created mothurOut class to handle logfiles

[mothur.git] / chimerarealigner.cpp

diff --git a/chimerarealigner.cpp b/chimerarealigner.cpp
index 57c3641d14f4f2664dd12c3e1a7f89d13722ab91..487e7ca8f0425d7ba22e61690a4e0e8bc4758206 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() {}       
 //***************************************************************************************************************
@@ -24,12 +24,12 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
                        
                        string qAligned = query->getAligned();
                        string newQuery = "";
-                       
+               
                        //sort parents by region start
                        sort(parents.begin(), parents.end(), compareRegionStart);
 
                        //make sure you don't cutoff beginning of query 
-                       if (parents[0].nastRegionStart > 0) {  newQuery += qAligned.substr(0, parents[0].nastRegionStart+1);  }
+                       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++) {
@@ -38,9 +38,10 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
                                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);
                                parent->setAligned(p);
                                
@@ -62,9 +63,10 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
                                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-1);  }
                        
+                       //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);  }
+               
                        //set query to new aligned string
                        query->setAligned(newQuery);
                        
@@ -76,7 +78,7 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
                
        }
        catch(exception& e) {
-               errorOut(e, "ChimeraReAligner", "reAlign");
+               m->errorOut(e, "ChimeraReAligner", "reAlign");
                exit(1);
        }
 }
@@ -94,14 +96,14 @@ 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);
        }
 }