changed how we count sequences in a fastafile to allow for '>' in sequence names

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index fa706eaa57b5d6c15942d274af3cc2471505d77a..b92e8c8d355f6d105c141857bd96c19538ba194b 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -10,6 +10,7 @@
 #include "chimeraslayer.h"
 #include "chimerarealigner.h"
 #include "kmerdb.hpp"
+#include "blastdb.hpp"
 
 //***************************************************************************************************************
 ChimeraSlayer::ChimeraSlayer(string file, string temp, string mode, int k, int ms, int mms, int win, float div, 
@@ -46,7 +47,6 @@ int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int num
 int ChimeraSlayer::doPrep() {
        try {
                
-               
                //read in all query seqs
                vector<Sequence*> tempQuerySeqs = readSeqs(fastafile);
                
@@ -148,6 +148,13 @@ int ChimeraSlayer::doPrep() {
                        
                        databaseRight->setNumSeqs(templateSeqs.size());
                #endif  
+               }else if (searchMethod == "blast") {
+               
+                       //generate blastdb
+                       databaseLeft = new BlastDB(-2.0, -1.0, match, misMatch);
+                       for (int i = 0; i < templateSeqs.size(); i++) {         databaseLeft->addSequence(*templateSeqs[i]);    }
+                       databaseLeft->generateDB();
+                       databaseLeft->setNumSeqs(templateSeqs.size());
                }
                
                return 0;
@@ -159,7 +166,11 @@ int ChimeraSlayer::doPrep() {
        }
 }
 //***************************************************************************************************************
-ChimeraSlayer::~ChimeraSlayer() {      delete decalc;  if (searchMethod == "kmer") {  delete databaseRight;  delete databaseLeft;  }    }
+ChimeraSlayer::~ChimeraSlayer() {      
+       delete decalc;  
+       if (searchMethod == "kmer") {  delete databaseRight;  delete databaseLeft;  }   
+       else if (searchMethod == "blast") {  delete databaseLeft; }
+}
 //***************************************************************************************************************
 void ChimeraSlayer::printHeader(ostream& out) {
        m->mothurOutEndLine();
@@ -185,7 +196,7 @@ int ChimeraSlayer::print(ostream& out, ostream& outAcc) {
                                }
                        }
                        
-                       printBlock(chimeraResults[0], out);
+                       printBlock(chimeraResults[0], chimeraFlag, out);
                        out << endl;
                }else {  out << querySeq->getName() << "\tno" << endl;  }
                
@@ -221,25 +232,38 @@ int ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) {
                                        
                                        //write to accnos file
                                        int length = outAccString.length();
-                                       char buf2[length];
-                                       strcpy(buf2, outAccString.c_str()); 
+                                       char* buf2 = new char[length];
+                                       memcpy(buf2, outAccString.c_str(), length);
                                
                                        MPI_File_write_shared(outAcc, buf2, length, MPI_CHAR, &status);
+                                       delete buf2;
                                }
                        }
                        
-                       outputString = getBlock(chimeraResults[0]);
+                       outputString = getBlock(chimeraResults[0], chimeraFlag);
                        outputString += "\n";
-                       
-               }else {  outputString += querySeq->getName() + "\tno\n";  }
+       //cout << outputString << endl;         
+                       //write to output file
+                       int length = outputString.length();
+                       char* buf = new char[length];
+                       memcpy(buf, outputString.c_str(), length);
+                               
+                       MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
+                       delete buf;
+
+               }else {  
+                       outputString += querySeq->getName() + "\tno\n";  
+       //cout << outputString << endl;
+                       //write to output file
+                       int length = outputString.length();
+                       char* buf = new char[length];
+                       memcpy(buf, outputString.c_str(), length);
+                               
+                       MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
+                       delete buf;
+               }
                
-               //write to output file
-               int length = outputString.length();
-               char buf[length];
-               strcpy(buf, outputString.c_str()); 
                
-               MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
-
                return results;
        }
        catch(exception& e) {
@@ -253,7 +277,7 @@ int ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) {
 int ChimeraSlayer::getChimeras(Sequence* query) {
        try {
                chimeraFlags = "no";
-               
+
                //filter query
                spotMap = runFilter(query);     
                
@@ -262,13 +286,13 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                //referenceSeqs, numWanted, matchScore, misMatchPenalty, divR, minSimilarity
                maligner = new Maligner(templateSeqs, numWanted, match, misMatch, divR, minSim, minCov, searchMethod, databaseLeft, databaseRight);
                slayer = new Slayer(window, increment, minSim, divR, iters, minSNP);
-               
+       
                if (m->control_pressed) {  return 0;  }
                
                string chimeraFlag = maligner->getResults(query, decalc);
                if (m->control_pressed) {  return 0;  }
                vector<results> Results = maligner->getOutput();
-                               
+                       
                //found in testing realigning only made things worse
                if (realign) {
                        ChimeraReAligner realigner(templateSeqs, match, misMatch);
@@ -363,7 +387,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
        }
 }
 //***************************************************************************************************************
-void ChimeraSlayer::printBlock(data_struct data, ostream& out){
+void ChimeraSlayer::printBlock(data_struct data, string flag, ostream& out){
        try {
        //out << ":)\n";
                
@@ -375,7 +399,7 @@ void ChimeraSlayer::printBlock(data_struct data, ostream& out){
                out << data.divr_qla_qrb << '\t' << data.qla_qrb << '\t' << data.bsa << '\t';
                out << data.divr_qlb_qra << '\t' << data.qlb_qra << '\t' << data.bsb << '\t';
                
-               out << "yes\t" << spotMap[data.winLStart] << "-" << spotMap[data.winLEnd] << '\t' << spotMap[data.winRStart] << "-" << spotMap[data.winREnd] << '\t';
+               out << flag << '\t' << spotMap[data.winLStart] << "-" << spotMap[data.winLEnd] << '\t' << spotMap[data.winRStart] << "-" << spotMap[data.winREnd] << '\t';
                
                //out << "Similarity of parents: " << data.ab << endl;
                //out << "Similarity of query to parentA: " << data.qa << endl;
@@ -398,7 +422,7 @@ void ChimeraSlayer::printBlock(data_struct data, ostream& out){
        }
 }
 //***************************************************************************************************************
-string ChimeraSlayer::getBlock(data_struct data){
+string ChimeraSlayer::getBlock(data_struct data, string flag){
        try {
                
                string outputString = "";
@@ -409,7 +433,7 @@ string ChimeraSlayer::getBlock(data_struct data){
                outputString += toString(data.divr_qla_qrb) + "\t" + toString(data.qla_qrb) + "\t" + toString(data.bsa) + "\t";
                outputString += toString(data.divr_qlb_qra) + "\t" + toString(data.qlb_qra) + "\t" + toString(data.bsb) + "\t";
                
-               outputString += "yes\t" + toString(spotMap[data.winLStart]) + "-" + toString(spotMap[data.winLEnd]) + "\t" + toString(spotMap[data.winRStart]) + "-" + toString(spotMap[data.winREnd]) + "\t";
+               outputString += flag + "\t" + toString(spotMap[data.winLStart]) + "-" + toString(spotMap[data.winLEnd]) + "\t" + toString(spotMap[data.winRStart]) + "-" + toString(spotMap[data.winREnd]) + "\t";
                
                return outputString;
        }