ffce;p=mothur.git

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 389235a..a68fbfc 100644
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -16,7 +16,7 @@
 
 #include "aligncommand.h"
 #include "referencedb.h"
-//test comm
+
 //**********************************************************************************************************************
 vector<string> AlignCommand::setParameters(){	
 	try {
@@ -75,6 +75,29 @@ string AlignCommand::getHelpString(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+string AlignCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string tag = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "fasta") {  tag = "align"; }
+            else if (type == "alignreport") {  tag = "align.report"; }
+            else if (type == "accnos") {  tag = "flip.accnos"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return tag;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "AlignCommand", "getOutputFileName");
+		exit(1);
+	}
+}
+
 //**********************************************************************************************************************
 AlignCommand::AlignCommand(){	
 	try {
@@ -305,9 +328,9 @@ int AlignCommand::execute(){
 			m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
 			
 			if (outputDir == "") {  outputDir += m->hasPath(candidateFileNames[s]); }
-			string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align";
-			string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report";
-			string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos";
+			string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("fasta");  
+			string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("alignreport");
+			string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("accnos");
 			bool hasAccnos = true;
 			
 			int numFastaSeqs = 0;
@@ -422,7 +445,7 @@ int AlignCommand::execute(){
 #else
 
 			vector<unsigned long long> positions; 
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			positions = m->divideFile(candidateFileNames[s], processors);
 			for (int i = 0; i < (positions.size()-1); i++) {	lines.push_back(new linePair(positions[i], positions[(i+1)]));	}
 		#else
@@ -430,7 +453,8 @@ int AlignCommand::execute(){
 				lines.push_back(new linePair(0, 1000));
 			}else {
 				positions = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); 
-				
+				if (positions.size() < processors) { processors = positions.size(); }
+                
 				//figure out how many sequences you have to process
 				int numSeqsPerProcessor = numFastaSeqs / processors;
 				for (int i = 0; i < processors; i++) {
@@ -617,7 +641,7 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
 			}
 			delete candidateSeq;
 			
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				unsigned long long pos = inFASTA.tellg();
 				if ((pos == -1) || (pos >= filePos->end)) { break; }
 			#else
@@ -826,7 +850,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
 	try {
 		int num = 0;
 		processIDS.resize(0);
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		int process = 1;
 		
 		//loop through and create all the processes you want
@@ -874,7 +898,7 @@ 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);
@@ -891,7 +915,7 @@ 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
@@ -956,7 +980,7 @@ 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);
@@ -972,7 +996,7 @@ 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
@@ -989,29 +1013,6 @@ 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) {
@@ -1024,10 +1025,11 @@ 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();