-/*
- * alignmentdb.cpp
- * Mothur
- *
- * Created by westcott on 11/4/09.
- * Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
-
-#include "alignmentdb.h"
-#include "kmerdb.hpp"
-#include "suffixdb.hpp"
-#include "blastdb.hpp"
-
-
-/**************************************************************************************************/
-AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch){ // This assumes that the template database is in fasta format, may
- try { // need to alter this in the future?
- m = MothurOut::getInstance();
- longest = 0;
- method = s;
- bool needToGenerate = true;
-
- m->mothurOutEndLine();
- m->mothurOut("Reading in the " + fastaFileName + " template sequences...\t"); cout.flush();
-
- #ifdef USE_MPI
- int pid;
- vector<long> positions;
-
- MPI_Status status;
- MPI_File inMPI;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
- char inFileName[fastaFileName.length()];
- strcpy(inFileName, fastaFileName.c_str());
-
- MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
-
- if (pid == 0) {
- positions = setFilePosFasta(fastaFileName, 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
- }
-
- //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[length];
- MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status);
-
- string tempBuf = buf4;
- if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
-
- istringstream iss (tempBuf,istringstream::in);
-
- Sequence temp(iss);
- if (temp.getName() != "") {
- templateSequences.push_back(temp);
- //save longest base
- if (temp.getUnaligned().length() > longest) { longest = temp.getUnaligned().length()+1; }
- }
- }
-
- MPI_File_close(&inMPI);
- #else
- ifstream fastaFile;
- openInputFile(fastaFileName, fastaFile);
-
- while (!fastaFile.eof()) {
- Sequence temp(fastaFile); gobble(fastaFile);
-
- if (m->control_pressed) { templateSequences.clear(); break; }
-
- if (temp.getName() != "") {
- templateSequences.push_back(temp);
- //save longest base
- if (temp.getUnaligned().length() > longest) { longest = temp.getUnaligned().length()+1; }
- }
- }
- 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();
- emptySequence.setName("no_match");
- emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
- emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
-
-
- string kmerDBName;
- if(method == "kmer") {
- search = new KmerDB(fastaFileName, kmerSize);
-
- #ifdef USE_MPI
- #else
- kmerDBName = fastaFileName.substr(0,fastaFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
- ifstream kmerFileTest(kmerDBName.c_str());
-
- if(kmerFileTest){ needToGenerate = false; }
- #endif
- }
- else if(method == "suffix") { search = new SuffixDB(numSeqs); }
- else if(method == "blast") { search = new BlastDB(gapOpen, gapExtend, match, misMatch); }
- else {
- m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
- m->mothurOutEndLine();
- search = new KmerDB(fastaFileName, 8);
- }
-
- if (!(m->control_pressed)) {
- if (needToGenerate) {
- //add sequences to search
- for (int i = 0; i < templateSequences.size(); i++) {
- search->addSequence(templateSequences[i]);
-
- if (m->control_pressed) { templateSequences.clear(); break; }
- }
-
- if (m->control_pressed) { templateSequences.clear(); }
-
- search->generateDB();
-
- }else if ((method == "kmer") && (!needToGenerate)) {
- ifstream kmerFileTest(kmerDBName.c_str());
- search->readKmerDB(kmerFileTest);
- }
-
- search->setNumSeqs(numSeqs);
- }
- }
- catch(exception& e) {
- m->errorOut(e, "AlignmentDB", "AlignmentDB");
- exit(1);
- }
-}
-/**************************************************************************************************/
-AlignmentDB::AlignmentDB(string s){
- try {
- m = MothurOut::getInstance();
- method = s;
-
- if(method == "suffix") { search = new SuffixDB(); }
- else if(method == "blast") { search = new BlastDB(); }
- else { search = new KmerDB(); }
-
-
- //in case you delete the seqs and then ask for them
- emptySequence = Sequence();
- emptySequence.setName("no_match");
- emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
- emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
-
- }
- catch(exception& e) {
- m->errorOut(e, "AlignmentDB", "AlignmentDB");
- exit(1);
- }
-}
-/**************************************************************************************************/
-AlignmentDB::~AlignmentDB() { delete search; }
-/**************************************************************************************************/
-Sequence AlignmentDB::findClosestSequence(Sequence* seq) {
- try{
-
- vector<int> spot = search->findClosestSequences(seq, 1);
-
- if (spot.size() != 0) { return templateSequences[spot[0]]; }
- else { return emptySequence; }
-
- }
- catch(exception& e) {
- m->errorOut(e, "AlignmentDB", "findClosestSequence");
- exit(1);
- }
-}
-#ifdef USE_MPI
-/**************************************************************************************************/
-int AlignmentDB::MPISend(int receiver) {
- try {
-
- //send numSeqs - int
- MPI_Send(&numSeqs, 1, MPI_INT, receiver, 2001, MPI_COMM_WORLD);
-
- //send longest - int
- MPI_Send(&longest, 1, MPI_INT, receiver, 2001, MPI_COMM_WORLD);
-
- //send templateSequences
- for (int i = 0; i < templateSequences.size(); i++) {
- templateSequences[i].MPISend(receiver);
- }
-
- //send Database
- search->MPISend(receiver);
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "AlignmentDB", "MPISend");
- exit(1);
- }
-}
-/**************************************************************************************************/
-int AlignmentDB::MPIRecv(int sender) {
- try {
- MPI_Status status;
- //receive numSeqs - int
- MPI_Recv(&numSeqs, 1, MPI_INT, sender, 2001, MPI_COMM_WORLD, &status);
-
- //receive longest - int
- MPI_Recv(&longest, 1, MPI_INT, sender, 2001, MPI_COMM_WORLD, &status);
-
- //receive templateSequences
- templateSequences.resize(numSeqs);
- for (int i = 0; i < templateSequences.size(); i++) {
- templateSequences[i].MPIRecv(sender);
- }
-
- //receive Database
- search->MPIRecv(sender);
-
- for (int i = 0; i < templateSequences.size(); i++) {
- search->addSequence(templateSequences[i]);
- }
- search->generateDB();
- search->setNumSeqs(numSeqs);
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "AlignmentDB", "MPIRecv");
- exit(1);
- }
-}
-#endif
-/**************************************************************************************************/
-
-
-
-
-
-
+/*\r
+ * alignmentdb.cpp\r
+ * Mothur\r
+ *\r
+ * Created by westcott on 11/4/09.\r
+ * Copyright 2009 Schloss Lab. All rights reserved.\r
+ *\r
+ */\r
+\r
+#include "alignmentdb.h"\r
+#include "kmerdb.hpp"\r
+#include "suffixdb.hpp"\r
+#include "blastdb.hpp"\r
+\r
+\r
+/**************************************************************************************************/\r
+AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch){ // This assumes that the template database is in fasta format, may \r
+ try { // need to alter this in the future?\r
+ m = MothurOut::getInstance();\r
+ longest = 0;\r
+ method = s;\r
+ bool needToGenerate = true;\r
+ \r
+ m->mothurOutEndLine();\r
+ m->mothurOut("Reading in the " + fastaFileName + " template sequences...\t"); cout.flush();\r
+ \r
+ #ifdef USE_MPI \r
+ int pid;\r
+ vector<long> positions;\r
+ \r
+ MPI_Status status; \r
+ MPI_File inMPI;\r
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are\r
+ \r
+ char inFileName[1024];\r
+ strcpy(inFileName, fastaFileName.c_str());\r
+ \r
+ MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer\r
+ \r
+ if (pid == 0) {\r
+ positions = setFilePosFasta(fastaFileName, numSeqs); //fills MPIPos, returns numSeqs\r
+\r
+ //send file positions to all processes\r
+ MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //send numSeqs\r
+ MPI_Bcast(&positions[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos \r
+ }else{\r
+ MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs\r
+ positions.resize(numSeqs+1);\r
+ MPI_Bcast(&positions[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions\r
+ }\r
+ \r
+ //read file \r
+ for(int i=0;i<numSeqs;i++){\r
+ \r
+ if (m->control_pressed) { templateSequences.clear(); break; }\r
+ \r
+ //read next sequence\r
+ int length = positions[i+1] - positions[i];\r
+ char* buf4 = new char[length];\r
+ \r
+ MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status);\r
+ \r
+ string tempBuf = buf4;\r
+ if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }\r
+ delete buf4;\r
+\r
+ istringstream iss (tempBuf,istringstream::in);\r
+ \r
+ Sequence temp(iss); \r
+ if (temp.getName() != "") {\r
+ templateSequences.push_back(temp);\r
+ //save longest base\r
+ if (temp.getUnaligned().length() > longest) { longest = temp.getUnaligned().length()+1; }\r
+ }\r
+ }\r
+ \r
+ MPI_File_close(&inMPI);\r
+ \r
+ #else\r
+ ifstream fastaFile;\r
+ openInputFile(fastaFileName, fastaFile);\r
+\r
+ while (!fastaFile.eof()) {\r
+ Sequence temp(fastaFile); gobble(fastaFile);\r
+ \r
+ if (m->control_pressed) { templateSequences.clear(); break; }\r
+ \r
+ if (temp.getName() != "") {\r
+ templateSequences.push_back(temp);\r
+ //save longest base\r
+ if (temp.getUnaligned().length() > longest) { longest = temp.getUnaligned().length()+1; }\r
+ }\r
+ }\r
+ fastaFile.close();\r
+ \r
+ #endif\r
+ \r
+ numSeqs = templateSequences.size();\r
+ //all of this is elsewhere already!\r
+ \r
+ m->mothurOut("DONE.");\r
+ m->mothurOutEndLine(); cout.flush();\r
+ \r
+ //in case you delete the seqs and then ask for them\r
+ emptySequence = Sequence();\r
+ emptySequence.setName("no_match");\r
+ emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");\r
+ emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");\r
+ \r
+ \r
+ string kmerDBName;\r
+ if(method == "kmer") { \r
+ search = new KmerDB(fastaFileName, kmerSize); \r
+ \r
+ #ifdef USE_MPI\r
+ #else\r
+ kmerDBName = fastaFileName.substr(0,fastaFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";\r
+ ifstream kmerFileTest(kmerDBName.c_str());\r
+ \r
+ if(kmerFileTest){ needToGenerate = false; }\r
+ #endif\r
+ }\r
+ else if(method == "suffix") { search = new SuffixDB(numSeqs); }\r
+ else if(method == "blast") { search = new BlastDB(gapOpen, gapExtend, match, misMatch); }\r
+ else {\r
+ m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");\r
+ m->mothurOutEndLine();\r
+ search = new KmerDB(fastaFileName, 8);\r
+ }\r
+ \r
+ if (!(m->control_pressed)) {\r
+ if (needToGenerate) {\r
+ //add sequences to search \r
+ for (int i = 0; i < templateSequences.size(); i++) {\r
+ search->addSequence(templateSequences[i]);\r
+ \r
+ if (m->control_pressed) { templateSequences.clear(); break; }\r
+ }\r
+ \r
+ if (m->control_pressed) { templateSequences.clear(); }\r
+ \r
+ search->generateDB();\r
+ \r
+ }else if ((method == "kmer") && (!needToGenerate)) {\r
+ ifstream kmerFileTest(kmerDBName.c_str());\r
+ search->readKmerDB(kmerFileTest); \r
+ }\r
+ \r
+ search->setNumSeqs(numSeqs);\r
+ }\r
+ }\r
+ catch(exception& e) {\r
+ m->errorOut(e, "AlignmentDB", "AlignmentDB");\r
+ exit(1);\r
+ }\r
+}\r
+/**************************************************************************************************/\r
+AlignmentDB::AlignmentDB(string s){ \r
+ try { \r
+ m = MothurOut::getInstance();\r
+ method = s;\r
+ \r
+ if(method == "suffix") { search = new SuffixDB(); }\r
+ else if(method == "blast") { search = new BlastDB(); }\r
+ else { search = new KmerDB(); }\r
+\r
+ \r
+ //in case you delete the seqs and then ask for them\r
+ emptySequence = Sequence();\r
+ emptySequence.setName("no_match");\r
+ emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");\r
+ emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");\r
+ \r
+ }\r
+ catch(exception& e) {\r
+ m->errorOut(e, "AlignmentDB", "AlignmentDB");\r
+ exit(1);\r
+ }\r
+}\r
+/**************************************************************************************************/\r
+AlignmentDB::~AlignmentDB() { delete search; }\r
+/**************************************************************************************************/\r
+Sequence AlignmentDB::findClosestSequence(Sequence* seq) {\r
+ try{\r
+ \r
+ vector<int> spot = search->findClosestSequences(seq, 1);\r
+\r
+ if (spot.size() != 0) { return templateSequences[spot[0]]; }\r
+ else { return emptySequence; }\r
+ \r
+ }\r
+ catch(exception& e) {\r
+ m->errorOut(e, "AlignmentDB", "findClosestSequence");\r
+ exit(1);\r
+ }\r
+}\r
+#ifdef USE_MPI \r
+/**************************************************************************************************/\r
+int AlignmentDB::MPISend(int receiver) {\r
+ try {\r
+ \r
+ //send numSeqs - int\r
+ MPI_Send(&numSeqs, 1, MPI_INT, receiver, 2001, MPI_COMM_WORLD); \r
+ \r
+ //send longest - int\r
+ MPI_Send(&longest, 1, MPI_INT, receiver, 2001, MPI_COMM_WORLD); \r
+ \r
+ //send templateSequences\r
+ for (int i = 0; i < templateSequences.size(); i++) {\r
+ templateSequences[i].MPISend(receiver);\r
+ }\r
+ \r
+ //send Database\r
+ search->MPISend(receiver);\r
+ \r
+ return 0;\r
+ }\r
+ catch(exception& e) {\r
+ m->errorOut(e, "AlignmentDB", "MPISend");\r
+ exit(1);\r
+ }\r
+}\r
+/**************************************************************************************************/\r
+int AlignmentDB::MPIRecv(int sender) {\r
+ try {\r
+ MPI_Status status;\r
+ //receive numSeqs - int\r
+ MPI_Recv(&numSeqs, 1, MPI_INT, sender, 2001, MPI_COMM_WORLD, &status);\r
+ \r
+ //receive longest - int\r
+ MPI_Recv(&longest, 1, MPI_INT, sender, 2001, MPI_COMM_WORLD, &status);\r
+\r
+ //receive templateSequences\r
+ templateSequences.resize(numSeqs);\r
+ for (int i = 0; i < templateSequences.size(); i++) {\r
+ templateSequences[i].MPIRecv(sender);\r
+ }\r
+\r
+ //receive Database\r
+ search->MPIRecv(sender);\r
+ \r
+ for (int i = 0; i < templateSequences.size(); i++) {\r
+ search->addSequence(templateSequences[i]);\r
+ }\r
+ search->generateDB();\r
+ search->setNumSeqs(numSeqs);\r
+\r
+ return 0;\r
+ }\r
+ catch(exception& e) {\r
+ m->errorOut(e, "AlignmentDB", "MPIRecv");\r
+ exit(1);\r
+ }\r
+}\r
+#endif\r
+/**************************************************************************************************/\r
+\r
+\r
+\r
+\r
+\r
+\r
projects / mothur.git / blobdiff