X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=ccode.cpp;h=00cd3f1948e009a86456e32bbcde2a40c6f889ac;hp=3aad3f6b48780505cb5f88c733b28027e28968b1;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3

diff --git a/ccode.cpp b/ccode.cpp
index 3aad3f6..00cd3f1 100644
--- a/ccode.cpp
+++ b/ccode.cpp
@@ -11,35 +11,80 @@
 #include "ignoregaps.h"
 #include "eachgapdist.h"
 
-
 //***************************************************************************************************************
-Ccode::Ccode(string filename, string o) {  
-	fastafile = filename;  outputDir = o; 
+Ccode::Ccode(string filename, string temp, bool f, string mask, int win, int numW, string o) : Chimera() {  
+ try {	
+	
+	fastafile = filename;  
+	outputDir = o; 
+	templateFileName = temp;  templateSeqs = readSeqs(temp); 
+	setMask(mask);
+	filter = f;
+	window = win;
+	numWanted = numW;
+	
 	distCalc = new eachGapDist();
 	decalc = new DeCalculator();
 	
-	mapInfo = outputDir + getRootName(getSimpleName(fastafile)) + "mapinfo";
-	ofstream out2;
-	openOutputFile(mapInfo, out2);
+	mapInfo = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "mapinfo";
+	
+	#ifdef USE_MPI
+		
+		//char* inFileName = new char[mapInfo.length()];
+		//memcpy(inFileName, mapInfo.c_str(), mapInfo.length());
+		
+		char inFileName[1024];
+		strcpy(inFileName, mapInfo.c_str());
+		
+		int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+
+		MPI_File_open(MPI_COMM_WORLD, inFileName, outMode, MPI_INFO_NULL, &outMap);  //comm, filename, mode, info, filepointer
+		
+		//delete inFileName;
+
+		int pid;
+		MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 		
-	out2 << "Place in masked, filtered and trimmed sequence\tPlace in original alignment" << endl;
-	out2.close();
+		if (pid == 0) {
+			string outString = "Place in masked, filtered and trimmed sequence\tPlace in original alignment\n";
+			
+			MPI_Status status;
+			int length = outString.length();
+			char* buf2 = new char[length];
+			memcpy(buf2, outString.c_str(), length);
+				
+			MPI_File_write_shared(outMap, buf2, length, MPI_CHAR, &status);
+			delete buf2;
+		}
+	#else
+
+		ofstream out2;
+		m->openOutputFile(mapInfo, out2);
+		
+		out2 << "Place in masked, filtered and trimmed sequence\tPlace in original alignment" << endl;
+		out2.close();
+	#endif
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Ccode", "Ccode");
+		exit(1);
+	}
 }
 //***************************************************************************************************************
 Ccode::~Ccode() {
 	delete distCalc;
 	delete decalc;
+	
+	#ifdef USE_MPI
+		MPI_File_close(&outMap);
+	#endif
 }	
 //***************************************************************************************************************
-void Ccode::printHeader(ostream& out) {
-	out << "For full window mapping info refer to " << mapInfo << endl << endl;
-}
-//***************************************************************************************************************
-int Ccode::print(ostream& out, ostream& outAcc) {
+Sequence Ccode::print(ostream& out, ostream& outAcc) {
 	try {
 		
 		ofstream out2;
-		openOutputFileAppend(mapInfo, out2);
+		m->openOutputFileAppend(mapInfo, out2);
 		
 		out2 << querySeq->getName() << endl;
 		for (it = spotMap.begin(); it!= spotMap.end(); it++) {
@@ -116,7 +161,115 @@ int Ccode::print(ostream& out, ostream& outAcc) {
 		//free memory
 		for (int i = 0; i < closest.size(); i++) {  delete closest[i].seq;  }
 
-		return 0;
+		return *querySeq;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Ccode", "print");
+		exit(1);
+	}
+}
+#ifdef USE_MPI
+//***************************************************************************************************************
+Sequence Ccode::print(MPI_File& out, MPI_File& outAcc) {
+	try {
+		
+		string outMapString = "";
+		
+		outMapString += querySeq->getName() + "\n";
+		for (it = spotMap.begin(); it!= spotMap.end(); it++) {
+			outMapString += toString(it->first)  + "\t" + toString(it->second)  + "\n";
+		}
+		printMapping(outMapString);
+		outMapString = "";
+		
+		string outString = "";
+		string outAccString = "";
+		
+		outString +=  querySeq->getName() + "\n\nReference sequences used and distance to query:\n";
+			
+		for (int j = 0; j < closest.size(); j++) {
+			outString += closest[j].seq->getName() + "\t" + toString(closest[j].dist) + "\n";
+		}
+		outString += "\n\nMapping information: ";
+		
+		//for each window
+		//window mapping info.
+		//you mask and did not filter
+		if ((seqMask != "") && (!filter)) { outString += "mask and trim."; }
+				
+		//you filtered and did not mask
+		if ((seqMask == "") && (filter)) { outString += "filter and trim."; }
+				
+		//you masked and filtered
+		if ((seqMask != "") && (filter)) { outString += "mask, filter and trim."; }
+			
+		outString += "\nWindow\tStartPos\tEndPos\n";
+		it = trim.begin();
+		for (int k = 0; k < windows.size()-1; k++) {
+			outString += toString(k+1) + "\t" + toString(spotMap[windows[k]-it->first]) + "\t" + toString(spotMap[windows[k]-it->first+windowSizes]) + "\n";
+		}
+			
+		outString += toString(windows.size()) + "\t" + toString(spotMap[windows[windows.size()-1]-it->first]) + "\t" + toString(spotMap[it->second-it->first-1]) + "\n\n";
+		
+		outString += "Window\tAvgQ\t(sdQ)\tAvgR\t(sdR)\tRatio\tAnova\n";
+		for (int k = 0; k < windows.size(); k++) {
+			float ds = averageQuery[k] / averageRef[k]; 
+			outString += toString(k+1) + "\t" + toString(averageQuery[k]) + "\t" + toString(sdQuery[k]) + "\t" + toString(averageRef[k]) + "\t" + toString(sdRef[k]) + "\t" + toString(ds) + "\t" + toString(anova[k]) + "\n";
+		}
+			
+		//varRef
+		//varQuery
+		/* F test for differences among variances.
+		* varQuery is expected to be higher or similar than varRef */
+		//float fs = varQuery[query] / varRef[query];	/* F-Snedecor, test for differences of variances */
+			
+		bool results = false;	
+					
+		//confidence limit, t - Student, anova
+		outString += "\nWindow\tConfidenceLimit\tt-Student\tAnova\n";
+			
+		for (int k = 0; k < windows.size(); k++) {
+			string temp = "";
+			if (isChimericConfidence[k]) {  temp += "*\t"; }
+			else { temp += "\t"; }
+				
+			if (isChimericTStudent[k]) {  temp += "*\t"; }
+			else { temp += "\t"; }
+				
+			if (isChimericANOVA[k]) {  temp += "*\t"; }
+			else { temp += "\t"; }
+			
+			outString += toString(k+1) + "\t" + temp + "\n";
+				
+			if (temp == "*\t*\t*\t") {  results = true;  }
+		}
+		outString += "\n";	
+		
+		MPI_Status status;
+		int length = outString.length();
+		char* buf2 = new char[length];
+		memcpy(buf2, outString.c_str(), length);
+				
+		MPI_File_write_shared(out, buf2, length, MPI_CHAR, &status);
+		delete buf2;
+
+		if (results) {
+			m->mothurOut(querySeq->getName() + " was found have at least one chimeric window."); m->mothurOutEndLine();
+			outAccString += querySeq->getName() + "\n";
+			
+			MPI_Status statusAcc;
+			length = outAccString.length();
+			char* buf = new char[length];
+			memcpy(buf, outAccString.c_str(), length);
+				
+			MPI_File_write_shared(outAcc, buf, length, MPI_CHAR, &statusAcc);
+			delete buf;
+		}
+
+		//free memory
+		for (int i = 0; i < closest.size(); i++) {  delete closest[i].seq;  }
+
+		return *querySeq;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "Ccode", "print");
@@ -124,6 +277,26 @@ int Ccode::print(ostream& out, ostream& outAcc) {
 	}
 }
 //***************************************************************************************************************
+int Ccode::printMapping(string& output) {
+	try {
+			MPI_Status status;
+			int length = output.length();
+			char* buf = new char[length];
+			memcpy(buf, output.c_str(), length);
+				
+			MPI_File_write_shared(outMap, buf, length, MPI_CHAR, &status);
+			delete buf;
+			
+			return 0;
+
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Ccode", "printMapping");
+		exit(1);
+	}
+}
+#endif
+//***************************************************************************************************************
 int Ccode::getChimeras(Sequence* query) {
 	try {