chimera.slayer

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 5b1075902d6a038a4e863913bee7969c0ae52154..ffba9f5ff734bbaa5d5a6d80767897c34757e4b1 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -72,10 +72,18 @@ ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, map<string, in
                
                createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
                
-               //run filter on template
-               for (int i = 0; i < templateSeqs.size(); i++) {  if (m->control_pressed) {  break; }  runFilter(templateSeqs[i]);  }
-
-               
+               if (searchMethod == "distance") { 
+                       createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
+                       
+                       //run filter on template copying templateSeqs into filteredTemplateSeqs
+                       for (int i = 0; i < templateSeqs.size(); i++) {  
+                               if (m->control_pressed) {  break; }
+                               
+                               Sequence* newSeq = new Sequence(templateSeqs[i]->getName(), templateSeqs[i]->getAligned());
+                               runFilter(newSeq);  
+                               filteredTemplateSeqs.push_back(newSeq);
+                       }
+               }
        }
        catch(exception& e) {
                m->errorOut(e, "ChimeraSlayer", "ChimeraSlayer");
@@ -835,7 +843,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                        //free memory
                        for (int k = 0; k < seqs.size(); k++) {  delete seqs[k].seq;   }
                }
-               
+               //cout << endl << endl;
                return 0;
        }
        catch(exception& e) {
@@ -1024,7 +1032,7 @@ vector<Sequence*> ChimeraSlayer::getBlastSeqs(Sequence* q, vector<Sequence*>& db
                string queryUnAligned = q->getUnaligned();
                string leftQuery = queryUnAligned.substr(0, int(queryUnAligned.length() * 0.33)); //first 1/3 of the sequence
                string rightQuery = queryUnAligned.substr(int(queryUnAligned.length() * 0.66)); //last 1/3 of the sequence
-               
+//cout << "whole length = " << queryUnAligned.length() << '\t' << "left length = " << leftQuery.length() << '\t' << "right length = "<< rightQuery.length() << endl;   
                Sequence* queryLeft = new Sequence(q->getName(), leftQuery);
                Sequence* queryRight = new Sequence(q->getName(), rightQuery);