more changes to error.seqs command and quality scores classses

[mothur.git] / qualityscores.cpp

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 2ee71e066f22e421b7f312be03da1279b2aa3a7a..aafa5794e206b936793cf6ffce6109f66eebaf86 100644 (file)
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -332,7 +332,7 @@ bool QualityScores::cullQualAverage(Sequence& sequence, double qAverage){
                return success;
        }
        catch(exception& e) {
-               m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
+               m->errorOut(e, "QualityScores", "cullQualAverage");
                exit(1);
        }
 }
@@ -341,19 +341,57 @@ bool QualityScores::cullQualAverage(Sequence& sequence, double qAverage){
 
 void QualityScores::updateQScoreErrorMap(map<char, vector<int> >& qualErrorMap, string errorSeq, int start, int stop, int weight){
        try {
-       
-               for(int i=start-1;i<stop;i++){
+
+               int seqLength = errorSeq.size();
+               int qIndex = start - 1;
+               for(int i=0;i<seqLength;i++){
                        
-                       if(errorSeq[i] == 'm')          {       qualErrorMap['m'][qScores[i]] += weight;        }
-                       else if(errorSeq[i] == 's')     {       qualErrorMap['s'][qScores[i]] += weight;        }
-                       else if(errorSeq[i] == 'i')     {       qualErrorMap['i'][qScores[i]] += weight;        }
-                       else if(errorSeq[i] == 'a')     {       qualErrorMap['a'][qScores[i]] += weight;        }
-                       else if(errorSeq[i] == 'd')     {       /*              nothing         */                                              }
+                       if(errorSeq[i] == 'm')          {       qualErrorMap['m'][qScores[qIndex]] += weight;   }
+                       else if(errorSeq[i] == 's')     {       qualErrorMap['s'][qScores[qIndex]] += weight;   }
+                       else if(errorSeq[i] == 'i')     {       qualErrorMap['i'][qScores[qIndex]] += weight;   }
+                       else if(errorSeq[i] == 'a')     {       qualErrorMap['a'][qScores[qIndex]] += weight;   }
+                       else if(errorSeq[i] == 'd')     {       /*      there are no qScores for deletions      */              }
+
+                       if(errorSeq[i] != 'd')          {       qIndex++;       }
 
                }       
        }
        catch(exception& e) {
-               m->errorOut(e, "TrimSeqsCommand", "updateQScoreErrorMap");
+               m->errorOut(e, "QualityScores", "updateQScoreErrorMap");
+               exit(1);
+       }
+}
+
+/**************************************************************************************************/
+
+void QualityScores::updateForwardMap(vector<vector<int> >& forwardMap, int start, int stop, int weight){
+       try {
+               
+               int index = 0;
+               for(int i=start-1;i<stop;i++){
+                       forwardMap[index++][qScores[i]] += weight;
+               }
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "QualityScores", "updateForwardMap");
+               exit(1);
+       }
+}
+
+/**************************************************************************************************/
+
+void QualityScores::updateReverseMap(vector<vector<int> >& reverseMap, int start, int stop, int weight){
+       try {
+               
+               int index = 0;
+               for(int i=stop-1;i>=start;i--){
+                       reverseMap[index++][qScores[i]] += weight;
+               }
+               
+       }       
+       catch(exception& e) {
+               m->errorOut(e, "QualityScores", "updateForwardMap");
                exit(1);
        }
 }