*/
#include "chimera.h"
+#include "referencedb.h"
//***************************************************************************************************************
//this is a vertical soft filter
if (m->control_pressed) { return filterString; }
string seqAligned = seqs[i]->getAligned();
+
+ if (seqAligned.length() != filterString.length()) { m->mothurOut(seqs[i]->getName() + " is not the same length as the template sequences. Aborting!\n"); exit(1); }
for (int j = 0; j < seqAligned.length(); j++) {
//if this spot is a gap
//***************************************************************************************************************
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();
+ ReferenceDB* rdb = ReferenceDB::getInstance();
- #ifdef USE_MPI
- int pid;
- vector<long> positions;
- int numSeqs;
-
- MPI_Status status;
- MPI_File inMPI;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
- char* inFileName = new char[file.length()];
- memcpy(inFileName, file.c_str(), file.length());
-
- 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 = setFilePosFasta(file, numSeqs); //fills MPIPos, returns numSeqs
-
- //send file positions to all processes
- MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //send numSeqs
- MPI_Bcast(&positions[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
- }else{
- MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
- positions.resize(numSeqs+1);
- MPI_Bcast(&positions[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
- }
+ if (file == "saved") {
- //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);
+ m->mothurOutEndLine(); m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory."); m->mothurOutEndLine();
+
+ 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);
- #else
-
- ifstream in;
- 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); 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();
return container;
}
MPI_Offset size;
MPI_Status status;
- char* inFileName = new char[filename.length()];
- memcpy(inFileName, filename.c_str(), filename.length());
+ //char* inFileName = new char[filename.length()];
+ //memcpy(inFileName, filename.c_str(), filename.length());
+
+ char inFileName[1024];
+ strcpy(inFileName, filename.c_str());
MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
MPI_File_get_size(inMPI, &size);
- delete inFileName;
+ //delete inFileName;
char* buffer = new char[size];
MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
#else
ifstream infile;
- openInputFile(filename, infile);
+ m->openInputFile(filename, infile);
if (!infile.eof()) {
Sequence temp(infile);
projects / mothur.git / blobdiff