worked on chimeras

[mothur.git] / pintail.h

diff --git a/pintail.h b/pintail.h
index 289af65b68cb2f37ddf3c392cf9c67572dd5560b..8c0dce4d4b802910cfad2f398871a9ba497bbe83 100644 (file)
--- a/pintail.h
+++ b/pintail.h
@@ -38,6 +38,7 @@ class Pintail : public Chimera {
                        int start;
                        int end;
                        linePair(int i, int j) : start(i), end(j) {}
+                       linePair(){}
                };
 
                Dist* distcalculator;
@@ -45,6 +46,7 @@ class Pintail : public Chimera {
                string fastafile, templateFile, consfile, quanfile;
                
                vector<linePair*> lines;
+               vector<linePair*> templateLines;
                vector<Sequence*> querySeqs;
                vector<Sequence*> templateSeqs;
                
@@ -53,10 +55,11 @@ class Pintail : public Chimera {
                vector< vector<float> > obsDistance;  //obsDistance[0] is the vector of observed distances for queryseqs[0]... 
                vector< vector<float> > expectedDistance;  //expectedDistance[0] is the vector of expected distances for queryseqs[0]... 
                vector<float> deviation;  //deviation[0] is the percentage of mismatched pairs over the whole seq between querySeqs[0] and its best match.
-               vector< vector<int> > windows;  // windows[0] is a vector containing the starting spot in queryseqs[0] aligned sequence for each window.
+               vector< vector<int> > windowsForeachQuery;  // windowsForeachQuery[0] is a vector containing the starting spot in queryseqs[0] aligned sequence for each window.
                                                                                //this is needed so you can move by bases and not just spots in the alignment
                                                                                
-               vector<int> windowSizes;    //windowSizes[0] = window size of querySeqs[0]
+               vector<int> windowSizes;                        //windowSizes[0] = window size of querySeqs[0]
+               vector<int> windowSizesTemplate;    //windowSizesTemplate[0] = window size of templateSeqs[0]
                
                vector< map<int, int> > trimmed;    //trimmed[0] = start and stop of trimmed sequences for querySeqs[0]
                map<int, int>::iterator it;
@@ -67,14 +70,12 @@ class Pintail : public Chimera {
                vector<float> probabilityProfile;
                vector< vector<float> > quantiles;  //quantiles[0] is the vector of deviations with ceiling score of 1, quantiles[1] is the vector of deviations with ceiling score of 2...
                
-               vector<Sequence*> readSeqs(string);
-               map<int, int> trimSeqs(Sequence*, Sequence, int);
+               void trimSeqs(Sequence*, Sequence, map<int, int>&);
                vector<float> readFreq();
                vector< vector<float> > readQuantiles();
                vector< vector<float> > getQuantiles(int, int);
                vector<float> calcFreq(vector<Sequence*>);
                
-               
                vector<Sequence> findPairs(int, int);
                vector<int> findWindows(Sequence*, int, int, int&);
                vector<float> calcObserved(Sequence*, Sequence, vector<int>, int);