changes to blastdb to make filenames given to blast unique, changes to split.abund...

[mothur.git] / chimerarealigner.cpp

diff --git a/chimerarealigner.cpp b/chimerarealigner.cpp
index f45b9a87f6829b68c81c8b137758ec3f6a096022..1da327819ab446fe62fb965f36b48211d484b97e 100644 (file)
--- a/chimerarealigner.cpp
+++ b/chimerarealigner.cpp
@@ -12,7 +12,7 @@
 #include "nast.hpp"
 
 //***************************************************************************************************************
-ChimeraReAligner::ChimeraReAligner(vector<Sequence*> t, int m, int mm) : match(m), misMatch(mm) {  templateSeqs = t;  }
+ChimeraReAligner::ChimeraReAligner(vector<Sequence*> t, int ms, int mm) : match(ms), misMatch(mm) {  templateSeqs = t;   m = MothurOut::getInstance(); }
 //***************************************************************************************************************
 ChimeraReAligner::~ChimeraReAligner() {}       
 //***************************************************************************************************************
@@ -31,45 +31,53 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
                        //make sure you don't cutoff beginning of query 
                        if (parents[0].nastRegionStart > 0) {  newQuery += qAligned.substr(0, parents[0].nastRegionStart);  }
                        int longest = 0;
+
                        //take query and break apart into pieces using breakpoints given by results of parents
                        for (int i = 0; i < parents.size(); i++) {
-       cout << parents[i].parent << '\t' << parents[i].nastRegionStart <<  '\t' << parents[i].nastRegionEnd    << endl;        
-                               int length = parents[i].nastRegionEnd - parents[i].nastRegionStart;
+                       
+                               int length = parents[i].nastRegionEnd - parents[i].nastRegionStart+1;
                                string q = qAligned.substr(parents[i].nastRegionStart, length);
-       cout << "query = " << q << endl;
                                Sequence* queryFrag = new Sequence(query->getName(), q);
-                               
+
                                queryParts.push_back(queryFrag);
-                               
+                       
                                Sequence* parent = getSequence(parents[i].parent);
                                string p = parent->getAligned();
                
                                p = p.substr(parents[i].nastRegionStart, length);
-       cout << "parent = " << p << endl;               
                                parent->setAligned(p);
                                
                                parentParts.push_back(parent);
-                               
+
                                if (q.length() > longest)       { longest = q.length(); }
                                if (p.length() > longest)       { longest = p.length(); }
                        }
-                                                                                       
+
                        //align each peice to correct parent from results
                        for (int i = 0; i < queryParts.size(); i++) {
                                alignment = new NeedlemanOverlap(-2.0, match, misMatch, longest+1); //default gapopen, match, mismatch, longestbase
                                Nast nast(alignment, queryParts[i], parentParts[i]);
                                delete alignment;
                        }
-                                                                                               
+
                        //recombine pieces to form new query sequence
                        for (int i = 0; i < queryParts.size(); i++) {
+                               //sometimes the parent regions do not meet, for example region 1 may end at 1000 and region 2 starts at 1100.  
+                               //we don't want to loose length so in this case we will leave query alone
+                               if (i != 0) {
+                                       int space = parents[i].nastRegionStart - parents[i-1].nastRegionEnd - 1;
+                                       if (space > 0) { //they don't meet and we need to add query piece
+                                               string q = qAligned.substr(parents[i-1].nastRegionEnd+1, space);
+                                               newQuery += q;
+                                       }
+                               }
+
                                newQuery += queryParts[i]->getAligned();
                        }
                        
-                       
                        //make sure you don't cutoff end of query 
-                       if (parents[parents.size()-1].nastRegionEnd < qAligned.length()) {  newQuery += qAligned.substr(parents[parents.size()-1].nastRegionEnd);  }
-                       
+                       if (parents[parents.size()-1].nastRegionEnd < (qAligned.length()-1)) {  newQuery += qAligned.substr(parents[parents.size()-1].nastRegionEnd+1);  }
+               
                        //set query to new aligned string
                        query->setAligned(newQuery);
                        
@@ -81,7 +89,7 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
                
        }
        catch(exception& e) {
-               errorOut(e, "ChimeraReAligner", "reAlign");
+               m->errorOut(e, "ChimeraReAligner", "reAlign");
                exit(1);
        }
 }
@@ -99,14 +107,14 @@ Sequence* ChimeraReAligner::getSequence(string name) {
                        }
                }
                
-               if(spot == -1) { mothurOut("Error: Could not find sequence."); mothurOutEndLine(); return NULL; }
+               if(spot == -1) { m->mothurOut("Error: Could not find sequence."); m->mothurOutEndLine(); return NULL; }
                
                temp = new Sequence(templateSeqs[spot]->getName(), templateSeqs[spot]->getAligned());
                
                return temp;
        }
        catch(exception& e) {
-               errorOut(e, "ChimeraReAligner", "getSequence");
+               m->errorOut(e, "ChimeraReAligner", "getSequence");
                exit(1);
        }
 }