added count.groups command and paralellized align.seqs for windows

[mothur.git] / alignmentdb.cpp

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index bac61c451854b96e256bae11545448fa38589ebd..6ccfd39edf3562d6795db6c9de131287b86241e0 100644 (file)
--- a/alignmentdb.cpp
+++ b/alignmentdb.cpp
@@ -13,7 +13,33 @@
 #include "blastdb.hpp"
 #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 
        try {                                                                                   //      need to alter this in the future?
@@ -22,10 +48,16 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                method = s;
                bool needToGenerate = true;
                ReferenceDB* rdb = ReferenceDB::getInstance();
+               bool silent = false;
+               
+               if (fastaFileName == "saved-silent") {
+                       fastaFileName = "saved"; silent = true;
+               }
                
                if (fastaFileName == "saved") {
                        int start = time(NULL);
-                       m->mothurOutEndLine();  m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory.");        m->mothurOutEndLine();
+                       
+                       if (!silent) { m->mothurOutEndLine();  m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory."); m->mothurOutEndLine(); }
 
                        for (int i = 0; i < rdb->referenceSeqs.size(); i++) {
                                templateSequences.push_back(rdb->referenceSeqs[i]);
@@ -35,7 +67,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                        fastaFileName = rdb->getSavedReference();
                        
                        numSeqs = templateSequences.size();
-                       m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(rdb->referenceSeqs.size()) + " sequences.");m->mothurOutEndLine();  
+                       if (!silent) { m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(rdb->referenceSeqs.size()) + " sequences.");m->mothurOutEndLine();  }
 
                }else {
                        int start = time(NULL);
@@ -159,6 +191,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                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 {
+                       method = "kmer";
                        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);