#include "kmerdb.hpp"
#include "suffixdb.hpp"
#include "blastdb.hpp"
+#include "referencedb.h"
/**************************************************************************************************/
longest = 0;
method = s;
bool needToGenerate = true;
+ ReferenceDB* rdb = ReferenceDB::getInstance();
- m->mothurOutEndLine();
- m->mothurOut("Reading in the " + fastaFileName + " template sequences...\t"); cout.flush();
+ if (fastaFileName == "saved") {
+ int start = time(NULL);
+ 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++) {
+ templateSequences.push_back(rdb->referenceSeqs[i]);
+ //save longest base
+ if (rdb->referenceSeqs[i].getUnaligned().length() >= longest) { longest = (rdb->referenceSeqs[i].getUnaligned().length()+1); }
+ }
+ fastaFileName = rdb->getSavedReference();
+
+ numSeqs = templateSequences.size();
+ m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(rdb->referenceSeqs.size()) + " sequences.");m->mothurOutEndLine();
+
+ }else {
+ int start = time(NULL);
+ m->mothurOutEndLine();
+ m->mothurOut("Reading in the " + fastaFileName + " template sequences...\t"); cout.flush();
+
+ #ifdef USE_MPI
+ int pid, processors;
+ vector<unsigned long int> positions;
+
+ 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);
+ int tag = 2001;
- #ifdef USE_MPI
- int pid, processors;
- vector<unsigned long int> positions;
+ char inFileName[1024];
+ strcpy(inFileName, fastaFileName.c_str());
- 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);
- int tag = 2001;
-
- char inFileName[1024];
- strcpy(inFileName, fastaFileName.c_str());
-
- MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+ MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+
+ if (pid == 0) {
+ positions = m->setFilePosFasta(fastaFileName, 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) { templateSequences.clear(); break; }
+
+ //read next sequence
+ int length = positions[i+1] - positions[i];
+ char* buf4 = new char[length];
+
+ MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status);
- if (pid == 0) {
- positions = m->setFilePosFasta(fastaFileName, numSeqs); //fills MPIPos, returns numSeqs
+ string tempBuf = buf4;
+ if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
+ delete buf4;
- //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);
+ istringstream iss (tempBuf,istringstream::in);
+
+ Sequence temp(iss);
+ if (temp.getName() != "") {
+ templateSequences.push_back(temp);
+
+ if (rdb->save) { rdb->referenceSeqs.push_back(temp); }
+
+ //save longest base
+ if (temp.getUnaligned().length() >= longest) { longest = temp.getUnaligned().length()+1; }
+ }
}
- }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) { templateSequences.clear(); break; }
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
- //read next sequence
- int length = positions[i+1] - positions[i];
- char* buf4 = new char[length];
+ MPI_File_close(&inMPI);
- MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status);
-
- string tempBuf = buf4;
- if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
- delete buf4;
+ #else
+ ifstream fastaFile;
+ m->openInputFile(fastaFileName, fastaFile);
- istringstream iss (tempBuf,istringstream::in);
-
- Sequence temp(iss);
+ while (!fastaFile.eof()) {
+ Sequence temp(fastaFile); m->gobble(fastaFile);
+
+ if (m->control_pressed) { templateSequences.clear(); break; }
+
if (temp.getName() != "") {
templateSequences.push_back(temp);
+
+ if (rdb->save) { rdb->referenceSeqs.push_back(temp); }
+
//save longest base
- if (temp.getUnaligned().length() >= longest) { longest = temp.getUnaligned().length()+1; }
+ if (temp.getUnaligned().length() >= longest) { longest = (temp.getUnaligned().length()+1); }
}
}
-
- MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
-
- MPI_File_close(&inMPI);
+ fastaFile.close();
+ #endif
- #else
- ifstream fastaFile;
- m->openInputFile(fastaFileName, fastaFile);
-
- while (!fastaFile.eof()) {
- Sequence temp(fastaFile); m->gobble(fastaFile);
-
- if (m->control_pressed) { templateSequences.clear(); break; }
+ numSeqs = templateSequences.size();
+ //all of this is elsewhere already!
- if (temp.getName() != "") {
- templateSequences.push_back(temp);
- //save longest base
- if (temp.getUnaligned().length() >= longest) { longest = (temp.getUnaligned().length()+1); }
- }
+ m->mothurOut("DONE.");
+ m->mothurOutEndLine(); cout.flush();
+ m->mothurOut("It took " + toString(time(NULL) - start) + " to read " + toString(rdb->referenceSeqs.size()) + " sequences."); m->mothurOutEndLine();
+
}
- fastaFile.close();
- #endif
-
- numSeqs = templateSequences.size();
- //all of this is elsewhere already!
- m->mothurOut("DONE.");
- m->mothurOutEndLine(); cout.flush();
//in case you delete the seqs and then ask for them
emptySequence = Sequence();
search->setNumSeqs(numSeqs);
}
+
}
catch(exception& e) {
m->errorOut(e, "AlignmentDB", "AlignmentDB");
try{
vector<int> spot = search->findClosestSequences(seq, 1);
-
+
if (spot.size() != 0) { return templateSequences[spot[0]]; }
else { return emptySequence; }
projects / mothur.git / blobdiff