X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimera.cpp;h=53e77322f52ba40eb478e0b385a84982de752d6b;hp=54124872b7a5e87ce4aa545585fcb4b94c759044;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=0571957d68cbbc0e425af1db8e808f826010b9e2

diff --git a/chimera.cpp b/chimera.cpp
index 5412487..53e7732 100644
--- a/chimera.cpp
+++ b/chimera.cpp
@@ -8,6 +8,7 @@
  */
 
 #include "chimera.h"
+#include "referencedb.h"
 
 //***************************************************************************************************************
 //this is a vertical soft filter
@@ -94,99 +95,163 @@ map<int, int> Chimera::runFilter(Sequence* seq) {
 //***************************************************************************************************************
 vector<Sequence*> Chimera::readSeqs(string file) {
 	try {
-	
+		
 		vector<Sequence*> container;
 		int count = 0;
 		length = 0;
 		unaligned = false;
-
-		m->mothurOut("Reading sequences from " + file + "..."); cout.flush();
-		
-		#ifdef USE_MPI	
-			int pid, processors;
-			vector<unsigned long int> positions;
-			int numSeqs;
-			int tag = 2001;
+		ReferenceDB* rdb = ReferenceDB::getInstance();
 		
-			MPI_Status status; 
-			MPI_File inMPI;
-			MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-			MPI_Comm_size(MPI_COMM_WORLD, &processors);
-
-			//char* inFileName = new char[file.length()];
-			//memcpy(inFileName, file.c_str(), file.length());
+		if (file == "saved") {
 			
-			char inFileName[1024];
-			strcpy(inFileName, file.c_str());
-	
-			MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
-			//delete inFileName;
-
-			if (pid == 0) {
-				positions = m->setFilePosFasta(file, numSeqs); //fills MPIPos, returns numSeqs
-
-				//send file positions to all processes
-				for(int i = 1; i < processors; i++) { 
-					MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
-					MPI_Send(&positions[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
-				}
-			}else{
-				MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
-				positions.resize(numSeqs+1);
-				MPI_Recv(&positions[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
-			}
 			
-			//read file 
-			for(int i=0;i<numSeqs;i++){
+			m->mothurOutEndLine();  m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory.");	m->mothurOutEndLine();
 			
-				if (m->control_pressed) { MPI_File_close(&inMPI); return container; }
-	
-				//read next sequence
-				int seqlength = positions[i+1] - positions[i];
-				char* buf4 = new char[seqlength];
-
-				MPI_File_read_at(inMPI, positions[i], buf4, seqlength, MPI_CHAR, &status);
+			for (int i = 0; i < rdb->referenceSeqs.size(); i++) {
+				Sequence* temp = new Sequence(rdb->referenceSeqs[i].getName(), rdb->referenceSeqs[i].getAligned());
+				
+				if (count == 0) {  length = temp->getAligned().length();  count++;  } //gets first seqs length
+				else if (length != temp->getAligned().length()) {	unaligned = true;	}
 				
-				string tempBuf = buf4;
-				if (tempBuf.length() > seqlength) { tempBuf = tempBuf.substr(0, seqlength); }
-				delete buf4;
+				if (temp->getName() != "") {  container.push_back(temp);  }
+			}
+			
+			templateFileName = rdb->getSavedReference();
+			
+		}else {
+			
+			m->mothurOut("Reading sequences from " + file + "..."); cout.flush();
+			
+			#ifdef USE_MPI
+				int pid, processors;
+				vector<unsigned long long> positions;
+				int numSeqs;
+				int tag = 2001;
+				MPI_File inMPI;
+				MPI_Status status; 
+			
+				if (byGroup) {
+					char inFileName[1024];
+					strcpy(inFileName, file.c_str());
+					
+					MPI_File_open(MPI_COMM_SELF, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
+					
+					positions = m->setFilePosFasta(file, numSeqs); //fills MPIPos, returns numSeqs
+					
+					//read file 
+					for(int i=0;i<numSeqs;i++){
+						
+						if (m->control_pressed) { MPI_File_close(&inMPI); return container; }
+						
+						//read next sequence
+						int seqlength = positions[i+1] - positions[i];
+						char* buf4 = new char[seqlength];
+						
+						MPI_File_read_at(inMPI, positions[i], buf4, seqlength, MPI_CHAR, &status);
+						
+						string tempBuf = buf4;
+						if (tempBuf.length() > seqlength) { tempBuf = tempBuf.substr(0, seqlength); }
+						delete buf4;
+						
+						istringstream iss (tempBuf,istringstream::in);
+						
+						Sequence* current = new Sequence(iss);   
+						if (current->getName() != "") {
+							if (count == 0) {  length = current->getAligned().length();  count++;  } //gets first seqs length
+							else if (length != current->getAligned().length()) {	unaligned = true;	}
+							
+							container.push_back(current);  
+							if (rdb->save) { rdb->referenceSeqs.push_back(*current); }
+						}
+					}
+					
+					MPI_File_close(&inMPI);
+					
+				}else {					
+					
+					MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+					MPI_Comm_size(MPI_COMM_WORLD, &processors);
+					
+					//char* inFileName = new char[file.length()];
+					//memcpy(inFileName, file.c_str(), file.length());
+					
+					char inFileName[1024];
+					strcpy(inFileName, file.c_str());
+					
+					MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
+					//delete inFileName;
+					
+					if (pid == 0) {
+						positions = m->setFilePosFasta(file, numSeqs); //fills MPIPos, returns numSeqs
+						
+						//send file positions to all processes
+						for(int i = 1; i < processors; i++) { 
+							MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+							MPI_Send(&positions[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+						}
+					}else{
+						MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+						positions.resize(numSeqs+1);
+						MPI_Recv(&positions[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
+					}
+					
+					//read file 
+					for(int i=0;i<numSeqs;i++){
+						
+						if (m->control_pressed) { MPI_File_close(&inMPI); return container; }
+						
+						//read next sequence
+						int seqlength = positions[i+1] - positions[i];
+						char* buf4 = new char[seqlength];
+						
+						MPI_File_read_at(inMPI, positions[i], buf4, seqlength, MPI_CHAR, &status);
+						
+						string tempBuf = buf4;
+						if (tempBuf.length() > seqlength) { tempBuf = tempBuf.substr(0, seqlength); }
+						delete buf4;
+						
+						istringstream iss (tempBuf,istringstream::in);
+						
+						Sequence* current = new Sequence(iss);   
+						if (current->getName() != "") {
+							if (count == 0) {  length = current->getAligned().length();  count++;  } //gets first seqs length
+							else if (length != current->getAligned().length()) {	unaligned = true;	}
+							
+							container.push_back(current);  
+							if (rdb->save) { rdb->referenceSeqs.push_back(*current); }
+						}
+					}
+					
+					MPI_File_close(&inMPI);
+					MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+				}
+		#else
 
-				istringstream iss (tempBuf,istringstream::in);
-		
-				Sequence* current = new Sequence(iss);   
-				if (current->getName() != "") {
-					if (count == 0) {  length = current->getAligned().length();  count++;  } //gets first seqs length
-					else if (length != current->getAligned().length()) {	unaligned = true;	}
+			ifstream in;
+			m->openInputFile(file, in);
 			
+			//read in seqs and store in vector
+			while(!in.eof()){
+				
+				if (m->control_pressed) { return container; }
+				
+				Sequence* current = new Sequence(in);  m->gobble(in);
+				
+				if (count == 0) {  length = current->getAligned().length();  count++;  } //gets first seqs length
+				else if (length != current->getAligned().length()) {   unaligned = true;	}
+							
+				if (current->getName() != "") {  
 					container.push_back(current);  
+					if (rdb->save) { rdb->referenceSeqs.push_back(*current); }
 				}
 			}
-			
-			MPI_File_close(&inMPI);
-			MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
-	#else
-
-		ifstream in;
-		m->openInputFile(file, in);
+			in.close();
+		#endif
 		
-		//read in seqs and store in vector
-		while(!in.eof()){
+			m->mothurOut("Done."); m->mothurOutEndLine();
 			
-			if (m->control_pressed) { return container; }
-			
-			Sequence* current = new Sequence(in);  m->gobble(in);
-			
-			if (count == 0) {  length = current->getAligned().length();  count++;  } //gets first seqs length
-			else if (length != current->getAligned().length()) {	unaligned = true;	}
-						
-			if (current->getName() != "") {  container.push_back(current);  }
+			filterString = (string(container[0]->getAligned().length(), '1'));
 		}
-		in.close();
-	#endif
-	
-		m->mothurOut("Done."); m->mothurOutEndLine();
-		
-		filterString = (string(container[0]->getAligned().length(), '1'));
 		
 		return container;
 	}