added versioning info to all shortcut files mothur makes.

[mothur.git] / bayesian.cpp

diff --git a/bayesian.cpp b/bayesian.cpp
index ae96a220ae2646c59a45a36152ed2d0b099c0c64..e596f672ed45f8f9f977e5264417e6781b959c38 100644 (file)
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -34,7 +34,13 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
                
                int start = time(NULL);
                
-               if(probFileTest && probFileTest2 && phyloTreeTest && probFileTest3){    
+               //if they are there make sure they were created after this release date
+               bool FilesGood = false;
+               if(probFileTest && probFileTest2 && phyloTreeTest && probFileTest3){
+                       FilesGood = checkReleaseDate(probFileTest, probFileTest2, phyloTreeTest, probFileTest3);
+               }
+               
+               if(probFileTest && probFileTest2 && phyloTreeTest && probFileTest3 && FilesGood){       
                        m->mothurOut("Reading template taxonomy...     "); cout.flush();
                        
                        phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
@@ -86,10 +92,16 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
                                
                                openOutputFile(probFileName, out);
                                
+                               //output mothur version
+                               out << "#" << m->getVersion() << endl;
+                               
                                out << numKmers << endl;
                                
                                openOutputFile(probFileName2, out2);
                                
+                               //output mothur version
+                               out2 << "#" << m->getVersion() << endl;
+                               
                                #ifdef USE_MPI
                                        }
                                #endif
@@ -416,12 +428,19 @@ void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string
                                positions2.resize(num2+1);
                                MPI_Recv(&positions2[0], (num2+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
                        }
-               
-                       //read numKmers
+                       
+                       //read version
                        int length = positions2[1] - positions2[0];
+                       char* buf5 = new char[length];
+
+                       MPI_File_read_at(inMPI2, positions2[0], buf5, length, MPI_CHAR, &status);
+                       delete buf5;
+
+                       //read numKmers
+                       length = positions2[2] - positions2[1];
                        char* buf = new char[length];
 
-                       MPI_File_read_at(inMPI2, positions2[0], buf, length, MPI_CHAR, &status);
+                       MPI_File_read_at(inMPI2, positions2[1], buf, length, MPI_CHAR, &status);
 
                        string tempBuf = buf;
                        if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
@@ -438,10 +457,17 @@ void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string
                        int kmer, name;  
                        vector<int> numbers; numbers.resize(numKmers);
                        float prob;
-                       vector<float> zeroCountProb; zeroCountProb.resize(numKmers);            
+                       vector<float> zeroCountProb; zeroCountProb.resize(numKmers);    
+                       
+                       //read version
+                       length = positions[1] - positions[0];
+                       char* buf6 = new char[length];
 
+                       MPI_File_read_at(inMPI2, positions[0], buf6, length, MPI_CHAR, &status);
+                       delete buf6;
+                       
                        //read file 
-                       for(int i=0;i<num;i++){
+                       for(int i=1;i<num;i++){
                                //read next sequence
                                length = positions[i+1] - positions[i];
                                char* buf4 = new char[length];
@@ -458,7 +484,7 @@ void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string
                        
                        MPI_File_close(&inMPI);
                        
-                       for(int i=1;i<num2;i++){
+                       for(int i=2;i<num2;i++){
                                //read next sequence
                                length = positions2[i+1] - positions2[i];
                                char* buf4 = new char[length];
@@ -488,7 +514,9 @@ void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string
                        MPI_File_close(&inMPI2);
                        MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
                #else
-               
+                       //read version
+                       string line = getline(in); gobble(in);
+                       
                        in >> numKmers; gobble(in);
                        
                        //initialze probabilities
@@ -500,7 +528,10 @@ void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string
                        vector<int> num; num.resize(numKmers);
                        float prob;
                        vector<float> zeroCountProb; zeroCountProb.resize(numKmers);            
-               
+                       
+                       //read version
+                       string line2 = getline(inNum); gobble(inNum);
+                       
                        while (inNum) {
                                inNum >> zeroCountProb[count] >> num[count];  
                                count++;
@@ -534,6 +565,61 @@ void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string
        }
 }
 /**************************************************************************************************/
+bool Bayesian::checkReleaseDate(ifstream& file1, ifstream& file2, ifstream& file3, ifstream& file4) {
+       try {
+               
+               bool good = true;
+               
+               vector<string> lines;
+               lines.push_back(getline(file1));  
+               lines.push_back(getline(file2)); 
+               lines.push_back(getline(file3)); 
+               lines.push_back(getline(file4)); 
+
+               //before we added this check
+               if ((lines[0][0] != '#') || (lines[1][0] != '#') || (lines[2][0] != '#') || (lines[3][0] != '#')) {  good = false;  }
+               else {
+                       //rip off #
+                       for (int i = 0; i < lines.size(); i++) { lines[i] = lines[i].substr(1);  }
+                       
+                       //get mothurs current version
+                       string version = m->getVersion();
+                       
+                       vector<string> versionVector;
+                       splitAtChar(version, versionVector, '.');
+                       
+                       //check each files version
+                       for (int i = 0; i < lines.size(); i++) { 
+                               vector<string> linesVector;
+                               splitAtChar(lines[i], linesVector, '.');
+                       
+                               if (versionVector.size() != linesVector.size()) { good = false; break; }
+                               else {
+                                       for (int j = 0; j < versionVector.size(); j++) {
+                                               int num1, num2;
+                                               convert(versionVector[j], num1);
+                                               convert(linesVector[j], num2);
+                                               
+                                               //if mothurs version is newer than this files version, then we want to remake it
+                                               if (num1 > num2) {  good = false; break;  }
+                                       }
+                               }
+                               
+                               if (!good) { break; }
+                       }
+               }
+               
+               if (!good) {  file1.close(); file2.close(); file3.close(); file4.close();  }
+               else { file1.seekg(0);  file2.seekg(0);  file3.seekg(0);  file4.seekg(0);  }
+               
+               return good;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Bayesian", "checkReleaseDate");
+               exit(1);
+       }
+}
+/**************************************************************************************************/