chimeras, fix to sabundvector and sharedsabundvector that caused getRabundVector...

[mothur.git] / chimera.cpp

diff --git a/chimera.cpp b/chimera.cpp
index bf16de4e34b795694d1a894ea1005f32353be110..9ad287b68d8457e6dffd6e101bbca007c64745eb 100644 (file)
--- a/chimera.cpp
+++ b/chimera.cpp
@@ -11,10 +11,10 @@
 
 //***************************************************************************************************************
 //this is a vertical soft filter
-void Chimera::createFilter(vector<Sequence*> seqs) {
+string Chimera::createFilter(vector<Sequence*> seqs, float t) {
        try {
                filterString = "";
-               int threshold = int (0.5 * seqs.size());
+               int threshold = int (t * seqs.size());
 //cout << "threshhold = " << threshold << endl;
                
                vector<int> gaps;       gaps.resize(seqs[0]->getAligned().length(), 0);
@@ -53,6 +53,7 @@ void Chimera::createFilter(vector<Sequence*> seqs) {
 //cout << "filter = " << filterString << endl; 
 
                mothurOut("Filter removed " + toString(numColRemoved) + " columns.");  mothurOutEndLine();
+               return filterString;
        }
        catch(exception& e) {
                errorOut(e, "Chimera", "createFilter");
@@ -60,18 +61,25 @@ void Chimera::createFilter(vector<Sequence*> seqs) {
        }
 }
 //***************************************************************************************************************
-void Chimera::runFilter(Sequence* seq) {
+map<int, int> Chimera::runFilter(Sequence* seq) {
        try {
-               
+               map<int, int> maskMap;
                string seqAligned = seq->getAligned();
                string newAligned = "";
+               int count = 0;
                        
                for (int j = 0; j < seqAligned.length(); j++) {
                        //if this spot is a gap
-                       if (filterString[j] == '1') { newAligned += seqAligned[j]; }
+                       if (filterString[j] == '1') { 
+                               newAligned += seqAligned[j]; 
+                               maskMap[count] = j;
+                               count++;
+                       }
                }
                        
                seq->setAligned(newAligned);
+               
+               return maskMap;
        }
        catch(exception& e) {
                errorOut(e, "Chimera", "runFilter");