added phylo.diversity command. added hard parameter to cluster, hcluster and read...

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index fa706eaa57b5d6c15942d274af3cc2471505d77a..2c4f7fba4253c2cb4c2693bb3cb18e676c5d938b 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();
@@ -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 += "\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);