changes while testing

[mothur.git] / alignmentdb.cpp

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index 6ccfd39edf3562d6795db6c9de131287b86241e0..9fec737778e01704e98f5c813e3c0554e7ab0981 100644 (file)
--- a/alignmentdb.cpp
+++ b/alignmentdb.cpp
@@ -14,34 +14,7 @@
 #include "referencedb.h"
 
 /**************************************************************************************************/
-//deep copy
-AlignmentDB::AlignmentDB(const AlignmentDB& adb) : numSeqs(adb.numSeqs), longest(adb.longest), method(adb.method), emptySequence(adb.emptySequence) {
-       try {
-               
-               m = MothurOut::getInstance();
-               if (adb.method == "blast") {
-                       search = new BlastDB(*((BlastDB*)adb.search));
-               }else if(adb.method == "kmer") {
-                       search = new KmerDB(*((KmerDB*)adb.search));
-               }else if(adb.method == "suffix") {
-                       search = new SuffixDB(*((SuffixDB*)adb.search));
-               }else {
-                       m->mothurOut("[ERROR]: cannot create copy of alignment database, unrecognized method - " + adb.method); m->mothurOutEndLine();
-               }
-               
-               for (int i = 0; i < adb.templateSequences.size(); i++) {
-                       Sequence temp(adb.templateSequences[i]);
-                       templateSequences.push_back(temp);
-               }
-       }
-       catch(exception& e) {
-               m->errorOut(e, "AlignmentDB", "AlignmentDB");
-               exit(1);
-       }
-       
-}
-/**************************************************************************************************/
-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 
+AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch, int tid){          //      This assumes that the template database is in fasta format, may 
        try {                                                                                   //      need to alter this in the future?
                m = MothurOut::getInstance();
                longest = 0;
@@ -49,6 +22,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                bool needToGenerate = true;
                ReferenceDB* rdb = ReferenceDB::getInstance();
                bool silent = false;
+               threadID = tid;
                
                if (fastaFileName == "saved-silent") {
                        fastaFileName = "saved"; silent = true;
@@ -68,15 +42,17 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                        
                        numSeqs = templateSequences.size();
                        if (!silent) { 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();
-                       
+                       //bool aligned = false;
+            int tempLength = 0;
+            
                        #ifdef USE_MPI  
                                int pid, processors;
-                               vector<unsigned long int> positions;
+                               vector<unsigned long long> positions;
                        
                                MPI_Status status; 
                                MPI_File inMPI;
@@ -128,6 +104,9 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                                                
                                                //save longest base
                                                if (temp.getUnaligned().length() >= longest)  { longest = temp.getUnaligned().length()+1; }
+                        if (tempLength != 0) {
+                            if (tempLength != temp.getAligned().length()) { m->mothurOut("[ERROR]: template is not aligned, aborting.\n"); m->control_pressed=true; }
+                        }else { tempLength = temp.getAligned().length(); }
                                        }
                                }
                                
@@ -151,6 +130,10 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                                        
                                        //save longest base
                                        if (temp.getUnaligned().length() >= longest)  { longest = (temp.getUnaligned().length()+1); }
+                    
+                    if (tempLength != 0) {
+                        if (tempLength != temp.getAligned().length()) { m->mothurOut("[ERROR]: template is not aligned, aborting.\n"); m->control_pressed=true; }
+                    }else { tempLength = temp.getAligned().length(); }
                                }
                        }
                        fastaFile.close();
@@ -189,7 +172,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                        #endif
                }
                else if(method == "suffix")             {       search = new SuffixDB(numSeqs);                                                         }
-               else if(method == "blast")              {       search = new BlastDB(fastaFileName.substr(0,fastaFileName.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "");       }
+               else if(method == "blast")              {       search = new BlastDB(fastaFileName.substr(0,fastaFileName.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", threadID);     }
                else {
                        method = "kmer";
                        m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
@@ -231,7 +214,7 @@ AlignmentDB::AlignmentDB(string s){
                method = s;
                
                if(method == "suffix")          {       search = new SuffixDB();        }
-               else if(method == "blast")      {       search = new BlastDB("");               }
+               else if(method == "blast")      {       search = new BlastDB("", 0);            }
                else                                            {       search = new KmerDB();          }