changed random forest output filename

[mothur.git] / alignment.cpp

diff --git a/alignment.cpp b/alignment.cpp
index 235216e8e59c82be596004559445c021312acb40..9ab17004bc146bc97168373995c98b932dcb9c3f 100644 (file)
--- a/alignment.cpp
+++ b/alignment.cpp
@@ -15,7 +15,7 @@
 
 /**************************************************************************************************/
 
-Alignment::Alignment() {       /*      do nothing      */      }
+Alignment::Alignment() {       m = MothurOut::getInstance(); /*        do nothing      */      }
 
 /**************************************************************************************************/
 
@@ -53,7 +53,8 @@ void Alignment::resize(int A) {
 
 void Alignment::traceBack(){                   //      This traceback routine is used by the dynamic programming algorithms
        try {   
-                                                                       //      to fill the values of seqAaln and seqBaln
+               BBaseMap.clear();
+        ABaseMap.clear(); //   to fill the values of seqAaln and seqBaln
                seqAaln = "";
                seqBaln = "";
                int row = lB-1;
@@ -65,31 +66,51 @@ void Alignment::traceBack(){                        //      This traceback routine is used by the dynamic
                //      matrix
                
                if(currentCell.prevCell == 'x'){        seqAaln = seqBaln = "NOALIGNMENT";              }//If there's an 'x' in the bottom-
-               else{                                                                                           //      right corner bail out because it means nothing got aligned
+               else{   //      right corner bail out because it means nothing got aligned
+            int count = 0;
                        while(currentCell.prevCell != 'x'){                             //      while the previous cell isn't an 'x', keep going...
                                
                                if(currentCell.prevCell == 'u'){                        //      if the pointer to the previous cell is 'u', go up in the
                                        seqAaln = '-' + seqAaln;                                //      matrix.  this indicates that we need to insert a gap in
                                        seqBaln = seqB[row] + seqBaln;                  //      seqA and a base in seqB
+                    BBaseMap[row] = count;
                                        currentCell = alignment[--row][column];
                                }
                                else if(currentCell.prevCell == 'l'){           //      if the pointer to the previous cell is 'l', go to the left
                                        seqBaln = '-' + seqBaln;                                //      in the matrix.  this indicates that we need to insert a gap
                                        seqAaln = seqA[column] + seqAaln;               //      in seqB and a base in seqA
+                    ABaseMap[column] = count;
                                        currentCell = alignment[row][--column];
                                }
                                else{
                                        seqAaln = seqA[column] + seqAaln;               //      otherwise we need to go diagonally up and to the left,
                                        seqBaln = seqB[row] + seqBaln;                  //      here we add a base to both alignments
+                    BBaseMap[row] = count;
+                    ABaseMap[column] = count;
                                        currentCell = alignment[--row][--column];
                                }
+                count++;
                        }
                }
                
-               pairwiseLength = seqAaln.length();
+       
+        pairwiseLength = seqAaln.length();
                seqAstart = 1;  seqAend = 0;
                seqBstart = 1;  seqBend = 0;
-               
+        //flip maps since we now know the total length
+        map<int, int> newAMap;
+        for (map<int, int>::iterator it = ABaseMap.begin(); it != ABaseMap.end(); it++) {
+            int spot = it->second;
+            newAMap[pairwiseLength-spot-1] = it->first-1;
+        }
+        ABaseMap = newAMap;
+        map<int, int> newBMap;
+        for (map<int, int>::iterator it = BBaseMap.begin(); it != BBaseMap.end(); it++) {
+            int spot = it->second;
+            newBMap[pairwiseLength-spot-1] = it->first-1;
+        }
+               BBaseMap = newBMap;
+        
                for(int i=0;i<seqAaln.length();i++){
                        if(seqAaln[i] != '-' && seqBaln[i] == '-')              {       seqAstart++;    }
                        else if(seqAaln[i] == '-' && seqBaln[i] != '-') {       seqBstart++;    }
@@ -156,7 +177,16 @@ int Alignment::getCandidateEndPos(){
 int Alignment::getTemplateStartPos(){
        return seqBstart;                                                                       //      this is called to report the quality of the alignment
 }
+/**************************************************************************************************/
+
+map<int, int> Alignment::getSeqAAlnBaseMap(){
+       return ABaseMap;                                                                        
+}
+/**************************************************************************************************/
 
+map<int, int> Alignment::getSeqBAlnBaseMap(){
+       return BBaseMap;                                                                        
+}
 /**************************************************************************************************/
 
 int Alignment::getTemplateEndPos(){